QTL Analysis - binary [ICI vs EOI]

Loading Data
Genome-wide scan
LOD peaks
QTL effects

Last updated: 2022-02-11

Checks: 6 1

Knit directory: Serreze-T1D_Workflow/

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Loading Data

We will load the data and subset indivials out that are in the groups of interest. We will create a binary phenotype from this (EOI ==0, ICI == 1).

load("data/gm_allqc_4.batches.RData")

#gm_allqc
gm=gm_allqc
gm

Object of class cross2 (crosstype "bc")

Total individuals               188
No. genotyped individuals       188
No. phenotyped individuals      188
No. with both geno & pheno      188

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131578

No. markers by chr:
    1     2     3     4     5     6     7     8     9    10    11    12    13 
 9977 10005  7858  7589  7621  7758  7413  6472  6725  6396  7154  6137  6085 
   14    15    16    17    18    19     X 
 5981  5346  5019  5093  4607  3564  4778

#pr <- readRDS("data/serreze_probs_allqc.rds")
#pr <- readRDS("data/serreze_probs.rds")

##extracting animals with ici and eoi group status
miceinfo <- gm$covar[gm$covar$group == "EOI" | gm$covar$group == "ICI",]
table(miceinfo$group)


EOI ICI 
 69  92

mice.ids <- rownames(miceinfo)

gm <- gm[mice.ids]
gm

Object of class cross2 (crosstype "bc")

Total individuals               161
No. genotyped individuals       161
No. phenotyped individuals      161
No. with both geno & pheno      161

No. phenotypes                    1
No. covariates                    6
No. phenotype covariates          0

No. chromosomes                  20
Total markers                131578

No. markers by chr:
    1     2     3     4     5     6     7     8     9    10    11    12    13 
 9977 10005  7858  7589  7621  7758  7413  6472  6725  6396  7154  6137  6085 
   14    15    16    17    18    19     X 
 5981  5346  5019  5093  4607  3564  4778

#pr.qc <- pr
#for (i in 1:20){pr.qc[[i]] = pr.qc[[i]][mice.ids,,]}

#bin_pheno <- NULL
#bin_pheno$EOI <- ifelse(gm$covar$group == "EOI", 1, 0)
#bin_pheno$ICI <- ifelse(gm$covar$group == "ICI", 1, 0)
#bin_pheno <- as.data.frame(bin_pheno)
#rownames(bin_pheno) <- rownames(gm$covar)

gm$covar$ICI.vs.EOI <- ifelse(gm$covar$group == "EOI", 0, 1)

##dropping monomorphic markers within the dataset

g <- do.call("cbind", gm$geno)
#g[1,1:ncol(g)]

gf_mar <- t(apply(g, 2, function(a) table(factor(a, 1:2))/sum(a != 0)))
#gn_mar <- t(apply(g, 2, function(a) table(factor(a, 1:2))))

gf_mar <- gf_mar[gf_mar[,2] != "NaN",]

count <- rowSums(gf_mar <=0.05)
low_freq_df <- merge(as.data.frame(gf_mar),as.data.frame(count), by="row.names",all=T)
low_freq_df[is.na(low_freq_df)] <- ''
low_freq_df <- low_freq_df[low_freq_df$count == 1,]
rownames(low_freq_df) <- low_freq_df$Row.names

low_freq <- find_markerpos(gm, rownames(low_freq_df))
low_freq$id <- rownames(low_freq)

nrow(low_freq)

[1] 99077

low_freq_bad <- merge(low_freq,low_freq_df, by="row.names",all=T)
names(low_freq_bad)[1] <- c("marker")

gf_mar <- gf_mar[gf_mar[,2] != "NaN",]
MAF <- apply(gf_mar, 1, function(x) min(x))
MAF <- as.data.frame(MAF)
MAF$index <- 1:nrow(gf_mar)
gf_mar_maf <- merge(gf_mar,as.data.frame(MAF), by="row.names")
gf_mar_maf <- gf_mar_maf[order(gf_mar_maf$index),]

gfmar <- NULL
gfmar$gfmar_mar_0 <- sum(gf_mar_maf$MAF==0)
gfmar$gfmar_mar_1 <- sum(gf_mar_maf$MAF< 0.01)
gfmar$gfmar_mar_5 <- sum(gf_mar_maf$MAF< 0.05)
gfmar$gfmar_mar_10 <- sum(gf_mar_maf$MAF< 0.10)
gfmar$gfmar_mar_15 <- sum(gf_mar_maf$MAF< 0.15)
gfmar$gfmar_mar_25 <- sum(gf_mar_maf$MAF< 0.25)
gfmar$gfmar_mar_50 <- sum(gf_mar_maf$MAF< 0.50)
gfmar$total_snps <- nrow(as.data.frame(gf_mar_maf))

gfmar <- t(as.data.frame(gfmar))
gfmar <- as.data.frame(gfmar)
gfmar$count <- gfmar$V1

gfmar[c(2)] %>%
  kable(escape = F,align = c("ccccccccc"),linesep ="\\hline") %>%
  kable_styling(full_width = F) %>%
  kable_styling("striped", full_width = F)  %>%
  row_spec(8 ,bold=T,color= "white",background = "black")

	count
gfmar_mar_0	89667
gfmar_mar_1	92615
gfmar_mar_5	99045
gfmar_mar_10	99502
gfmar_mar_15	99619
gfmar_mar_25	100097
gfmar_mar_50	131139
total_snps	131578

gm_qc <- drop_markers(gm, low_freq_bad$marker)
gm_qc <- drop_nullmarkers(gm_qc)
 
gm = gm_qc
gm

Object of class cross2 (crosstype "bc")

Total individuals              161
No. genotyped individuals      161
No. phenotyped individuals     161
No. with both geno & pheno     161

No. phenotypes                   1
No. covariates                   7
No. phenotype covariates         0

No. chromosomes                 20
Total markers                32501

No. markers by chr:
   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
2940 2853 2033 2045 1931 2041 1858 1677 1991 1208 2057 1387 1617 1685 1194  922 
  17   18   19    X 
 382 1073 1052  555

markers <- marker_names(gm)
gmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_hh/genetic_map.csv")
pmapdf <- read.csv("/Users/corneb/Documents/MyJax/CS/Projects/Serreze/haplotype.reconstruction/output_hh/physical_map.csv")
mapdf <- merge(gmapdf,pmapdf, by=c("marker","chr"), all=T)
rownames(mapdf) <- mapdf$marker
mapdf <- mapdf[markers,]
names(mapdf) <- c('marker','chr','gmapdf','pmapdf')
mapdf <- mapdf[!duplicated(mapdf[c(2:3)]),]

pr.qc <- calc_genoprob(gm)

Genome-wide scan

For each of the phenotype analyzed, permutations were used for each model to obtain genome-wide LOD significance threshold for p < 0.01, p < 0.05, p < 0.10, respectively, separately for X and automsomes (A).

The table shows the estimated significance thresholds from permutation test.

We also looked at the kinship to see how correlated each sample is. Kinship values between pairs of samples range between 0 (no relationship) and 1.0 (completely identical). The darker the colour the more indentical the pairs are.

Xcovar <- get_x_covar(gm)
#addcovar = model.matrix(~Sex, data = covars)[,-1]

#K <- calc_kinship(pr.qc, type = "loco")
#heatmap(K[[1]])
#K.overall <- calc_kinship(pr.qc, type = "overall")
#heatmap(K.overall)
kinship <- calc_kinship(pr.qc)
heatmap(kinship)

Version	Author	Date
1218e08	Belinda Cornes	2022-02-11

#operm <- scan1perm(pr.qc, gm$covar$phenos, Xcovar=Xcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, addcovar = addcovar, n_perm=2000)
#operm <- scan1perm(pr.qc, gm$covar$phenos, n_perm=2000)
operm <- scan1perm(pr.qc, gm$covar["ICI.vs.EOI"], model="binary", n_perm=10, perm_Xsp=TRUE, chr_lengths=chr_lengths(gm$gmap))

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))
names(summary_table) <- c("autosomes","X")
summary_table$significance.level <- rownames(summary_table)

rownames(summary_table) <- NULL

summary_table[c(3,1:2)] %>%
  kable(escape = F,align = c("ccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

significance.level	autosomes	X
0.01	4.033409	2.907967
0.05	3.877426	2.847949
0.1	3.681965	2.769463

The figures below show QTL maps for each phenotype

out <- scan1(pr.qc, gm$covar["ICI.vs.EOI"], Xcovar=Xcovar, model="binary")

summary_table<-data.frame(unclass(summary(operm, alpha=c(0.01,  0.05, 0.1))))

plot_lod<-function(out,map){
  for (i in 1:dim(out)[2]){
    #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/",colnames(out)[i],  "_lod.png"))
    
    #par(mar=c(5.1, 6.1, 1.1, 1.1))
    ymx <- maxlod(out) # overall maximum LOD score
    plot(out, gm$gmap, lodcolumn=i, col="slateblue", ylim=c(0, ymx+0.5))
    legend("topright", lwd=2, colnames(out)[i], bg="gray90")
    title(main = colnames(out)[i])
    #for (j in 1: dim(summary_table)[1]){
    #  abline(h=summary_table[j, i],col="red")
    #  text(x=400, y =summary_table[j, i]+0.12, labels = paste("p=", row.names(summary_table)[j]))
    #}
    #dev.off()
  }
}

plot_lod(out,gm$gmap)

Version	Author	Date
1218e08	Belinda Cornes	2022-02-11

LOD peaks

The table below shows QTL peaks associated with the phenotype. We use the 95% threshold from the permutations to find peaks.

peaks<-find_peaks(out, gm$gmap, threshold=4, drop=1.5)

rownames(peaks) <- NULL
peaks[] %>%
  kable(escape = F,align = c("ccccccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

lodindex	lodcolumn	chr	pos	lod	ci_lo	ci_hi
1	ICI.vs.EOI	3	18.624	8.058029	5.566	21.449

peaks_mbl <- list()
#corresponding info in Mb
for(i in 1:nrow(peaks)){
  lodindex <- peaks$lodindex[i]
  lodcolumn <- peaks$lodcolumn[i]
  chr <- peaks$chr[i]
  lod <- peaks$lod[i]
  pos <- mapdf$pmapdf[which(mapdf$gmapdf == peaks$pos[i] & mapdf$chr == peaks$chr[i])]
  ci_lo <- mapdf$pmapdf[which(mapdf$gmapdf == peaks$ci_lo[i] & mapdf$chr == peaks$chr[i])]
  ci_hi <- mapdf$pmapdf[which(mapdf$gmapdf == peaks$ci_hi[i] & mapdf$chr == peaks$chr[i])]
  peaks_mb=cbind(lodindex, lodcolumn, chr, pos, lod, ci_lo, ci_hi)
  peaks_mbl[[i]] <- peaks_mb
}
peaks_mba <- do.call(rbind, peaks_mbl)
peaks_mba <- as.data.frame(peaks_mba)
#peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")] <- sapply(peaks_mba[,c("chr", "pos", "lod", "ci_lo", "ci_hi")], as.numeric)

rownames(peaks_mba) <- NULL
peaks_mba[] %>%
  kable(escape = F,align = c("ccccccc")) %>%
  kable_styling("striped", full_width = T) %>%
  column_spec(1, bold=TRUE)

lodindex	lodcolumn	chr	pos	lod	ci_lo	ci_hi
1	ICI.vs.EOI	3	38.523543	8.05802845906476	19.493219	48.682283

QTL effects

For each peak LOD location we give a list of gene

query_variants <- create_variant_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/cc_variants.sqlite")
query_genes <- create_gene_query_func("/Users/corneb/Documents/MyJax/CS/Projects/support.files/qtl2/mouse_genes_mgi.sqlite")

for (i in 1:nrow(peaks)){
#for (i in 1:1){
  #Plot 1
  marker = find_marker(gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i])
  #g <- maxmarg(pr.qc, gm$gmap, chr=peaks$chr[i], pos=peaks$pos[i], return_char=TRUE, minprob = 0.5)
  gp <- g[,marker]
  gp[gp==1] <- "AA"
  gp[gp==2] <- "AB"
  gp[gp==0] <- NA
  #png(filename=paste0("/Users/chenm/Documents/qtl/Jai/","qtl_effect_", i, ".png"))
  #par(mar=c(4.1, 4.1, 1.5, 0.6))
  plot_pxg(gp, gm$covar[,peaks$lodcolumn[i]], ylab=peaks$lodcolumn[i], sort=FALSE)
  title(main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")"), line=0.2)
  ##dev.off()

  chr = peaks$chr[i]

# Plot 2
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar)
  #coeff <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], Xcovar=Xcovar)
  coeff <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary")
  blup <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]])
  #plot_coef(coeff, 
  #     gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i]," [scan1coeff])")
  #     )

  plot_coef(blup, 
       gm$gmap[chr], columns=1:2,
       bgcolor="gray95", legend="bottomleft", 
       main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i]," [scan1blup])")
       )
  #last_coef <- unclass(coeff)[nrow(coeff),1:3]
  #for(t in seq(along=last_coef))
  #axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


 # Plot 3
  #c2effB <- scan1coef(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], model="binary", contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  #c2effBb <- scan1blup(pr.qc[,chr], gm$covar[peaks$lodcolumn[i]], contrasts=cbind(a=c(-1, 0), d=c(0, -1)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]], addcovar = addcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  ##c2effB <- scan1coef(pr[,chr], cross$pheno[,peaks$lodcolumn[i]],Xcovar=Xcovar, contrasts=cbind(mu=c(1,1,1), a=c(-1, 0, 1), d=c(0, 1, 0)))
  #plot(c2effB, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  #plot(c2effBb, gm$gmap[chr], columns=1:2,
  #     bgcolor="gray95", legend="bottomleft", 
  #     main = paste("chr", chr=peaks$chr[i], "pos", peaks$pos[i], "(",peaks$lodcolumn[i],")")
  #     )
  ##last_coef <- unclass(c2effB)[nrow(c2effB),2:3] # last two coefficients
  ##for(t in seq(along=last_coef))
  ##  axis(side=4, at=last_coef[t], names(last_coef)[t], tick=FALSE)


  #Table 1
  chr = peaks_mba$chr[i]
  start=as.numeric(peaks_mba$ci_lo[i])
  end=as.numeric(peaks_mba$ci_hi[i])

  genesgss = query_genes(chr, start, end)

  rownames(genesgss) <- NULL
  genesgss$strand_old = genesgss$strand
  genesgss$strand[genesgss$strand=="+"] <- "positive"
  genesgss$strand[genesgss$strand=="-"] <- "negative"

  #genesgss <- 
  #table <- 
  #genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")] %>%
  #kable(escape = F,align = c("ccccccccccc")) %>%
  #kable_styling("striped", full_width = T) #%>% 
  #cat #%>%
  #column_spec(1, bold=TRUE)
#
  #print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], escape = F,align = c("ccccccccccc")))

  print(kable(genesgss[,c("chr","type","start","stop","strand","ID","Name","Dbxref","gene_id","mgi_type","description")], "html") %>% kable_styling("striped", full_width = T))

  #table
  

}

Version	Author	Date
1218e08	Belinda Cornes	2022-02-11

Version	Author	Date
1218e08	Belinda Cornes	2022-02-11

chr	type	start	stop	strand	ID	Name	Dbxref	gene_id	mgi_type	description
3	gene	19.50859	19.61086	positive	MGI_C57BL6J_1913576	Dnajc5b	NCBI_Gene:66326,ENSEMBL:ENSMUSG00000027606	MGI:1913576	protein coding gene	DnaJ heat shock protein family (Hsp40) member C5 beta
3	gene	19.56025	19.56042	positive	MGI_C57BL6J_5453107	Gm23330	ENSEMBL:ENSMUSG00000096211	MGI:5453107	snRNA gene	predicted gene, 23330
3	pseudogene	19.58479	19.58554	positive	MGI_C57BL6J_3646012	Gm6141	NCBI_Gene:620290,ENSEMBL:ENSMUSG00000084339	MGI:3646012	pseudogene	predicted pseudogene 6141
3	gene	19.61037	19.62948	negative	MGI_C57BL6J_1920674	1700064H15Rik	NCBI_Gene:102633032,ENSEMBL:ENSMUSG00000082766	MGI:1920674	protein coding gene	RIKEN cDNA 1700064H15 gene
3	gene	19.62796	19.62803	negative	MGI_C57BL6J_4413716	n-TRacg3	NCBI_Gene:102467637	MGI:4413716	tRNA gene	nuclear encoded tRNA arginine 3 (anticodon ACG)
3	gene	19.62835	19.62845	positive	MGI_C57BL6J_4414074	n-TYgta1	NCBI_Gene:102467442	MGI:4414074	tRNA gene	nuclear encoded tRNA tyrosine 1 (anticodon GTA)
3	gene	19.62878	19.62887	positive	MGI_C57BL6J_4414075	n-TYgta2	NCBI_Gene:102467395	MGI:4414075	tRNA gene	nuclear encoded tRNA tyrosine 2 (anticodon GTA)
3	gene	19.62899	19.62907	positive	MGI_C57BL6J_4413687	n-TAagc14	NCBI_Gene:102467233	MGI:4413687	tRNA gene	nuclear encoded tRNA alanine 14 (anticodon AGC)
3	gene	19.64434	19.69242	positive	MGI_C57BL6J_3036269	Trim55	NCBI_Gene:381485,ENSEMBL:ENSMUSG00000060913	MGI:3036269	protein coding gene	tripartite motif-containing 55
3	gene	19.68597	19.68657	positive	MGI_C57BL6J_3642300	BC002189	ENSEMBL:ENSMUSG00000104465	MGI:3642300	lncRNA gene	cDNA sequence BC002189
3	gene	19.69340	19.69540	negative	MGI_C57BL6J_88496	Crh	NCBI_Gene:12918,ENSEMBL:ENSMUSG00000049796	MGI:88496	protein coding gene	corticotropin releasing hormone
3	gene	19.69449	19.70735	positive	MGI_C57BL6J_5625074	Gm42189	NCBI_Gene:105247005	MGI:5625074	lncRNA gene	predicted gene, 42189
3	pseudogene	19.70825	19.70932	negative	MGI_C57BL6J_5011049	Gm18864	NCBI_Gene:100417853,ENSEMBL:ENSMUSG00000102261	MGI:5011049	pseudogene	predicted gene, 18864
3	pseudogene	19.76883	19.76933	positive	MGI_C57BL6J_3644940	Gm7442	NCBI_Gene:665002,ENSEMBL:ENSMUSG00000106182	MGI:3644940	pseudogene	predicted gene 7442
3	pseudogene	19.88087	19.88175	negative	MGI_C57BL6J_3780317	Gm2148	NCBI_Gene:102633274	MGI:3780317	pseudogene	predicted gene 2148
3	pseudogene	19.89487	19.90103	positive	MGI_C57BL6J_1918058	4632415L05Rik	NCBI_Gene:70808,ENSEMBL:ENSMUSG00000048106	MGI:1918058	pseudogene	RIKEN cDNA 4632415L05 gene
3	pseudogene	19.91380	19.91436	positive	MGI_C57BL6J_5610751	Gm37523	ENSEMBL:ENSMUSG00000103781	MGI:5610751	pseudogene	predicted gene, 37523
3	pseudogene	19.93424	19.93539	positive	MGI_C57BL6J_5009935	Gm17771	NCBI_Gene:100046095,ENSEMBL:ENSMUSG00000104031	MGI:5009935	pseudogene	predicted gene, 17771
3	gene	19.94515	19.95395	negative	MGI_C57BL6J_5625075	Gm42190	NCBI_Gene:105247006	MGI:5625075	lncRNA gene	predicted gene, 42190
3	gene	19.95698	20.00975	positive	MGI_C57BL6J_88476	Cp	NCBI_Gene:12870,ENSEMBL:ENSMUSG00000003617	MGI:88476	protein coding gene	ceruloplasmin
3	gene	19.99594	20.03538	negative	MGI_C57BL6J_2153839	Hps3	NCBI_Gene:12807,ENSEMBL:ENSMUSG00000027615	MGI:2153839	protein coding gene	HPS3, biogenesis of lysosomal organelles complex 2 subunit 1
3	gene	20.05657	20.05816	negative	MGI_C57BL6J_2445023	D830024F11Rik	NA	NA	unclassified gene	RIKEN cDNA D830024F11 gene
3	gene	20.05781	20.11849	positive	MGI_C57BL6J_1196437	Hltf	NCBI_Gene:20585,ENSEMBL:ENSMUSG00000002428	MGI:1196437	protein coding gene	helicase-like transcription factor
3	gene	20.12208	20.15532	negative	MGI_C57BL6J_1351614	Gyg	NCBI_Gene:27357,ENSEMBL:ENSMUSG00000019528	MGI:1351614	protein coding gene	glycogenin
3	gene	20.21562	20.24221	negative	MGI_C57BL6J_88479	Cpa3	NCBI_Gene:12873,ENSEMBL:ENSMUSG00000001865	MGI:88479	protein coding gene	carboxypeptidase A3, mast cell
3	gene	20.22229	20.22236	negative	MGI_C57BL6J_5531279	Mir7007	miRBase:MI0022856,NCBI_Gene:102465609,ENSEMBL:ENSMUSG00000099105	MGI:5531279	miRNA gene	microRNA 7007
3	gene	20.22229	20.22948	positive	MGI_C57BL6J_5590479	Gm31320	NCBI_Gene:102633510	MGI:5590479	lncRNA gene	predicted gene, 31320
3	pseudogene	20.22377	20.22469	negative	MGI_C57BL6J_3647720	Gm7428	NCBI_Gene:664965	MGI:3647720	pseudogene	predicted gene 7428
3	gene	20.24826	20.27573	negative	MGI_C57BL6J_1923953	Cpb1	NCBI_Gene:76703,ENSEMBL:ENSMUSG00000011463	MGI:1923953	protein coding gene	carboxypeptidase B1 (tissue)
3	gene	20.27671	20.28605	negative	MGI_C57BL6J_5826434	Gm46797	NCBI_Gene:108168859	MGI:5826434	lncRNA gene	predicted gene, 46797
3	gene	20.30841	20.30992	positive	MGI_C57BL6J_5663662	Gm43525	ENSEMBL:ENSMUSG00000105208	MGI:5663662	lncRNA gene	predicted gene 43525
3	gene	20.31447	20.36718	negative	MGI_C57BL6J_87965	Agtr1b	NCBI_Gene:11608,ENSEMBL:ENSMUSG00000054988	MGI:87965	protein coding gene	angiotensin II receptor, type 1b
3	pseudogene	20.39101	20.39198	negative	MGI_C57BL6J_5010611	Gm18426	NCBI_Gene:100417153,ENSEMBL:ENSMUSG00000103573	MGI:5010611	pseudogene	predicted gene, 18426
3	gene	20.40250	20.50621	negative	MGI_C57BL6J_5590625	Gm31466	NCBI_Gene:108168860,ENSEMBL:ENSMUSG00000102636	MGI:5590625	lncRNA gene	predicted gene, 31466
3	gene	20.40467	20.40491	positive	MGI_C57BL6J_5662731	Gm42594	ENSEMBL:ENSMUSG00000106442	MGI:5662731	unclassified gene	predicted gene 42594
3	pseudogene	20.78247	20.78407	negative	MGI_C57BL6J_5010676	Gm18491	NCBI_Gene:100417265,ENSEMBL:ENSMUSG00000103460	MGI:5010676	pseudogene	predicted gene, 18491
3	pseudogene	20.78794	20.78815	positive	MGI_C57BL6J_5611551	Gm38323	ENSEMBL:ENSMUSG00000102986	MGI:5611551	pseudogene	predicted gene, 38323
3	pseudogene	20.80448	20.80609	positive	MGI_C57BL6J_5010678	Gm18493	NCBI_Gene:100417268,ENSEMBL:ENSMUSG00000103533	MGI:5010678	pseudogene	predicted gene, 18493
3	gene	20.81639	20.82236	negative	MGI_C57BL6J_5590711	Gm31552	NCBI_Gene:102633820	MGI:5590711	lncRNA gene	predicted gene, 31552
3	gene	20.81962	20.82369	positive	MGI_C57BL6J_5610708	Gm37480	ENSEMBL:ENSMUSG00000102807	MGI:5610708	unclassified gene	predicted gene, 37480
3	pseudogene	21.04945	21.05053	positive	MGI_C57BL6J_3647006	Gm7488	NCBI_Gene:665094,ENSEMBL:ENSMUSG00000039617	MGI:3647006	pseudogene	predicted gene 7488
3	pseudogene	21.11358	21.11400	negative	MGI_C57BL6J_5663297	Gm43160	ENSEMBL:ENSMUSG00000106051	MGI:5663297	pseudogene	predicted gene 43160
3	gene	21.26837	21.26909	negative	MGI_C57BL6J_5579843	Gm29137	ENSEMBL:ENSMUSG00000101897	MGI:5579843	lncRNA gene	predicted gene 29137
3	gene	21.42179	21.48966	negative	MGI_C57BL6J_5590769	Gm31610	NCBI_Gene:102633894	MGI:5590769	lncRNA gene	predicted gene, 31610
3	pseudogene	21.60381	21.60551	positive	MGI_C57BL6J_5663812	Gm43675	ENSEMBL:ENSMUSG00000106085	MGI:5663812	pseudogene	predicted gene 43675
3	pseudogene	21.64839	21.64918	positive	MGI_C57BL6J_5010120	Gm17935	NCBI_Gene:100416137,ENSEMBL:ENSMUSG00000106460	MGI:5010120	pseudogene	predicted gene, 17935
3	gene	21.70282	21.71246	positive	MGI_C57BL6J_5590852	Gm31693	NCBI_Gene:102634003,ENSEMBL:ENSMUSG00000105440	MGI:5590852	lncRNA gene	predicted gene, 31693
3	gene	21.75353	21.80080	negative	MGI_C57BL6J_2442162	7530428D23Rik	NCBI_Gene:319506,ENSEMBL:ENSMUSG00000103441	MGI:2442162	lncRNA gene	RIKEN cDNA 7530428D23 gene
3	gene	21.86417	21.96435	negative	MGI_C57BL6J_5590972	Gm31813	NCBI_Gene:102634161	MGI:5590972	lncRNA gene	predicted gene, 31813
3	gene	21.99768	21.99847	negative	MGI_C57BL6J_5663811	Gm43674	ENSEMBL:ENSMUSG00000106321	MGI:5663811	lncRNA gene	predicted gene 43674
3	pseudogene	22.02120	22.02163	positive	MGI_C57BL6J_5663808	Gm43671	ENSEMBL:ENSMUSG00000106527	MGI:5663808	pseudogene	predicted gene 43671
3	gene	22.07441	22.07614	negative	MGI_C57BL6J_5663809	Gm43672	ENSEMBL:ENSMUSG00000106019	MGI:5663809	lncRNA gene	predicted gene 43672
3	gene	22.07441	22.07620	negative	MGI_C57BL6J_1914374	2810416G20Rik	NA	NA	protein coding gene	RIKEN cDNA 2810416G20 gene
3	gene	22.07659	22.21659	positive	MGI_C57BL6J_2441730	Tbl1xr1	NCBI_Gene:81004,ENSEMBL:ENSMUSG00000027630	MGI:2441730	protein coding gene	transducin (beta)-like 1X-linked receptor 1
3	pseudogene	22.08040	22.08125	negative	MGI_C57BL6J_3645251	Gm5842	NCBI_Gene:545506,ENSEMBL:ENSMUSG00000103293	MGI:3645251	pseudogene	predicted gene 5842
3	gene	22.25137	22.25166	positive	MGI_C57BL6J_105104	Rprl2	NCBI_Gene:19784,ENSEMBL:ENSMUSG00000087775	MGI:105104	RNase P RNA gene	ribonuclease P RNA-like 2
3	gene	22.28508	22.29783	negative	MGI_C57BL6J_5611552	Gm38324	ENSEMBL:ENSMUSG00000102987	MGI:5611552	lncRNA gene	predicted gene, 38324
3	pseudogene	22.34885	22.34961	negative	MGI_C57BL6J_5610864	Gm37636	NCBI_Gene:108168850,ENSEMBL:ENSMUSG00000102866	MGI:5610864	pseudogene	predicted gene, 37636
3	gene	22.40992	22.41005	negative	MGI_C57BL6J_5456131	Gm26354	ENSEMBL:ENSMUSG00000088846	MGI:5456131	snoRNA gene	predicted gene, 26354
3	pseudogene	22.52501	22.52624	positive	MGI_C57BL6J_3780056	Spin3-ps	NCBI_Gene:675593,ENSEMBL:ENSMUSG00000103801	MGI:3780056	pseudogene	spindlin family, member 3, pseudogene
3	gene	22.81221	22.81246	positive	MGI_C57BL6J_5611117	Gm37889	ENSEMBL:ENSMUSG00000102233	MGI:5611117	unclassified gene	predicted gene, 37889
3	pseudogene	23.07242	23.07492	positive	MGI_C57BL6J_5610211	Gm36983	ENSEMBL:ENSMUSG00000103275	MGI:5610211	pseudogene	predicted gene, 36983
3	gene	23.08598	23.08895	positive	MGI_C57BL6J_5610249	Gm37021	ENSEMBL:ENSMUSG00000103607	MGI:5610249	lncRNA gene	predicted gene, 37021
3	pseudogene	23.37494	23.37532	negative	MGI_C57BL6J_5610720	Gm37492	ENSEMBL:ENSMUSG00000102214	MGI:5610720	pseudogene	predicted gene, 37492
3	gene	23.46105	23.52140	positive	MGI_C57BL6J_1924114	4930412E21Rik	NCBI_Gene:100039548,ENSEMBL:ENSMUSG00000102203	MGI:1924114	lncRNA gene	RIKEN cDNA 4930412E21 gene
3	gene	23.79810	25.14426	negative	MGI_C57BL6J_2685867	Naaladl2	NCBI_Gene:635702,ENSEMBL:ENSMUSG00000102758	MGI:2685867	protein coding gene	N-acetylated alpha-linked acidic dipeptidase-like 2
3	pseudogene	23.93096	23.93200	positive	MGI_C57BL6J_5011009	Gm18824	NCBI_Gene:100417784	MGI:5011009	pseudogene	predicted gene, 18824
3	gene	23.94002	23.94593	positive	MGI_C57BL6J_5625076	Gm42191	NCBI_Gene:105247007	MGI:5625076	lncRNA gene	predicted gene, 42191
3	gene	24.16303	24.16311	negative	MGI_C57BL6J_4413931	n-TLcag1	NCBI_Gene:102467553	MGI:4413931	tRNA gene	nuclear encoded tRNA leucine 1 (anticodon CAG)
3	pseudogene	24.33304	24.33355	positive	MGI_C57BL6J_3645137	Gm7536	NCBI_Gene:665189,ENSEMBL:ENSMUSG00000057036	MGI:3645137	pseudogene	predicted gene 7536
3	gene	24.48671	24.48749	positive	MGI_C57BL6J_1920306	2900080J11Rik	NA	NA	unclassified gene	RIKEN cDNA 2900080J11 gene
3	gene	24.56207	24.56218	positive	MGI_C57BL6J_5454481	Gm24704	ENSEMBL:ENSMUSG00000070227	MGI:5454481	snRNA gene	predicted gene, 24704
3	gene	24.71872	24.71898	positive	MGI_C57BL6J_5453839	Gm24062	ENSEMBL:ENSMUSG00000088115	MGI:5453839	unclassified non-coding RNA gene	predicted gene, 24062
3	pseudogene	25.00742	25.00771	negative	MGI_C57BL6J_5662911	Gm42774	ENSEMBL:ENSMUSG00000105009	MGI:5662911	pseudogene	predicted gene 42774
3	gene	25.14407	25.14426	positive	MGI_C57BL6J_5610364	Gm37136	ENSEMBL:ENSMUSG00000102876	MGI:5610364	unclassified gene	predicted gene, 37136
3	pseudogene	25.18480	25.18498	negative	MGI_C57BL6J_5611230	Gm38002	ENSEMBL:ENSMUSG00000102855	MGI:5611230	pseudogene	predicted gene, 38002
3	pseudogene	25.21076	25.21273	negative	MGI_C57BL6J_3704211	Gm10259	NCBI_Gene:100039592,ENSEMBL:ENSMUSG00000069083	MGI:3704211	pseudogene	predicted pseudogene 10259
3	gene	25.42621	26.33286	negative	MGI_C57BL6J_2179435	Nlgn1	NCBI_Gene:192167,ENSEMBL:ENSMUSG00000063887	MGI:2179435	protein coding gene	neuroligin 1
3	gene	25.54602	25.54615	positive	MGI_C57BL6J_5454027	Gm24250	ENSEMBL:ENSMUSG00000087945	MGI:5454027	rRNA gene	predicted gene, 24250
3	gene	25.64956	25.65077	negative	MGI_C57BL6J_1920377	3110039C02Rik	NA	NA	unclassified gene	RIKEN cDNA 3110039C02 gene
3	gene	25.69519	25.70030	negative	MGI_C57BL6J_5610801	Gm37573	ENSEMBL:ENSMUSG00000102397	MGI:5610801	lncRNA gene	predicted gene, 37573
3	pseudogene	25.73123	25.73261	positive	MGI_C57BL6J_3647151	Gm6197	NCBI_Gene:621017,ENSEMBL:ENSMUSG00000104295	MGI:3647151	pseudogene	predicted gene 6197
3	gene	25.86566	25.86752	negative	MGI_C57BL6J_2443798	A830010M09Rik	NA	NA	unclassified gene	RIKEN cDNA A830010M09 gene
3	gene	26.33115	26.33688	positive	MGI_C57BL6J_3698881	A830092H15Rik	NCBI_Gene:100379095,ENSEMBL:ENSMUSG00000074664	MGI:3698881	lncRNA gene	RIKEN cDNA A830092H15 gene
3	pseudogene	26.38044	26.38256	positive	MGI_C57BL6J_3648363	Gm4855	NCBI_Gene:229152,ENSEMBL:ENSMUSG00000102274	MGI:3648363	pseudogene	predicted gene 4855
3	gene	26.62618	26.62631	negative	MGI_C57BL6J_5455550	Gm25773	ENSEMBL:ENSMUSG00000080368	MGI:5455550	miRNA gene	predicted gene, 25773
3	gene	26.63762	26.98321	positive	MGI_C57BL6J_1918112	Spata16	NCBI_Gene:70862,ENSEMBL:ENSMUSG00000039335	MGI:1918112	protein coding gene	spermatogenesis associated 16
3	gene	26.85020	26.87914	negative	MGI_C57BL6J_5591617	Gm32458	NCBI_Gene:102635017	MGI:5591617	lncRNA gene	predicted gene, 32458
3	pseudogene	27.01276	27.01287	positive	MGI_C57BL6J_5610887	Gm37659	ENSEMBL:ENSMUSG00000103712	MGI:5610887	pseudogene	predicted gene, 37659
3	gene	27.02642	27.02655	negative	MGI_C57BL6J_5690856	Gm44464	ENSEMBL:ENSMUSG00000105670	MGI:5690856	miRNA gene	predicted gene, 44464
3	pseudogene	27.04674	27.04798	negative	MGI_C57BL6J_3645515	Gm7558	NCBI_Gene:665258,ENSEMBL:ENSMUSG00000102908	MGI:3645515	pseudogene	predicted gene 7558
3	gene	27.09722	27.15391	negative	MGI_C57BL6J_95281	Ect2	NCBI_Gene:13605,ENSEMBL:ENSMUSG00000027699	MGI:95281	protein coding gene	ect2 oncogene
3	gene	27.10898	27.10909	positive	MGI_C57BL6J_5454929	Gm25152	ENSEMBL:ENSMUSG00000087742	MGI:5454929	snoRNA gene	predicted gene, 25152
3	gene	27.15403	27.15702	positive	MGI_C57BL6J_1923907	1700125G22Rik	NCBI_Gene:76657,ENSEMBL:ENSMUSG00000097584	MGI:1923907	lncRNA gene	RIKEN cDNA 1700125G22 gene
3	gene	27.18296	27.28461	positive	MGI_C57BL6J_2443191	Nceh1	NCBI_Gene:320024,ENSEMBL:ENSMUSG00000027698	MGI:2443191	protein coding gene	neutral cholesterol ester hydrolase 1
3	gene	27.26033	27.28446	positive	MGI_C57BL6J_5625077	Gm42192	NCBI_Gene:105247008	MGI:5625077	lncRNA gene	predicted gene, 42192
3	pseudogene	27.27806	27.27845	positive	MGI_C57BL6J_5610419	Gm37191	ENSEMBL:ENSMUSG00000102186	MGI:5610419	pseudogene	predicted gene, 37191
3	pseudogene	27.30841	27.30867	negative	MGI_C57BL6J_5663482	Gm43345	ENSEMBL:ENSMUSG00000105806	MGI:5663482	pseudogene	predicted gene 43345
3	gene	27.31703	27.34243	positive	MGI_C57BL6J_107414	Tnfsf10	NCBI_Gene:22035,ENSEMBL:ENSMUSG00000039304	MGI:107414	protein coding gene	tumor necrosis factor (ligand) superfamily, member 10
3	gene	27.37131	27.37923	positive	MGI_C57BL6J_2441906	Ghsr	NCBI_Gene:208188,ENSEMBL:ENSMUSG00000051136	MGI:2441906	protein coding gene	growth hormone secretagogue receptor
3	gene	27.41511	27.41615	negative	MGI_C57BL6J_1924904	C430049A07Rik	NA	NA	unclassified gene	RIKEN cDNA C430049A07 gene
3	gene	27.41616	27.71311	negative	MGI_C57BL6J_1919257	Fndc3b	NCBI_Gene:72007,ENSEMBL:ENSMUSG00000039286	MGI:1919257	protein coding gene	fibronectin type III domain containing 3B
3	gene	27.44166	27.44411	positive	MGI_C57BL6J_5625078	Gm42193	NCBI_Gene:105247009	MGI:5625078	lncRNA gene	predicted gene, 42193
3	gene	27.48228	27.48424	positive	MGI_C57BL6J_5591897	Gm32738	NCBI_Gene:102635381	MGI:5591897	lncRNA gene	predicted gene, 32738
3	gene	27.54664	27.54787	positive	MGI_C57BL6J_5663481	Gm43344	ENSEMBL:ENSMUSG00000106625	MGI:5663481	unclassified gene	predicted gene 43344
3	gene	27.58490	27.58499	negative	MGI_C57BL6J_4834306	Mir3092	miRBase:MI0014085,NCBI_Gene:100526525,ENSEMBL:ENSMUSG00000092695	MGI:4834306	miRNA gene	microRNA 3092
3	gene	27.77786	27.84092	positive	MGI_C57BL6J_5625079	Gm42194	NCBI_Gene:105247010	MGI:5625079	lncRNA gene	predicted gene, 42194
3	gene	27.79788	27.81538	negative	MGI_C57BL6J_5591954	Gm32795	NCBI_Gene:102635463	MGI:5591954	lncRNA gene	predicted gene, 32795
3	gene	27.86606	27.89639	negative	MGI_C57BL6J_2685410	Tmem212	NCBI_Gene:208613,ENSEMBL:ENSMUSG00000043164	MGI:2685410	protein coding gene	transmembrane protein 212
3	gene	27.86811	27.86827	positive	MGI_C57BL6J_5455817	Gm26040	ENSEMBL:ENSMUSG00000088772	MGI:5455817	snoRNA gene	predicted gene, 26040
3	gene	27.89680	27.90023	negative	MGI_C57BL6J_5625080	Gm42195	NCBI_Gene:105247011	MGI:5625080	lncRNA gene	predicted gene, 42195
3	gene	27.93841	28.13336	positive	MGI_C57BL6J_109585	Pld1	NCBI_Gene:18805,ENSEMBL:ENSMUSG00000027695	MGI:109585	protein coding gene	phospholipase D1
3	gene	28.17651	28.21221	positive	MGI_C57BL6J_5625081	Gm42196	NCBI_Gene:105247012,ENSEMBL:ENSMUSG00000109716	MGI:5625081	lncRNA gene	predicted gene, 42196
3	pseudogene	28.24552	28.24577	positive	MGI_C57BL6J_5610326	Gm37098	ENSEMBL:ENSMUSG00000103729	MGI:5610326	pseudogene	predicted gene, 37098
3	gene	28.26321	28.67586	positive	MGI_C57BL6J_1916264	Tnik	NCBI_Gene:665113,ENSEMBL:ENSMUSG00000027692	MGI:1916264	protein coding gene	TRAF2 and NCK interacting kinase
3	gene	28.26928	28.26983	positive	MGI_C57BL6J_2139599	AA589472	NA	NA	unclassified gene	expressed sequence AA589472
3	gene	28.32436	28.32609	positive	MGI_C57BL6J_5610765	Gm37537	ENSEMBL:ENSMUSG00000103420	MGI:5610765	unclassified gene	predicted gene, 37537
3	gene	28.41994	28.42002	positive	MGI_C57BL6J_4950412	Mir466q	miRBase:MI0018032,NCBI_Gene:100628591,ENSEMBL:ENSMUSG00000092990	MGI:4950412	miRNA gene	microRNA 466q
3	gene	28.69790	28.73136	positive	MGI_C57BL6J_1095438	Slc2a2	NCBI_Gene:20526,ENSEMBL:ENSMUSG00000027690	MGI:1095438	protein coding gene	solute carrier family 2 (facilitated glucose transporter), member 2
3	gene	28.70267	28.78111	negative	MGI_C57BL6J_1920861	1700112D23Rik	NCBI_Gene:73611,ENSEMBL:ENSMUSG00000091329	MGI:1920861	lncRNA gene	RIKEN cDNA 1700112D23 gene
3	pseudogene	28.76353	28.76539	negative	MGI_C57BL6J_3648080	Gm6505	NCBI_Gene:624446,ENSEMBL:ENSMUSG00000070522	MGI:3648080	pseudogene	predicted pseudogene 6505
3	gene	28.78127	28.79885	positive	MGI_C57BL6J_1933735	Eif5a2	NCBI_Gene:208691,ENSEMBL:ENSMUSG00000050192	MGI:1933735	protein coding gene	eukaryotic translation initiation factor 5A2
3	gene	28.79064	28.80542	negative	MGI_C57BL6J_5592109	Gm32950	NCBI_Gene:102635671,ENSEMBL:ENSMUSG00000103827	MGI:5592109	lncRNA gene	predicted gene, 32950
3	gene	28.80544	28.80742	positive	MGI_C57BL6J_1915278	Rpl22l1	NCBI_Gene:68028,ENSEMBL:ENSMUSG00000039221	MGI:1915278	protein coding gene	ribosomal protein L22 like 1
3	gene	28.80720	28.81618	negative	MGI_C57BL6J_5592210	Gm33051	NCBI_Gene:102635804,ENSEMBL:ENSMUSG00000104444	MGI:5592210	lncRNA gene	predicted gene, 33051
3	gene	28.85203	28.85426	negative	MGI_C57BL6J_5611095	Gm37867	ENSEMBL:ENSMUSG00000104275	MGI:5611095	lncRNA gene	predicted gene, 37867
3	gene	28.87981	28.88346	positive	MGI_C57BL6J_5611152	Gm37924	ENSEMBL:ENSMUSG00000102482	MGI:5611152	unclassified gene	predicted gene, 37924
3	gene	28.88346	28.89728	negative	MGI_C57BL6J_5592261	Gm33102	NCBI_Gene:102635876	MGI:5592261	lncRNA gene	predicted gene, 33102
3	gene	28.89262	28.92672	positive	MGI_C57BL6J_2686373	Gm1527	NCBI_Gene:385263,ENSEMBL:ENSMUSG00000074655	MGI:2686373	protein coding gene	predicted gene 1527
3	gene	29.04377	29.04555	negative	MGI_C57BL6J_5592313	Gm33154	NCBI_Gene:102635945	MGI:5592313	lncRNA gene	predicted gene, 33154
3	gene	29.08072	29.69121	positive	MGI_C57BL6J_1922990	Egfem1	NCBI_Gene:75740,ENSEMBL:ENSMUSG00000063600	MGI:1922990	protein coding gene	EGF-like and EMI domain containing 1
3	gene	29.17484	29.17693	positive	MGI_C57BL6J_5611257	Gm38029	ENSEMBL:ENSMUSG00000103992	MGI:5611257	unclassified gene	predicted gene, 38029
3	gene	29.20934	29.21198	positive	MGI_C57BL6J_2442122	D230021J17Rik	NA	NA	unclassified gene	RIKEN cDNA D230021J17 gene
3	gene	29.21989	29.22125	positive	MGI_C57BL6J_5611193	Gm37965	ENSEMBL:ENSMUSG00000102579	MGI:5611193	unclassified gene	predicted gene, 37965
3	gene	29.26628	29.26684	negative	MGI_C57BL6J_2139582	AA516838	NA	NA	unclassified gene	expressed sequence AA516838
3	gene	29.41682	29.41692	positive	MGI_C57BL6J_3691605	Mir551b	miRBase:MI0004131,NCBI_Gene:791072,ENSEMBL:ENSMUSG00000076120	MGI:3691605	miRNA gene	microRNA 551b
3	gene	29.63674	29.63685	positive	MGI_C57BL6J_5531333	Mir21b	miRBase:MI0021906,NCBI_Gene:102466637,ENSEMBL:ENSMUSG00000098315	MGI:5531333	miRNA gene	microRNA 21b
3	gene	29.66251	29.69656	negative	MGI_C57BL6J_5625082	Gm42197	NCBI_Gene:105247013	MGI:5625082	lncRNA gene	predicted gene, 42197
3	gene	29.76404	29.89323	negative	MGI_C57BL6J_5592365	Gm33206	NCBI_Gene:102636014,ENSEMBL:ENSMUSG00000102574	MGI:5592365	lncRNA gene	predicted gene, 33206
3	pseudogene	29.77128	29.77142	positive	MGI_C57BL6J_5610785	Gm37557	ENSEMBL:ENSMUSG00000103095	MGI:5610785	pseudogene	predicted gene, 37557
3	gene	29.89101	29.92419	positive	MGI_C57BL6J_5564803	Mannr	NCBI_Gene:102636083,ENSEMBL:ENSMUSG00000102590	MGI:5564803	lncRNA gene	Mecom adjacent non-protein coding RNA
3	pseudogene	29.92654	29.92697	positive	MGI_C57BL6J_5610509	Gm37281	ENSEMBL:ENSMUSG00000102884	MGI:5610509	pseudogene	predicted gene, 37281
3	gene	29.95130	30.54801	negative	MGI_C57BL6J_95457	Mecom	NCBI_Gene:14013,ENSEMBL:ENSMUSG00000027684	MGI:95457	protein coding gene	MDS1 and EVI1 complex locus
3	gene	30.01238	30.05481	positive	MGI_C57BL6J_4439646	Mecomos	ENSEMBL:ENSMUSG00000085702	MGI:4439646	antisense lncRNA gene	MDS1 and EVI1 complex locus, opposite strand
3	gene	30.16025	30.16189	negative	MGI_C57BL6J_5611294	Gm38066	ENSEMBL:ENSMUSG00000104486	MGI:5611294	unclassified gene	predicted gene, 38066
3	gene	30.22557	30.22769	negative	MGI_C57BL6J_5611425	Gm38197	ENSEMBL:ENSMUSG00000102460	MGI:5611425	unclassified gene	predicted gene, 38197
3	gene	30.26684	30.28019	negative	MGI_C57BL6J_3648282	Gm10258	NCBI_Gene:545510,ENSEMBL:ENSMUSG00000069074	MGI:3648282	unclassified non-coding RNA gene	predicted gene 10258
3	gene	30.27232	30.27438	negative	MGI_C57BL6J_5611590	Gm38362	ENSEMBL:ENSMUSG00000103870	MGI:5611590	unclassified gene	predicted gene, 38362
3	gene	30.34998	30.35132	negative	MGI_C57BL6J_1924752	9530010C24Rik	NA	NA	unclassified gene	RIKEN cDNA 9530010C24 gene
3	gene	30.48843	30.48929	positive	MGI_C57BL6J_5610252	Gm37024	ENSEMBL:ENSMUSG00000104079	MGI:5610252	unclassified gene	predicted gene, 37024
3	gene	30.50172	30.50381	negative	MGI_C57BL6J_5610880	Gm37652	ENSEMBL:ENSMUSG00000103738	MGI:5610880	unclassified gene	predicted gene, 37652
3	gene	30.55270	30.56424	negative	MGI_C57BL6J_5611486	Gm38258	ENSEMBL:ENSMUSG00000102256	MGI:5611486	lncRNA gene	predicted gene, 38258
3	pseudogene	30.56166	30.56213	negative	MGI_C57BL6J_5611381	Gm38153	ENSEMBL:ENSMUSG00000104243	MGI:5611381	pseudogene	predicted gene, 38153
3	gene	30.59484	30.59576	negative	MGI_C57BL6J_1920499	1600017P15Rik	ENSEMBL:ENSMUSG00000102505,ENSEMBL:ENSMUSG00000065361	MGI:1920499	unclassified gene	RIKEN cDNA 1600017P15 gene
3	gene	30.59707	30.59994	negative	MGI_C57BL6J_1923902	Actrt3	NCBI_Gene:76652,ENSEMBL:ENSMUSG00000037737	MGI:1923902	protein coding gene	actin related protein T3
3	gene	30.60127	30.60134	positive	MGI_C57BL6J_4414091	n-TVaac8	NCBI_Gene:102467402	MGI:4414091	tRNA gene	nuclear encoded tRNA valine 8 (anticodon AAC)
3	gene	30.60206	30.61987	positive	MGI_C57BL6J_1931415	Mynn	NCBI_Gene:80732,ENSEMBL:ENSMUSG00000037730	MGI:1931415	protein coding gene	myoneurin
3	gene	30.62427	30.64787	negative	MGI_C57BL6J_1919077	Lrrc34	NCBI_Gene:71827,ENSEMBL:ENSMUSG00000027702	MGI:1919077	protein coding gene	leucine rich repeat containing 34
3	gene	30.64451	30.67243	positive	MGI_C57BL6J_1915557	Lrriq4	NCBI_Gene:68307,ENSEMBL:ENSMUSG00000027703	MGI:1915557	protein coding gene	leucine-rich repeats and IQ motif containing 4
3	gene	30.67855	30.69984	negative	MGI_C57BL6J_2443864	Lrrc31	NCBI_Gene:320352,ENSEMBL:ENSMUSG00000074653	MGI:2443864	protein coding gene	leucine rich repeat containing 31
3	gene	30.68594	30.69301	positive	MGI_C57BL6J_3705271	Gm15462	NCBI_Gene:108168861,ENSEMBL:ENSMUSG00000086189	MGI:3705271	lncRNA gene	predicted gene 15462
3	gene	30.74629	30.76717	positive	MGI_C57BL6J_1923203	Samd7	NCBI_Gene:75953,ENSEMBL:ENSMUSG00000051860	MGI:1923203	protein coding gene	sterile alpha motif domain containing 7
3	gene	30.75231	30.75665	negative	MGI_C57BL6J_5592749	Gm33590	NCBI_Gene:102636556	MGI:5592749	lncRNA gene	predicted gene, 33590
3	gene	30.79257	30.79356	negative	MGI_C57BL6J_1918530	4933429H19Rik	ENSEMBL:ENSMUSG00000097786	MGI:1918530	lncRNA gene	RIKEN cDNA 4933429H19 gene
3	gene	30.79276	30.82126	positive	MGI_C57BL6J_1916526	Sec62	NCBI_Gene:69276,ENSEMBL:ENSMUSG00000027706	MGI:1916526	protein coding gene	SEC62 homolog (S. cerevisiae)
3	pseudogene	30.82857	30.82883	negative	MGI_C57BL6J_5611308	Gm38080	ENSEMBL:ENSMUSG00000104361	MGI:5611308	pseudogene	predicted gene, 38080
3	gene	30.84154	30.85199	negative	MGI_C57BL6J_5625083	Gm42198	NCBI_Gene:105247015	MGI:5625083	lncRNA gene	predicted gene, 42198
3	gene	30.85248	30.85586	negative	MGI_C57BL6J_5625084	Gm42199	NCBI_Gene:105247016	MGI:5625084	lncRNA gene	predicted gene, 42199
3	gene	30.85587	30.89719	positive	MGI_C57BL6J_1919112	Gpr160	NCBI_Gene:71862,ENSEMBL:ENSMUSG00000037661	MGI:1919112	protein coding gene	G protein-coupled receptor 160
3	gene	30.89929	30.96948	negative	MGI_C57BL6J_2181434	Phc3	NCBI_Gene:241915,ENSEMBL:ENSMUSG00000037652	MGI:2181434	protein coding gene	polyhomeotic 3
3	gene	30.95733	30.95764	negative	MGI_C57BL6J_1924590	9530022L04Rik	ENSEMBL:ENSMUSG00000102369	MGI:1924590	unclassified gene	RIKEN cDNA 9530022L04 gene
3	pseudogene	30.97291	30.97511	positive	MGI_C57BL6J_3781157	Gm2979	NCBI_Gene:100040809,ENSEMBL:ENSMUSG00000102741	MGI:3781157	pseudogene	predicted gene 2979
3	gene	30.99574	31.05296	positive	MGI_C57BL6J_99260	Prkci	NCBI_Gene:18759,ENSEMBL:ENSMUSG00000037643	MGI:99260	protein coding gene	protein kinase C, iota
3	gene	31.03897	31.03903	positive	MGI_C57BL6J_5531134	Mir7008	miRBase:MI0022857,NCBI_Gene:102465610,ENSEMBL:ENSMUSG00000098890	MGI:5531134	miRNA gene	microRNA 7008
3	gene	31.06130	31.06669	positive	MGI_C57BL6J_5592800	Gm33641	NCBI_Gene:102636630	MGI:5592800	lncRNA gene	predicted gene, 33641
3	gene	31.06243	31.07994	negative	MGI_C57BL6J_5592853	Gm33694	NCBI_Gene:102636694	MGI:5592853	lncRNA gene	predicted gene, 33694
3	gene	31.09480	31.12292	positive	MGI_C57BL6J_106203	Skil	NCBI_Gene:20482,ENSEMBL:ENSMUSG00000027660	MGI:106203	protein coding gene	SKI-like
3	gene	31.14992	31.16433	positive	MGI_C57BL6J_106925	Cldn11	NCBI_Gene:18417,ENSEMBL:ENSMUSG00000037625	MGI:106925	protein coding gene	claudin 11
3	gene	31.20285	31.31057	negative	MGI_C57BL6J_3040688	Slc7a14	NCBI_Gene:241919,ENSEMBL:ENSMUSG00000069072	MGI:3040688	protein coding gene	solute carrier family 7 (cationic amino acid transporter, y+ system), member 14
3	gene	31.23262	31.23736	positive	MGI_C57BL6J_5592993	Gm33834	NCBI_Gene:102636884	MGI:5592993	lncRNA gene	predicted gene, 33834
3	gene	31.24614	31.31690	positive	MGI_C57BL6J_3782942	Gm15496	NCBI_Gene:102636803,ENSEMBL:ENSMUSG00000085953	MGI:3782942	lncRNA gene	predicted gene 15496
3	gene	31.34101	31.34528	positive	MGI_C57BL6J_5611253	Gm38025	ENSEMBL:ENSMUSG00000103998	MGI:5611253	lncRNA gene	predicted gene, 38025
3	pseudogene	31.64480	31.69058	negative	MGI_C57BL6J_3779607	Gm6558	NCBI_Gene:625125,ENSEMBL:ENSMUSG00000103499	MGI:3779607	pseudogene	predicted gene 6558
3	gene	31.68642	31.69214	positive	MGI_C57BL6J_5593045	Gm33886	NCBI_Gene:102636961	MGI:5593045	lncRNA gene	predicted gene, 33886
3	gene	31.89883	31.90212	negative	MGI_C57BL6J_5593190	Gm34031	NCBI_Gene:102637147	MGI:5593190	lncRNA gene	predicted gene, 34031
3	gene	31.90213	32.20018	positive	MGI_C57BL6J_1919663	Kcnmb2	NCBI_Gene:72413,ENSEMBL:ENSMUSG00000037610	MGI:1919663	protein coding gene	potassium large conductance calcium-activated channel, subfamily M, beta member 2
3	gene	31.95476	31.95780	positive	MGI_C57BL6J_5611062	Gm37834	ENSEMBL:ENSMUSG00000103539	MGI:5611062	unclassified gene	predicted gene, 37834
3	gene	32.23753	32.32631	negative	MGI_C57BL6J_5625086	Gm42201	NCBI_Gene:105247019	MGI:5625086	lncRNA gene	predicted gene, 42201
3	pseudogene	32.26033	32.26111	positive	MGI_C57BL6J_5610998	Gm37770	NCBI_Gene:108168862,ENSEMBL:ENSMUSG00000103643	MGI:5610998	pseudogene	predicted gene, 37770
3	gene	32.33479	32.36601	negative	MGI_C57BL6J_1195270	Zmat3	NCBI_Gene:22401,ENSEMBL:ENSMUSG00000027663	MGI:1195270	protein coding gene	zinc finger matrin type 3
3	gene	32.36549	32.36744	positive	MGI_C57BL6J_1914826	4930429B21Rik	NCBI_Gene:67576	MGI:1914826	lncRNA gene	RIKEN cDNA 4930429B21 gene
3	gene	32.37158	32.37299	negative	MGI_C57BL6J_5610218	Gm36990	ENSEMBL:ENSMUSG00000102825	MGI:5610218	unclassified gene	predicted gene, 36990
3	gene	32.37898	32.38470	negative	MGI_C57BL6J_5625087	Gm42202	NCBI_Gene:105247020	MGI:5625087	lncRNA gene	predicted gene, 42202
3	gene	32.39707	32.46849	positive	MGI_C57BL6J_1206581	Pik3ca	NCBI_Gene:18706,ENSEMBL:ENSMUSG00000027665	MGI:1206581	protein coding gene	phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
3	gene	32.45459	32.45576	positive	MGI_C57BL6J_5610351	Gm37123	ENSEMBL:ENSMUSG00000103039	MGI:5610351	unclassified gene	predicted gene, 37123
3	gene	32.46778	32.50290	negative	MGI_C57BL6J_3612244	Kcnmb3	NCBI_Gene:100502876,ENSEMBL:ENSMUSG00000091091	MGI:3612244	protein coding gene	potassium large conductance calcium-activated channel, subfamily M, beta member 3
3	gene	32.51026	32.52083	positive	MGI_C57BL6J_1915028	Zfp639	NCBI_Gene:67778,ENSEMBL:ENSMUSG00000027667	MGI:1915028	protein coding gene	zinc finger protein 639
3	gene	32.51180	32.51234	negative	MGI_C57BL6J_5610820	Gm37592	ENSEMBL:ENSMUSG00000104231	MGI:5610820	lncRNA gene	predicted gene, 37592
3	gene	32.52946	32.57924	positive	MGI_C57BL6J_1914664	Mfn1	NCBI_Gene:67414,ENSEMBL:ENSMUSG00000027668	MGI:1914664	protein coding gene	mitofusin 1
3	gene	32.58033	32.61659	negative	MGI_C57BL6J_104581	Gnb4	NCBI_Gene:14696,ENSEMBL:ENSMUSG00000027669	MGI:104581	protein coding gene	guanine nucleotide binding protein (G protein), beta 4
3	gene	32.61086	32.61351	positive	MGI_C57BL6J_5610868	Gm37640	ENSEMBL:ENSMUSG00000102862	MGI:5610868	lncRNA gene	predicted gene, 37640
3	gene	32.70630	32.72697	positive	MGI_C57BL6J_1861453	Actl6a	NCBI_Gene:56456,ENSEMBL:ENSMUSG00000027671	MGI:1861453	protein coding gene	actin-like 6A
3	gene	32.72178	32.72209	negative	MGI_C57BL6J_5610581	Gm37353	ENSEMBL:ENSMUSG00000103590	MGI:5610581	unclassified gene	predicted gene, 37353
3	gene	32.72540	32.73761	negative	MGI_C57BL6J_1921850	Mrpl47	NCBI_Gene:74600,ENSEMBL:ENSMUSG00000037531	MGI:1921850	protein coding gene	mitochondrial ribosomal protein L47
3	gene	32.73610	32.73761	negative	MGI_C57BL6J_3704212	Gm9859	NA	NA	unclassified gene	predicted gene 9859
3	gene	32.73699	32.75157	positive	MGI_C57BL6J_1913296	Ndufb5	NCBI_Gene:66046,ENSEMBL:ENSMUSG00000027673	MGI:1913296	protein coding gene	NADH:ubiquinone oxidoreductase subunit B5
3	gene	32.81702	32.93807	positive	MGI_C57BL6J_1919857	Usp13	NCBI_Gene:72607,ENSEMBL:ENSMUSG00000056900	MGI:1919857	protein coding gene	ubiquitin specific peptidase 13 (isopeptidase T-3)
3	pseudogene	32.88001	32.88061	negative	MGI_C57BL6J_3783022	Gm15574	ENSEMBL:ENSMUSG00000081883	MGI:3783022	pseudogene	predicted gene 15574
3	gene	32.93931	32.98330	positive	MGI_C57BL6J_5610687	Gm37459	ENSEMBL:ENSMUSG00000104283	MGI:5610687	lncRNA gene	predicted gene, 37459
3	gene	32.94793	33.14327	negative	MGI_C57BL6J_1916672	Pex5l	NCBI_Gene:58869,ENSEMBL:ENSMUSG00000027674	MGI:1916672	protein coding gene	peroxisomal biogenesis factor 5-like
3	gene	33.01196	33.01211	positive	MGI_C57BL6J_5452991	Gm23214	ENSEMBL:ENSMUSG00000084665	MGI:5452991	snRNA gene	predicted gene, 23214
3	gene	33.02478	33.08861	positive	MGI_C57BL6J_1921124	4930419G24Rik	NCBI_Gene:73874,ENSEMBL:ENSMUSG00000087625	MGI:1921124	lncRNA gene	RIKEN cDNA 4930419G24 gene
3	gene	33.03423	33.03705	negative	MGI_C57BL6J_5610671	Gm37443	ENSEMBL:ENSMUSG00000102581	MGI:5610671	unclassified gene	predicted gene, 37443
3	gene	33.07392	33.07636	negative	MGI_C57BL6J_5011630	Gm19445	ENSEMBL:ENSMUSG00000102498	MGI:5011630	unclassified gene	predicted gene, 19445
3	pseudogene	33.19080	33.19104	positive	MGI_C57BL6J_5610356	Gm37128	ENSEMBL:ENSMUSG00000103896	MGI:5610356	pseudogene	predicted gene, 37128
3	gene	33.26072	33.26082	negative	MGI_C57BL6J_5531356	Gm27974	ENSEMBL:ENSMUSG00000098622	MGI:5531356	miRNA gene	predicted gene, 27974
3	gene	33.28312	33.28565	positive	MGI_C57BL6J_5610259	Gm37031	ENSEMBL:ENSMUSG00000104384	MGI:5610259	unclassified gene	predicted gene, 37031
3	gene	33.39306	33.39320	negative	MGI_C57BL6J_5454557	Gm24780	ENSEMBL:ENSMUSG00000088260	MGI:5454557	snoRNA gene	predicted gene, 24780
3	gene	33.39338	33.39485	negative	MGI_C57BL6J_5610626	Gm37398	ENSEMBL:ENSMUSG00000104203	MGI:5610626	unclassified gene	predicted gene, 37398
3	gene	33.54027	33.54342	positive	MGI_C57BL6J_5593364	Gm34205	NCBI_Gene:102637377	MGI:5593364	lncRNA gene	predicted gene, 34205
3	pseudogene	33.62159	33.62245	positive	MGI_C57BL6J_3649050	Gm5845	NCBI_Gene:545512,ENSEMBL:ENSMUSG00000103423	MGI:3649050	pseudogene	predicted gene 5845
3	pseudogene	33.68451	33.68487	negative	MGI_C57BL6J_5662831	Gm42694	ENSEMBL:ENSMUSG00000104954	MGI:5662831	pseudogene	predicted gene 42694
3	gene	33.68696	33.69200	negative	MGI_C57BL6J_5625088	Gm42203	NCBI_Gene:105247021	MGI:5625088	lncRNA gene	predicted gene, 42203
3	gene	33.70336	33.75962	negative	MGI_C57BL6J_5663803	Gm43666	ENSEMBL:ENSMUSG00000104588	MGI:5663803	lncRNA gene	predicted gene 43666
3	pseudogene	33.73060	33.73353	positive	MGI_C57BL6J_5010796	Gm18611	NCBI_Gene:100417436,ENSEMBL:ENSMUSG00000106231	MGI:5010796	pseudogene	predicted gene, 18611
3	gene	33.79983	33.81486	positive	MGI_C57BL6J_1914370	Ttc14	NCBI_Gene:67120,ENSEMBL:ENSMUSG00000027677	MGI:1914370	protein coding gene	tetratricopeptide repeat domain 14
3	gene	33.81076	33.84432	negative	MGI_C57BL6J_1289263	Ccdc39	NCBI_Gene:51938,ENSEMBL:ENSMUSG00000027676	MGI:1289263	protein coding gene	coiled-coil domain containing 39
3	gene	33.81726	33.81795	positive	MGI_C57BL6J_5663277	Gm43140	ENSEMBL:ENSMUSG00000105286	MGI:5663277	lncRNA gene	predicted gene 43140
3	gene	33.86681	33.89758	negative	MGI_C57BL6J_1921204	4930431L21Rik	ENSEMBL:ENSMUSG00000105475	MGI:1921204	lncRNA gene	RIKEN cDNA 4930431L21 gene
3	gene	33.90684	33.90823	positive	MGI_C57BL6J_5625089	Gm42204	NCBI_Gene:105247022	MGI:5625089	lncRNA gene	predicted gene, 42204
3	gene	33.95620	33.95715	positive	MGI_C57BL6J_1922225	4930502C17Rik	ENSEMBL:ENSMUSG00000106584	MGI:1922225	unclassified gene	RIKEN cDNA 4930502C17 gene
3	gene	33.95907	33.95920	negative	MGI_C57BL6J_5452952	Gm23175	ENSEMBL:ENSMUSG00000077559	MGI:5452952	snoRNA gene	predicted gene, 23175
3	gene	33.97218	33.97545	negative	MGI_C57BL6J_5826470	Gm46833	NCBI_Gene:108168913	MGI:5826470	lncRNA gene	predicted gene, 46833
3	pseudogene	34.00477	34.00551	negative	MGI_C57BL6J_3642317	Gm9791	NCBI_Gene:100040232,ENSEMBL:ENSMUSG00000044434	MGI:3642317	pseudogene	predicted pseudogene 9791
3	gene	34.00880	34.01188	negative	MGI_C57BL6J_5826435	Gm46798	NCBI_Gene:108168863	MGI:5826435	lncRNA gene	predicted gene, 46798
3	gene	34.01771	34.01988	negative	MGI_C57BL6J_5663214	Gm43077	ENSEMBL:ENSMUSG00000105535	MGI:5663214	lncRNA gene	predicted gene 43077
3	gene	34.01994	34.07032	positive	MGI_C57BL6J_104860	Fxr1	NCBI_Gene:14359,ENSEMBL:ENSMUSG00000027680	MGI:104860	protein coding gene	fragile X mental retardation gene 1, autosomal homolog
3	gene	34.05434	34.05543	negative	MGI_C57BL6J_5663804	Gm43667	ENSEMBL:ENSMUSG00000105135	MGI:5663804	unclassified gene	predicted gene 43667
3	gene	34.05602	34.08135	negative	MGI_C57BL6J_1914963	Dnajc19	NCBI_Gene:67713,ENSEMBL:ENSMUSG00000027679	MGI:1914963	protein coding gene	DnaJ heat shock protein family (Hsp40) member C19
3	gene	34.07066	34.07600	positive	MGI_C57BL6J_5663805	Gm43668	ENSEMBL:ENSMUSG00000105176	MGI:5663805	unclassified gene	predicted gene 43668
3	gene	34.10427	34.68262	positive	MGI_C57BL6J_2444112	Sox2ot	NCBI_Gene:320478,ENSEMBL:ENSMUSG00000105265	MGI:2444112	lncRNA gene	SOX2 overlapping transcript (non-protein coding)
3	pseudogene	34.18331	34.18419	positive	MGI_C57BL6J_3647478	Gm5708	NCBI_Gene:435727,ENSEMBL:ENSMUSG00000105739	MGI:3647478	pseudogene	predicted gene 5708
3	gene	34.28133	34.35199	negative	MGI_C57BL6J_5621390	Gm38505	NCBI_Gene:102638008,ENSEMBL:ENSMUSG00000092196	MGI:5621390	lncRNA gene	predicted gene, 38505
3	gene	34.41544	34.41816	positive	MGI_C57BL6J_5593758	Gm34599	NCBI_Gene:102637903,ENSEMBL:ENSMUSG00000105577	MGI:5593758	lncRNA gene	predicted gene, 34599
3	gene	34.42737	34.43510	negative	MGI_C57BL6J_5141980	Gm20515	ENSEMBL:ENSMUSG00000092242	MGI:5141980	lncRNA gene	predicted gene 20515
3	gene	34.48143	34.48221	negative	MGI_C57BL6J_5579841	Gm29135	ENSEMBL:ENSMUSG00000099437	MGI:5579841	lncRNA gene	predicted gene 29135
3	gene	34.56034	34.56055	positive	MGI_C57BL6J_5530785	Gm27403	ENSEMBL:ENSMUSG00000098795	MGI:5530785	unclassified non-coding RNA gene	predicted gene, 27403
3	gene	34.56526	34.57220	negative	MGI_C57BL6J_5662832	Gm42695	ENSEMBL:ENSMUSG00000106525	MGI:5662832	lncRNA gene	predicted gene 42695
3	gene	34.59782	34.60488	negative	MGI_C57BL6J_5625090	Gm42205	NCBI_Gene:105247023,ENSEMBL:ENSMUSG00000105222	MGI:5625090	lncRNA gene	predicted gene, 42205
3	gene	34.63846	34.63854	positive	MGI_C57BL6J_3811407	Mir1897	miRBase:MI0008314,NCBI_Gene:100316679,ENSEMBL:ENSMUSG00000104797	MGI:3811407	miRNA gene	microRNA 1897
3	gene	34.64326	34.64610	positive	MGI_C57BL6J_5662829	Gm42692	ENSEMBL:ENSMUSG00000104901	MGI:5662829	unclassified gene	predicted gene 42692
3	gene	34.64999	34.65246	positive	MGI_C57BL6J_98364	Sox2	NCBI_Gene:20674,ENSEMBL:ENSMUSG00000074637	MGI:98364	protein coding gene	SRY (sex determining region Y)-box 2
3	gene	34.65318	34.65328	positive	MGI_C57BL6J_5530993	Gm27611	ENSEMBL:ENSMUSG00000098254	MGI:5530993	unclassified non-coding RNA gene	predicted gene, 27611
3	gene	34.66366	34.66429	negative	MGI_C57BL6J_5662830	Gm42693	ENSEMBL:ENSMUSG00000105284	MGI:5662830	unclassified gene	predicted gene 42693
3	gene	34.68263	34.68275	positive	MGI_C57BL6J_5663343	Gm43206	ENSEMBL:ENSMUSG00000105101	MGI:5663343	unclassified gene	predicted gene 43206
3	gene	34.68938	34.69292	positive	MGI_C57BL6J_5594100	Gm34941	NCBI_Gene:102638356	MGI:5594100	lncRNA gene	predicted gene, 34941
3	gene	34.69964	34.71666	negative	MGI_C57BL6J_3781322	Gm3143	NCBI_Gene:100041108,ENSEMBL:ENSMUSG00000105153	MGI:3781322	lncRNA gene	predicted gene 3143
3	gene	34.77208	34.78235	positive	MGI_C57BL6J_5621394	Gm38509	NCBI_Gene:102638436,ENSEMBL:ENSMUSG00000106519	MGI:5621394	lncRNA gene	predicted gene, 38509
3	gene	34.82656	34.87928	positive	MGI_C57BL6J_5434743	Gm21388	NCBI_Gene:100861998,ENSEMBL:ENSMUSG00000114832	MGI:5434743	lncRNA gene	predicted gene, 21388
3	gene	34.92254	34.92265	negative	MGI_C57BL6J_5531088	Mir6378	miRBase:MI0021909,NCBI_Gene:102466155,ENSEMBL:ENSMUSG00000098862	MGI:5531088	miRNA gene	microRNA 6378
3	gene	34.95023	34.95953	positive	MGI_C57BL6J_5594414	Gm35255	NCBI_Gene:102638771	MGI:5594414	lncRNA gene	predicted gene, 35255
3	gene	35.25646	35.27613	negative	MGI_C57BL6J_1923648	1700017M07Rik	NCBI_Gene:76398,ENSEMBL:ENSMUSG00000105651	MGI:1923648	lncRNA gene	RIKEN cDNA 1700017M07 gene
3	gene	35.31844	35.33011	positive	MGI_C57BL6J_5594584	Gm35425	NCBI_Gene:102639001	MGI:5594584	lncRNA gene	predicted gene, 35425
3	gene	35.32561	35.32570	positive	MGI_C57BL6J_5455219	Gm25442	ENSEMBL:ENSMUSG00000093499	MGI:5455219	miRNA gene	predicted gene, 25442
3	gene	35.33770	35.40595	negative	MGI_C57BL6J_5621397	Gm38512	NCBI_Gene:102638848	MGI:5621397	lncRNA gene	predicted gene, 38512
3	gene	35.41383	35.41400	positive	MGI_C57BL6J_5663215	Gm43078	ENSEMBL:ENSMUSG00000106512	MGI:5663215	unclassified gene	predicted gene 43078
3	pseudogene	35.53688	35.53780	negative	MGI_C57BL6J_3643628	Gm7733	NCBI_Gene:665655,ENSEMBL:ENSMUSG00000106496	MGI:3643628	pseudogene	predicted gene 7733
3	pseudogene	35.54589	35.54633	positive	MGI_C57BL6J_1347022	Ube2l3-ps1	ENSEMBL:ENSMUSG00000105040	MGI:1347022	pseudogene	ubiquitin-conjugating enzyme E2L 3, pseudogene 1
3	gene	35.59715	35.66616	negative	MGI_C57BL6J_3779620	Gm6639	NCBI_Gene:625963,ENSEMBL:ENSMUSG00000105662	MGI:3779620	lncRNA gene	predicted gene 6639
3	gene	35.73537	35.73548	positive	MGI_C57BL6J_5455473	Gm25696	ENSEMBL:ENSMUSG00000064834	MGI:5455473	snRNA gene	predicted gene, 25696
3	gene	35.75406	35.85628	positive	MGI_C57BL6J_1923545	Atp11b	NCBI_Gene:76295,ENSEMBL:ENSMUSG00000037400	MGI:1923545	protein coding gene	ATPase, class VI, type 11B
3	gene	35.84534	35.84590	positive	MGI_C57BL6J_5663340	Gm43203	ENSEMBL:ENSMUSG00000104897	MGI:5663340	unclassified gene	predicted gene 43203
3	gene	35.86162	35.86212	positive	MGI_C57BL6J_1915850	1110021P09Rik	NA	NA	unclassified gene	RIKEN cDNA 1110021P09 gene
3	pseudogene	35.86386	35.86507	positive	MGI_C57BL6J_3647088	Gm7741	NCBI_Gene:665667,ENSEMBL:ENSMUSG00000097713	MGI:3647088	pseudogene	predicted gene 7741
3	pseudogene	35.87565	35.88335	negative	MGI_C57BL6J_5295701	Gm20595	NCBI_Gene:100463514	MGI:5295701	pseudogene	predicted gene, 20595
3	gene	35.89211	35.93744	negative	MGI_C57BL6J_2150386	Dcun1d1	NCBI_Gene:114893,ENSEMBL:ENSMUSG00000027708	MGI:2150386	protein coding gene	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)
3	gene	35.93304	35.99084	positive	MGI_C57BL6J_3802149	Gm15952	NCBI_Gene:102639351,ENSEMBL:ENSMUSG00000085655	MGI:3802149	lncRNA gene	predicted gene 15952
3	gene	35.95544	35.95626	negative	MGI_C57BL6J_1925753	8430422M14Rik	ENSEMBL:ENSMUSG00000105095	MGI:1925753	unclassified gene	RIKEN cDNA 8430422M14 gene
3	gene	35.95629	36.00068	negative	MGI_C57BL6J_1919289	Mccc1	NCBI_Gene:72039,ENSEMBL:ENSMUSG00000027709	MGI:1919289	protein coding gene	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)
3	gene	35.96938	35.97203	negative	MGI_C57BL6J_5663217	Gm43080	ENSEMBL:ENSMUSG00000105556	MGI:5663217	unclassified gene	predicted gene 43080
3	pseudogene	35.97377	35.97409	positive	MGI_C57BL6J_3704213	B230207O21Rik	ENSEMBL:ENSMUSG00000106096	MGI:3704213	pseudogene	RIKEN cDNA B230207O21 gene
3	gene	35.99983	36.02511	positive	MGI_C57BL6J_3590669	Mccc1os	NCBI_Gene:654424,ENSEMBL:ENSMUSG00000086392	MGI:3590669	antisense lncRNA gene	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha), opposite strand
3	gene	36.00724	36.05355	negative	MGI_C57BL6J_2681852	Ccdc144b	NCBI_Gene:241943,ENSEMBL:ENSMUSG00000047696	MGI:2681852	protein coding gene	coiled-coil domain containing 144B
3	gene	36.06598	36.09286	positive	MGI_C57BL6J_1914272	Acad9	NCBI_Gene:229211,ENSEMBL:ENSMUSG00000027710	MGI:1914272	protein coding gene	acyl-Coenzyme A dehydrogenase family, member 9
3	gene	36.08886	36.09145	positive	MGI_C57BL6J_5663216	Gm43079	ENSEMBL:ENSMUSG00000105055	MGI:5663216	lncRNA gene	predicted gene 43079
3	gene	36.09718	36.09914	positive	MGI_C57BL6J_5663342	Gm43205	ENSEMBL:ENSMUSG00000105419	MGI:5663342	unclassified gene	predicted gene 43205
3	gene	36.15102	36.17034	positive	MGI_C57BL6J_1098769	Zfp267	NCBI_Gene:241944,ENSEMBL:ENSMUSG00000033883	MGI:1098769	protein coding gene	zinc finger protein 267
3	gene	36.17942	36.22231	negative	MGI_C57BL6J_2677633	Qrfpr	NCBI_Gene:229214,ENSEMBL:ENSMUSG00000058400	MGI:2677633	protein coding gene	pyroglutamylated RFamide peptide receptor
3	gene	36.20329	36.20562	positive	MGI_C57BL6J_5663392	Gm43255	ENSEMBL:ENSMUSG00000104568	MGI:5663392	lncRNA gene	predicted gene 43255
3	pseudogene	36.21381	36.21476	negative	MGI_C57BL6J_5011078	Gm18893	NCBI_Gene:100417907,ENSEMBL:ENSMUSG00000106180	MGI:5011078	pseudogene	predicted gene, 18893
3	gene	36.27233	36.27896	negative	MGI_C57BL6J_5625093	Gm42208	NCBI_Gene:105247026,ENSEMBL:ENSMUSG00000106140	MGI:5625093	lncRNA gene	predicted gene, 42208
3	gene	36.35422	36.40651	negative	MGI_C57BL6J_5625094	Gm42209	NCBI_Gene:105247027	MGI:5625094	lncRNA gene	predicted gene, 42209
3	pseudogene	36.39470	36.39520	negative	MGI_C57BL6J_5010020	Gm17835	NCBI_Gene:100415952,ENSEMBL:ENSMUSG00000105281	MGI:5010020	pseudogene	predicted gene, 17835
3	pseudogene	36.42158	36.42212	positive	MGI_C57BL6J_5010072	Gm17887	NCBI_Gene:100416041,ENSEMBL:ENSMUSG00000105792	MGI:5010072	pseudogene	predicted gene, 17887
3	gene	36.44892	36.47589	negative	MGI_C57BL6J_106008	Anxa5	NCBI_Gene:11747,ENSEMBL:ENSMUSG00000027712	MGI:106008	protein coding gene	annexin A5
3	gene	36.47546	36.47552	negative	MGI_C57BL6J_5530854	Mir7009	miRBase:MI0022858,NCBI_Gene:102466786,ENSEMBL:ENSMUSG00000098808	MGI:5530854	miRNA gene	microRNA 7009
3	gene	36.47594	36.48230	positive	MGI_C57BL6J_1919532	1810062G17Rik	NCBI_Gene:72282,ENSEMBL:ENSMUSG00000027713	MGI:1919532	protein coding gene	RIKEN cDNA 1810062G17 gene
3	gene	36.49980	36.50681	negative	MGI_C57BL6J_3650340	Gm11548	NCBI_Gene:329623,ENSEMBL:ENSMUSG00000085320	MGI:3650340	lncRNA gene	predicted gene 11548
3	gene	36.51506	36.52181	negative	MGI_C57BL6J_3650339	Gm11549	NCBI_Gene:100503068,ENSEMBL:ENSMUSG00000085007	MGI:3650339	lincRNA gene	predicted gene 11549
3	gene	36.52922	36.53233	negative	MGI_C57BL6J_5663674	Gm43537	ENSEMBL:ENSMUSG00000105022	MGI:5663674	unclassified gene	predicted gene 43537
3	pseudogene	36.53917	36.54010	negative	MGI_C57BL6J_3650891	Gm11550	NCBI_Gene:665709,ENSEMBL:ENSMUSG00000083388	MGI:3650891	pseudogene	predicted gene 11550
3	gene	36.55261	36.56573	positive	MGI_C57BL6J_1355319	Exosc9	NCBI_Gene:50911,ENSEMBL:ENSMUSG00000027714	MGI:1355319	protein coding gene	exosome component 9
3	gene	36.56486	36.57303	negative	MGI_C57BL6J_108069	Ccna2	NCBI_Gene:12428,ENSEMBL:ENSMUSG00000027715	MGI:108069	protein coding gene	cyclin A2
3	gene	36.57314	36.61349	negative	MGI_C57BL6J_1918742	Bbs7	NCBI_Gene:71492,ENSEMBL:ENSMUSG00000037325	MGI:1918742	protein coding gene	Bardet-Biedl syndrome 7 (human)
3	gene	36.62048	36.69022	negative	MGI_C57BL6J_109526	Trpc3	NCBI_Gene:22065,ENSEMBL:ENSMUSG00000027716	MGI:109526	protein coding gene	transient receptor potential cation channel, subfamily C, member 3
3	gene	36.65407	36.65501	negative	MGI_C57BL6J_5595015	Gm35856	NCBI_Gene:102639576	MGI:5595015	lncRNA gene	predicted gene, 35856
3	pseudogene	36.69480	36.69505	negative	MGI_C57BL6J_3651607	Gm12377	ENSEMBL:ENSMUSG00000082548	MGI:3651607	pseudogene	predicted gene 12377
3	pseudogene	36.82435	36.82506	negative	MGI_C57BL6J_3651608	Gm12376	NCBI_Gene:100417988,ENSEMBL:ENSMUSG00000084027	MGI:3651608	pseudogene	predicted gene 12376
3	gene	36.86306	37.05303	positive	MGI_C57BL6J_2444631	4932438A13Rik	NCBI_Gene:229227,ENSEMBL:ENSMUSG00000037270	MGI:2444631	protein coding gene	RIKEN cDNA 4932438A13 gene
3	gene	37.05221	37.06003	negative	MGI_C57BL6J_3650531	Gm12531	ENSEMBL:ENSMUSG00000086090	MGI:3650531	lncRNA gene	predicted gene 12531
3	gene	37.06309	37.12193	positive	MGI_C57BL6J_103258	Adad1	NCBI_Gene:21744,ENSEMBL:ENSMUSG00000027719	MGI:103258	protein coding gene	adenosine deaminase domain containing 1 (testis specific)
3	pseudogene	37.07756	37.07891	positive	MGI_C57BL6J_3651489	Gm12582	NCBI_Gene:652987,ENSEMBL:ENSMUSG00000081705	MGI:3651489	pseudogene	predicted gene 12582
3	pseudogene	37.10808	37.10933	positive	MGI_C57BL6J_3651485	Gm12583	NCBI_Gene:100416060,ENSEMBL:ENSMUSG00000082878	MGI:3651485	pseudogene	predicted gene 12583
3	pseudogene	37.11673	37.11784	positive	MGI_C57BL6J_3651486	Gm12584	ENSEMBL:ENSMUSG00000083857	MGI:3651486	pseudogene	predicted gene 12584
3	gene	37.12052	37.12596	negative	MGI_C57BL6J_96548	Il2	NCBI_Gene:16183,ENSEMBL:ENSMUSG00000027720	MGI:96548	protein coding gene	interleukin 2
3	gene	37.16972	37.17665	negative	MGI_C57BL6J_5595159	Gm36000	NCBI_Gene:102639768	MGI:5595159	lncRNA gene	predicted gene, 36000
3	gene	37.18218	37.18860	positive	MGI_C57BL6J_3650618	Gm12532	NCBI_Gene:102639848,ENSEMBL:ENSMUSG00000084754	MGI:3650618	lncRNA gene	predicted gene 12532
3	gene	37.22276	37.23264	negative	MGI_C57BL6J_1890474	Il21	NCBI_Gene:60505,ENSEMBL:ENSMUSG00000027718	MGI:1890474	protein coding gene	interleukin 21
3	gene	37.22538	37.22711	positive	MGI_C57BL6J_5595327	Gm36168	NCBI_Gene:102639985	MGI:5595327	lncRNA gene	predicted gene, 36168
3	gene	37.23133	37.23247	positive	MGI_C57BL6J_3650303	Gm12534	ENSEMBL:ENSMUSG00000086517	MGI:3650303	lncRNA gene	predicted gene 12534
3	gene	37.23287	37.23334	positive	MGI_C57BL6J_5663959	Gm43822	ENSEMBL:ENSMUSG00000104998	MGI:5663959	unclassified gene	predicted gene 43822
3	gene	37.25678	37.25689	negative	MGI_C57BL6J_5453946	Gm24169	ENSEMBL:ENSMUSG00000094007	MGI:5453946	miRNA gene	predicted gene, 24169
3	gene	37.30775	37.31271	negative	MGI_C57BL6J_2677454	Cetn4	NCBI_Gene:207175,ENSEMBL:ENSMUSG00000045031	MGI:2677454	protein coding gene	centrin 4
3	gene	37.31249	37.32145	positive	MGI_C57BL6J_2686651	Bbs12	NCBI_Gene:241950,ENSEMBL:ENSMUSG00000051444	MGI:2686651	protein coding gene	Bardet-Biedl syndrome 12 (human)
3	gene	37.31252	37.40487	positive	MGI_C57BL6J_5663576	Gm43439	ENSEMBL:ENSMUSG00000106407	MGI:5663576	lncRNA gene	predicted gene 43439
3	pseudogene	37.31253	37.32919	positive	MGI_C57BL6J_3651849	Gm12540	NCBI_Gene:102640067,ENSEMBL:ENSMUSG00000083353	MGI:3651849	pseudogene	predicted gene 12540
3	gene	37.33329	37.35103	negative	MGI_C57BL6J_3649376	Fgf2os	NCBI_Gene:329626,ENSEMBL:ENSMUSG00000054779	MGI:3649376	antisense lncRNA gene	fibroblast growth factor 2, opposite strand
3	gene	37.33902	37.34152	positive	MGI_C57BL6J_5663625	Gm43488	ENSEMBL:ENSMUSG00000105063	MGI:5663625	unclassified gene	predicted gene 43488
3	gene	37.34835	37.41011	positive	MGI_C57BL6J_95516	Fgf2	NCBI_Gene:14173,ENSEMBL:ENSMUSG00000037225	MGI:95516	protein coding gene	fibroblast growth factor 2
3	gene	37.39221	37.39510	negative	MGI_C57BL6J_5663060	Gm42923	ENSEMBL:ENSMUSG00000105134	MGI:5663060	unclassified gene	predicted gene 42923
3	gene	37.40491	37.42021	negative	MGI_C57BL6J_2387618	Nudt6	NCBI_Gene:229228,ENSEMBL:ENSMUSG00000050174	MGI:2387618	protein coding gene	nudix (nucleoside diphosphate linked moiety X)-type motif 6
3	gene	37.41990	37.57910	positive	MGI_C57BL6J_1927170	Spata5	NCBI_Gene:57815,ENSEMBL:ENSMUSG00000027722	MGI:1927170	protein coding gene	spermatogenesis associated 5
3	gene	37.48883	37.49479	positive	MGI_C57BL6J_5663621	Gm43484	ENSEMBL:ENSMUSG00000106166	MGI:5663621	unclassified gene	predicted gene 43484
3	gene	37.54188	37.60239	negative	MGI_C57BL6J_5595571	Gm36412	NCBI_Gene:102640314	MGI:5595571	lncRNA gene	predicted gene, 36412
3	pseudogene	37.55618	37.55650	negative	MGI_C57BL6J_3652207	Gm12564	ENSEMBL:ENSMUSG00000080723	MGI:3652207	pseudogene	predicted gene 12564
3	pseudogene	37.59942	37.60007	negative	MGI_C57BL6J_3652206	Gm12565	NCBI_Gene:665778,ENSEMBL:ENSMUSG00000081093	MGI:3652206	pseudogene	predicted gene 12565
3	gene	37.60989	37.61528	positive	MGI_C57BL6J_1923197	4930594O21Rik	NCBI_Gene:75947,ENSEMBL:ENSMUSG00000085677	MGI:1923197	lncRNA gene	RIKEN cDNA 4930594O21 gene
3	gene	37.63858	37.64066	negative	MGI_C57BL6J_5663059	Gm42922	ENSEMBL:ENSMUSG00000104605	MGI:5663059	unclassified gene	predicted gene 42922
3	gene	37.63995	37.64460	positive	MGI_C57BL6J_1345139	Spry1	NCBI_Gene:24063,ENSEMBL:ENSMUSG00000037211	MGI:1345139	protein coding gene	sprouty RTK signaling antagonist 1
3	gene	37.64461	37.64795	positive	MGI_C57BL6J_5663957	Gm43820	ENSEMBL:ENSMUSG00000106062	MGI:5663957	unclassified gene	predicted gene 43820
3	gene	37.65268	37.65652	negative	MGI_C57BL6J_5826436	Gm46799	NCBI_Gene:108168864	MGI:5826436	lncRNA gene	predicted gene, 46799
3	gene	37.69046	37.69486	negative	MGI_C57BL6J_5625096	Gm42211	NCBI_Gene:105247029	MGI:5625096	lncRNA gene	predicted gene, 42211
3	gene	37.70802	37.71121	positive	MGI_C57BL6J_5663551	Gm43414	ENSEMBL:ENSMUSG00000104935	MGI:5663551	unclassified gene	predicted gene 43414
3	gene	37.71419	37.72449	negative	MGI_C57BL6J_3646006	Gm5148	NCBI_Gene:381438,ENSEMBL:ENSMUSG00000058174	MGI:3646006	protein coding gene	predicted gene 5148
3	pseudogene	37.71471	37.71522	positive	MGI_C57BL6J_3705429	Rps23-ps1	NCBI_Gene:100038875,ENSEMBL:ENSMUSG00000100755	MGI:3705429	pseudogene	ribosomal protein S23, pseudogene 1
3	gene	37.72423	37.74132	positive	MGI_C57BL6J_5595779	Gm36620	NCBI_Gene:102640592	MGI:5595779	lncRNA gene	predicted gene, 36620
3	pseudogene	37.73468	37.73514	positive	MGI_C57BL6J_3643738	Rpl31-ps15	NCBI_Gene:626367,ENSEMBL:ENSMUSG00000097304	MGI:3643738	pseudogene	ribosomal protein L31, pseudogene 15
3	gene	37.75320	37.77440	positive	MGI_C57BL6J_5625095	Gm42210	NCBI_Gene:105247028	MGI:5625095	lncRNA gene	predicted gene, 42210
3	gene	37.76104	37.76730	positive	MGI_C57BL6J_5663058	Gm42921	ENSEMBL:ENSMUSG00000106441	MGI:5663058	lncRNA gene	predicted gene 42921
3	gene	37.80254	37.80265	negative	MGI_C57BL6J_5456181	Gm26404	ENSEMBL:ENSMUSG00000089123	MGI:5456181	snoRNA gene	predicted gene, 26404
3	gene	37.82822	37.84829	positive	MGI_C57BL6J_1925294	4930556A17Rik	NCBI_Gene:102640520	MGI:1925294	lncRNA gene	RIKEN cDNA 4930556A17 gene
3	gene	37.83847	37.83957	positive	MGI_C57BL6J_5662889	Gm42752	ENSEMBL:ENSMUSG00000106621	MGI:5662889	unclassified gene	predicted gene 42752
3	gene	37.84180	37.84307	positive	MGI_C57BL6J_5662890	Gm42753	ENSEMBL:ENSMUSG00000105252	MGI:5662890	unclassified gene	predicted gene 42753
3	gene	37.89881	37.99273	positive	MGI_C57BL6J_5434111	Gm20755	NCBI_Gene:626410,ENSEMBL:ENSMUSG00000106461	MGI:5434111	lncRNA gene	predicted gene, 20755
3	pseudogene	37.95961	37.96009	negative	MGI_C57BL6J_3643378	Gm7799	ENSEMBL:ENSMUSG00000087457	MGI:3643378	pseudogene	predicted gene 7799
3	gene	37.98279	37.98335	positive	MGI_C57BL6J_5662888	Gm42751	ENSEMBL:ENSMUSG00000105099	MGI:5662888	unclassified gene	predicted gene 42751
3	gene	37.99511	37.99524	negative	MGI_C57BL6J_5452676	Gm22899	ENSEMBL:ENSMUSG00000077728	MGI:5452676	snoRNA gene	predicted gene, 22899
3	gene	38.09463	38.13019	negative	MGI_C57BL6J_5663958	Gm43821	ENSEMBL:ENSMUSG00000105219	MGI:5663958	lncRNA gene	predicted gene 43821
3	pseudogene	38.10123	38.10798	negative	MGI_C57BL6J_3643358	Rpl21-ps10	NCBI_Gene:665821,ENSEMBL:ENSMUSG00000105359	MGI:3643358	pseudogene	ribosomal protein L21, pseudogene 10
3	gene	38.15191	38.15915	positive	MGI_C57BL6J_5595839	Gm36680	NCBI_Gene:102640666	MGI:5595839	lncRNA gene	predicted gene, 36680
3	gene	38.20315	38.20812	negative	MGI_C57BL6J_1918592	5430434I15Rik	NCBI_Gene:71342,ENSEMBL:ENSMUSG00000106002	MGI:1918592	lncRNA gene	RIKEN cDNA 5430434I15 gene
3	pseudogene	38.22345	38.22382	positive	MGI_C57BL6J_3781143	Gm2965	NCBI_Gene:100040785,ENSEMBL:ENSMUSG00000105943	MGI:3781143	pseudogene	predicted gene 2965
3	pseudogene	38.25402	38.25480	positive	MGI_C57BL6J_5010140	Gm17955	NCBI_Gene:100416169	MGI:5010140	pseudogene	predicted gene, 17955
3	gene	38.26784	38.26808	negative	MGI_C57BL6J_5455351	Gm25574	ENSEMBL:ENSMUSG00000092986	MGI:5455351	unclassified non-coding RNA gene	predicted gene, 25574
3	gene	38.36615	38.36888	negative	MGI_C57BL6J_5625098	Gm42213	NCBI_Gene:105247031	MGI:5625098	lncRNA gene	predicted gene, 42213
3	gene	38.36940	38.37364	positive	MGI_C57BL6J_5663057	Gm42920	ENSEMBL:ENSMUSG00000106008	MGI:5663057	lncRNA gene	predicted gene 42920
3	gene	38.41897	38.42015	negative	MGI_C57BL6J_1917958	3830422I06Rik	ENSEMBL:ENSMUSG00000106485	MGI:1917958	unclassified gene	RIKEN cDNA 3830422I06 gene
3	gene	38.42655	38.44387	negative	MGI_C57BL6J_5595982	Gm36823	NCBI_Gene:102640855,ENSEMBL:ENSMUSG00000105516	MGI:5595982	lncRNA gene	predicted gene, 36823
3	pseudogene	38.43895	38.43984	negative	MGI_C57BL6J_3646285	Gm7815	NCBI_Gene:665838,ENSEMBL:ENSMUSG00000106201	MGI:3646285	pseudogene	predicted gene 7815
3	gene	38.44926	38.48486	negative	MGI_C57BL6J_2139777	Ankrd50	NCBI_Gene:99696,ENSEMBL:ENSMUSG00000044864	MGI:2139777	protein coding gene	ankyrin repeat domain 50
3	pseudogene	38.55797	38.55886	negative	MGI_C57BL6J_3779766	Gm7824	NCBI_Gene:665855,ENSEMBL:ENSMUSG00000105360	MGI:3779766	pseudogene	predicted gene 7824
3	gene	38.55811	38.55821	negative	MGI_C57BL6J_5454239	Gm24462	ENSEMBL:ENSMUSG00000076385	MGI:5454239	miRNA gene	predicted gene, 24462
3	gene	38.61425	38.61556	positive	MGI_C57BL6J_5663675	Gm43538	ENSEMBL:ENSMUSG00000106168	MGI:5663675	lncRNA gene	predicted gene 43538
3	gene	38.66361	38.70922	positive	MGI_C57BL6J_5589038	Gm29879	NCBI_Gene:102631576	MGI:5589038	lncRNA gene	predicted gene, 29879
3	gene	38.76048	38.76195	negative	MGI_C57BL6J_5589118	Gm29959	NCBI_Gene:102631683	MGI:5589118	lncRNA gene	predicted gene, 29959
3	gene	38.87457	38.88826	negative	MGI_C57BL6J_2441892	C230034O21Rik	NCBI_Gene:102632538,ENSEMBL:ENSMUSG00000086181	MGI:2441892	lncRNA gene	RIKEN cDNA C230034O21 gene
3	gene	38.88563	39.01199	positive	MGI_C57BL6J_3045256	Fat4	NCBI_Gene:329628,ENSEMBL:ENSMUSG00000046743	MGI:3045256	protein coding gene	FAT atypical cadherin 4
3	gene	39.00860	39.00968	negative	MGI_C57BL6J_5663676	Gm43539	ENSEMBL:ENSMUSG00000105910	MGI:5663676	lncRNA gene	predicted gene 43539
3	pseudogene	39.12853	39.12891	negative	MGI_C57BL6J_5663445	Gm43308	ENSEMBL:ENSMUSG00000104792	MGI:5663445	pseudogene	predicted gene 43308
3	gene	39.15083	39.15967	negative	MGI_C57BL6J_5589170	Gm30011	NCBI_Gene:102631750	MGI:5589170	lncRNA gene	predicted gene, 30011
3	pseudogene	39.21756	39.21785	negative	MGI_C57BL6J_5663145	Gm43008	ENSEMBL:ENSMUSG00000107333	MGI:5663145	pseudogene	predicted gene 43008
3	gene	39.27713	39.30593	positive	MGI_C57BL6J_5625099	Gm42214	NCBI_Gene:105247032	MGI:5625099	lncRNA gene	predicted gene, 42214
3	pseudogene	39.35737	39.35913	negative	MGI_C57BL6J_3704215	Gm9845	NCBI_Gene:100040853,ENSEMBL:ENSMUSG00000050533	MGI:3704215	pseudogene	predicted pseudogene 9845
3	pseudogene	39.44389	39.44435	positive	MGI_C57BL6J_5295673	Gm20566	NCBI_Gene:100047050	MGI:5295673	pseudogene	predicted gene, 20566
3	gene	39.46078	39.59865	positive	MGI_C57BL6J_5589222	Gm30063	NCBI_Gene:102631823	MGI:5589222	lncRNA gene	predicted gene, 30063
3	gene	39.52552	39.53415	negative	MGI_C57BL6J_5625100	Gm42215	NCBI_Gene:105247033	MGI:5625100	lncRNA gene	predicted gene, 42215
3	gene	39.63596	39.63608	negative	MGI_C57BL6J_4422060	n-R5s195	ENSEMBL:ENSMUSG00000093952	MGI:4422060	rRNA gene	nuclear encoded rRNA 5S 195
3	gene	39.63606	39.63878	positive	MGI_C57BL6J_5662918	Gm42781	ENSEMBL:ENSMUSG00000106786	MGI:5662918	unclassified gene	predicted gene 42781
3	gene	39.66629	39.66645	positive	MGI_C57BL6J_5453573	Gm23796	ENSEMBL:ENSMUSG00000065945	MGI:5453573	snRNA gene	predicted gene, 23796
3	gene	39.71315	39.72565	positive	MGI_C57BL6J_5826471	Gm46834	NCBI_Gene:108168914	MGI:5826471	lncRNA gene	predicted gene, 46834
3	gene	39.79963	39.79972	negative	MGI_C57BL6J_5453608	Gm23831	ENSEMBL:ENSMUSG00000089520	MGI:5453608	snoRNA gene	predicted gene, 23831
3	pseudogene	39.82048	39.82076	negative	MGI_C57BL6J_5662923	Gm42786	ENSEMBL:ENSMUSG00000106846	MGI:5662923	pseudogene	predicted gene 42786
3	pseudogene	39.82358	39.82741	positive	MGI_C57BL6J_5662922	Gm42785	ENSEMBL:ENSMUSG00000106948	MGI:5662922	pseudogene	predicted gene 42785
3	gene	40.42571	40.45380	negative	MGI_C57BL6J_5589343	Gm30184	NCBI_Gene:102632001	MGI:5589343	lncRNA gene	predicted gene, 30184
3	gene	40.45843	40.46115	positive	MGI_C57BL6J_5625101	Gm42216	NCBI_Gene:105247034	MGI:5625101	lncRNA gene	predicted gene, 42216
3	gene	40.48090	40.48573	positive	MGI_C57BL6J_5625102	Gm42217	NCBI_Gene:105247035	MGI:5625102	lncRNA gene	predicted gene, 42217
3	gene	40.48702	40.48993	positive	MGI_C57BL6J_5826438	Gm46801	NCBI_Gene:108168866	MGI:5826438	lncRNA gene	predicted gene, 46801
3	gene	40.50487	40.52291	negative	MGI_C57BL6J_1919477	1700017G19Rik	NCBI_Gene:100040882,ENSEMBL:ENSMUSG00000037884	MGI:1919477	lncRNA gene	RIKEN cDNA 1700017G19 gene
3	gene	40.50998	40.51183	positive	MGI_C57BL6J_5826437	Gm46800	NCBI_Gene:108168865	MGI:5826437	lncRNA gene	predicted gene, 46800
3	gene	40.51882	40.51889	positive	MGI_C57BL6J_5453587	Gm23810	ENSEMBL:ENSMUSG00000092891	MGI:5453587	miRNA gene	predicted gene, 23810
3	gene	40.53129	40.70478	positive	MGI_C57BL6J_2443752	Intu	NCBI_Gene:380614,ENSEMBL:ENSMUSG00000060798	MGI:2443752	protein coding gene	inturned planar cell polarity protein
3	pseudogene	40.65887	40.65917	negative	MGI_C57BL6J_3801939	Gm16114	ENSEMBL:ENSMUSG00000089932	MGI:3801939	pseudogene	predicted gene 16114
3	gene	40.70885	40.72610	positive	MGI_C57BL6J_1920583	Slc25a31	NCBI_Gene:73333,ENSEMBL:ENSMUSG00000069041	MGI:1920583	protein coding gene	solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 31
3	gene	40.74440	40.79610	positive	MGI_C57BL6J_107422	Hspa4l	NCBI_Gene:18415,ENSEMBL:ENSMUSG00000025757	MGI:107422	protein coding gene	heat shock protein 4 like
3	gene	40.79364	40.79846	positive	MGI_C57BL6J_1918107	4921509J17Rik	NA	NA	unclassified gene	RIKEN cDNA 4921509J17 gene
3	gene	40.79995	40.81688	positive	MGI_C57BL6J_101783	Plk4	NCBI_Gene:20873,ENSEMBL:ENSMUSG00000025758	MGI:101783	protein coding gene	polo like kinase 4
3	gene	40.81810	40.84689	negative	MGI_C57BL6J_1919425	Mfsd8	NCBI_Gene:72175,ENSEMBL:ENSMUSG00000025759	MGI:1919425	protein coding gene	major facilitator superfamily domain containing 8
3	pseudogene	40.84682	40.87561	positive	MGI_C57BL6J_3780180	Gm2011	NCBI_Gene:100039027,ENSEMBL:ENSMUSG00000107741	MGI:3780180	pseudogene	predicted gene 2011
3	gene	40.84697	40.93814	positive	MGI_C57BL6J_1915468	Abhd18	NCBI_Gene:269423,ENSEMBL:ENSMUSG00000037818	MGI:1915468	protein coding gene	abhydrolase domain containing 18
3	pseudogene	40.85348	40.85529	negative	MGI_C57BL6J_3795712	Gm10731	NCBI_Gene:100039043,ENSEMBL:ENSMUSG00000074620	MGI:3795712	pseudogene	predicted gene 10731
3	gene	40.86395	40.86505	negative	MGI_C57BL6J_5690528	Gm44136	ENSEMBL:ENSMUSG00000107524	MGI:5690528	unclassified gene	predicted gene, 44136
3	gene	40.87665	40.89455	negative	MGI_C57BL6J_3648839	6430590A07Rik	NCBI_Gene:619719,ENSEMBL:ENSMUSG00000097583	MGI:3648839	lncRNA gene	RIKEN cDNA 6430590A07 gene
3	pseudogene	40.87698	40.87725	negative	MGI_C57BL6J_5753100	Gm44524	ENSEMBL:ENSMUSG00000107892	MGI:5753100	pseudogene	predicted gene 44524
3	gene	40.90020	40.90254	negative	MGI_C57BL6J_1920547	1700034I23Rik	NCBI_Gene:73297,ENSEMBL:ENSMUSG00000074619	MGI:1920547	protein coding gene	RIKEN cDNA 1700034I23 gene
3	gene	40.94869	40.94986	negative	MGI_C57BL6J_5826439	Gm46802	NCBI_Gene:108168867	MGI:5826439	lncRNA gene	predicted gene, 46802
3	gene	40.94972	41.04023	positive	MGI_C57BL6J_1914604	Larp1b	NCBI_Gene:214048,ENSEMBL:ENSMUSG00000025762	MGI:1914604	protein coding gene	La ribonucleoprotein domain family, member 1B
3	gene	40.97850	41.00609	positive	MGI_C57BL6J_5589448	Gm30289	NA	NA	protein coding gene	predicted gene%2c 30289
3	gene	40.99269	40.99285	positive	MGI_C57BL6J_5451820	Gm22043	ENSEMBL:ENSMUSG00000064927	MGI:5451820	snRNA gene	predicted gene, 22043
3	gene	41.00243	41.00609	positive	MGI_C57BL6J_5662573	Gm42436	ENSEMBL:ENSMUSG00000105517	MGI:5662573	unclassified gene	predicted gene 42436
3	gene	41.00552	41.00644	negative	MGI_C57BL6J_5662574	Gm42437	ENSEMBL:ENSMUSG00000105674	MGI:5662574	unclassified gene	predicted gene 42437
3	gene	41.06633	41.08305	negative	MGI_C57BL6J_1918054	Pgrmc2	NCBI_Gene:70804,ENSEMBL:ENSMUSG00000049940	MGI:1918054	protein coding gene	progesterone receptor membrane component 2
3	gene	41.15803	41.17346	negative	MGI_C57BL6J_5622923	Gm40038	NCBI_Gene:105244429,ENSEMBL:ENSMUSG00000105258	MGI:5622923	lncRNA gene	predicted gene, 40038
3	gene	41.28606	41.29059	negative	MGI_C57BL6J_3642810	Gm16508	ENSEMBL:ENSMUSG00000106000	MGI:3642810	lncRNA gene	predicted gene 16508
3	gene	41.35415	41.40446	positive	MGI_C57BL6J_1920712	1700052H01Rik	NCBI_Gene:73462,ENSEMBL:ENSMUSG00000105297	MGI:1920712	lncRNA gene	RIKEN cDNA 1700052H01 gene
3	gene	41.44134	41.44147	negative	MGI_C57BL6J_5455264	Gm25487	ENSEMBL:ENSMUSG00000089350	MGI:5455264	snoRNA gene	predicted gene, 25487
3	gene	41.47491	41.48400	negative	MGI_C57BL6J_5622925	Gm40040	NCBI_Gene:105244431,ENSEMBL:ENSMUSG00000105260	MGI:5622925	lncRNA gene	predicted gene, 40040
3	gene	41.48402	41.49320	negative	MGI_C57BL6J_1925956	Platr4	NCBI_Gene:78706,ENSEMBL:ENSMUSG00000097639	MGI:1925956	lncRNA gene	pluripotency associated transcript 4
3	pseudogene	41.48569	41.48641	positive	MGI_C57BL6J_3648422	Gm6069	NCBI_Gene:606542,ENSEMBL:ENSMUSG00000104616	MGI:3648422	pseudogene	predicted gene 6069
3	gene	41.50093	41.52847	negative	MGI_C57BL6J_1925898	2400006E01Rik	NCBI_Gene:78648,ENSEMBL:ENSMUSG00000106223	MGI:1925898	lncRNA gene	RIKEN cDNA 2400006E01 gene
3	gene	41.55573	41.61686	positive	MGI_C57BL6J_1925835	Jade1	NCBI_Gene:269424,ENSEMBL:ENSMUSG00000025764	MGI:1925835	protein coding gene	jade family PHD finger 1
3	gene	41.56050	41.56370	negative	MGI_C57BL6J_5590425	Gm31266	NCBI_Gene:105244433,ENSEMBL:ENSMUSG00000103843	MGI:5590425	lncRNA gene	predicted gene, 31266
3	gene	41.61755	41.62371	negative	MGI_C57BL6J_5622926	Gm40041	NCBI_Gene:105244432	MGI:5622926	lncRNA gene	predicted gene, 40041
3	gene	41.62671	41.74253	negative	MGI_C57BL6J_1914411	Sclt1	NCBI_Gene:67161,ENSEMBL:ENSMUSG00000059834	MGI:1914411	protein coding gene	sodium channel and clathrin linker 1
3	gene	41.64812	41.64925	negative	MGI_C57BL6J_5611275	Gm38047	ENSEMBL:ENSMUSG00000102436	MGI:5611275	unclassified gene	predicted gene, 38047
3	gene	41.74261	41.80332	positive	MGI_C57BL6J_1289213	D3Ertd751e	NCBI_Gene:73852,ENSEMBL:ENSMUSG00000025766	MGI:1289213	protein coding gene	DNA segment, Chr 3, ERATO Doi 751, expressed
3	gene	41.77318	41.77579	positive	MGI_C57BL6J_5610496	Gm37268	ENSEMBL:ENSMUSG00000103952	MGI:5610496	unclassified gene	predicted gene, 37268
3	pseudogene	41.97607	41.97812	negative	MGI_C57BL6J_3645044	Gm7899	NCBI_Gene:666031,ENSEMBL:ENSMUSG00000103823	MGI:3645044	pseudogene	predicted gene 7899
3	pseudogene	41.97633	41.97812	positive	MGI_C57BL6J_5610576	Gm37348	ENSEMBL:ENSMUSG00000102972	MGI:5610576	pseudogene	predicted gene, 37348
3	gene	42.16387	42.16764	positive	MGI_C57BL6J_5611074	Gm37846	ENSEMBL:ENSMUSG00000102610	MGI:5611074	unclassified gene	predicted gene, 37846
3	pseudogene	42.36263	42.36278	negative	MGI_C57BL6J_5611502	Gm38274	ENSEMBL:ENSMUSG00000104089	MGI:5611502	pseudogene	predicted gene, 38274
3	gene	42.57246	42.57300	positive	MGI_C57BL6J_5610761	Gm37533	ENSEMBL:ENSMUSG00000103426	MGI:5610761	unclassified gene	predicted gene, 37533
3	pseudogene	42.58511	42.58560	negative	MGI_C57BL6J_5611272	Gm38044	ENSEMBL:ENSMUSG00000104294	MGI:5611272	pseudogene	predicted gene, 38044
3	pseudogene	43.25039	43.25093	positive	MGI_C57BL6J_3780131	Gm9723	NCBI_Gene:677788,ENSEMBL:ENSMUSG00000102149	MGI:3780131	pseudogene	predicted gene 9723
3	pseudogene	43.39077	43.39194	negative	MGI_C57BL6J_5011050	Gm18865	NCBI_Gene:100417854,ENSEMBL:ENSMUSG00000102334	MGI:5011050	pseudogene	predicted gene, 18865
3	gene	43.54717	43.54828	positive	MGI_C57BL6J_5610204	Gm36976	ENSEMBL:ENSMUSG00000104303	MGI:5610204	unclassified gene	predicted gene, 36976
3	pseudogene	43.76405	43.76476	negative	MGI_C57BL6J_5588898	Gm29739	NCBI_Gene:101055891,ENSEMBL:ENSMUSG00000104083	MGI:5588898	pseudogene	predicted gene, 29739
3	gene	43.92557	43.92586	positive	MGI_C57BL6J_5455491	Gm25714	ENSEMBL:ENSMUSG00000089251	MGI:5455491	unclassified non-coding RNA gene	predicted gene, 25714
3	pseudogene	43.92760	43.92795	negative	MGI_C57BL6J_5591334	Gm32175	ENSEMBL:ENSMUSG00000102792	MGI:5591334	pseudogene	predicted gene, 32175
3	gene	43.95572	43.95592	positive	MGI_C57BL6J_5610974	Gm37746	ENSEMBL:ENSMUSG00000103148	MGI:5610974	unclassified gene	predicted gene, 37746
3	pseudogene	44.49350	44.49390	negative	MGI_C57BL6J_5610593	Gm37365	ENSEMBL:ENSMUSG00000104013	MGI:5610593	pseudogene	predicted gene, 37365
3	gene	44.65990	44.66315	positive	MGI_C57BL6J_5611356	Gm38128	ENSEMBL:ENSMUSG00000104051	MGI:5611356	unclassified gene	predicted gene, 38128
3	pseudogene	44.71813	44.71851	negative	MGI_C57BL6J_5610825	Gm37597	ENSEMBL:ENSMUSG00000103353	MGI:5610825	pseudogene	predicted gene, 37597
3	pseudogene	44.72516	44.72574	positive	MGI_C57BL6J_5011051	Gm18866	NCBI_Gene:100417856	MGI:5011051	pseudogene	predicted gene, 18866
3	gene	44.98320	44.98330	positive	MGI_C57BL6J_5454774	Gm24997	ENSEMBL:ENSMUSG00000088535	MGI:5454774	snRNA gene	predicted gene, 24997
3	gene	45.16069	45.16080	positive	MGI_C57BL6J_5531371	Gm27989	ENSEMBL:ENSMUSG00000099285	MGI:5531371	miRNA gene	predicted gene, 27989
3	pseudogene	45.17179	45.17324	negative	MGI_C57BL6J_5434370	Gm21015	NCBI_Gene:100534291	MGI:5434370	pseudogene	predicted gene, 21015
3	gene	45.26999	45.27257	negative	MGI_C57BL6J_5611352	Gm38124	ENSEMBL:ENSMUSG00000103082	MGI:5611352	unclassified gene	predicted gene, 38124
3	gene	45.27342	45.27497	negative	MGI_C57BL6J_1924316	5930409G06Rik	ENSEMBL:ENSMUSG00000103477	MGI:1924316	unclassified gene	RIKEN cDNA 5930409G06 gene
3	gene	45.28044	45.37826	negative	MGI_C57BL6J_1919761	2610316D01Rik	NCBI_Gene:72511,ENSEMBL:ENSMUSG00000097040	MGI:1919761	lncRNA gene	RIKEN cDNA 2610316D01 gene
3	pseudogene	45.33216	45.33241	negative	MGI_C57BL6J_5610224	Gm36996	ENSEMBL:ENSMUSG00000103430	MGI:5610224	pseudogene	predicted gene, 36996
3	gene	45.37840	45.43562	positive	MGI_C57BL6J_1338042	Pcdh10	NCBI_Gene:18526,ENSEMBL:ENSMUSG00000049100	MGI:1338042	protein coding gene	protocadherin 10
3	gene	45.38548	45.38960	positive	MGI_C57BL6J_2442672	6330566A10Rik	NA	NA	unclassified gene	RIKEN cDNA 6330566A10 gene
3	gene	45.39986	45.40200	positive	MGI_C57BL6J_2444936	D930002L09Rik	NA	NA	unclassified gene	RIKEN cDNA D930002L09 gene
3	gene	45.41658	45.43931	negative	MGI_C57BL6J_1919524	1700027H10Rik	NCBI_Gene:72274,ENSEMBL:ENSMUSG00000100799	MGI:1919524	lncRNA gene	RIKEN cDNA 1700027H10 gene
3	gene	45.43838	45.44096	positive	MGI_C57BL6J_3780305	Gm2136	ENSEMBL:ENSMUSG00000103713	MGI:3780305	protein coding gene	predicted gene 2136
3	gene	45.44567	45.44881	positive	MGI_C57BL6J_5610573	Gm37345	ENSEMBL:ENSMUSG00000103947	MGI:5610573	unclassified gene	predicted gene, 37345
3	pseudogene	45.69054	45.69090	negative	MGI_C57BL6J_5611063	Gm37835	ENSEMBL:ENSMUSG00000103534	MGI:5611063	pseudogene	predicted gene, 37835
3	gene	45.77542	45.77589	negative	MGI_C57BL6J_5611394	Gm38166	ENSEMBL:ENSMUSG00000102190	MGI:5611394	unclassified gene	predicted gene, 38166
3	pseudogene	45.77587	45.86058	negative	MGI_C57BL6J_5591499	Gm32340	NCBI_Gene:102634856,ENSEMBL:ENSMUSG00000104491	MGI:5591499	pseudogene	predicted gene, 32340
3	gene	45.81774	45.81790	positive	MGI_C57BL6J_5455573	Gm25796	ENSEMBL:ENSMUSG00000064579	MGI:5455573	snRNA gene	predicted gene, 25796
3	pseudogene	45.86121	45.86995	negative	MGI_C57BL6J_5591575	Gm32416	NCBI_Gene:102634958	MGI:5591575	pseudogene	predicted gene, 32416
3	gene	45.97858	45.97870	positive	MGI_C57BL6J_5453114	Gm23337	ENSEMBL:ENSMUSG00000089584	MGI:5453114	snRNA gene	predicted gene, 23337
3	gene	46.28983	46.28996	positive	MGI_C57BL6J_5455858	Gm26081	ENSEMBL:ENSMUSG00000077256	MGI:5455858	snoRNA gene	predicted gene, 26081
3	pseudogene	46.41340	46.41412	positive	MGI_C57BL6J_5011028	Gm18843	NCBI_Gene:100417811,ENSEMBL:ENSMUSG00000104511	MGI:5011028	pseudogene	predicted gene, 18843
3	gene	46.44085	46.44822	negative	MGI_C57BL6J_3643087	Pabpc4l	NCBI_Gene:241989,ENSEMBL:ENSMUSG00000090919	MGI:3643087	protein coding gene	poly(A) binding protein, cytoplasmic 4-like
3	pseudogene	46.62112	46.62136	positive	MGI_C57BL6J_5610673	Gm37445	ENSEMBL:ENSMUSG00000102589	MGI:5610673	pseudogene	predicted gene, 37445
3	gene	46.90067	46.90078	negative	MGI_C57BL6J_5531112	Mir6379	miRBase:MI0021910,NCBI_Gene:102465199,ENSEMBL:ENSMUSG00000098417	MGI:5531112	miRNA gene	microRNA 6379
3	pseudogene	47.04911	47.05178	negative	MGI_C57BL6J_3641761	Gm10356	NCBI_Gene:545517,ENSEMBL:ENSMUSG00000072387	MGI:3641761	pseudogene	predicted gene 10356
3	pseudogene	47.08453	47.08575	negative	MGI_C57BL6J_3646161	Gm5274	NCBI_Gene:383849,ENSEMBL:ENSMUSG00000097985	MGI:3646161	pseudogene	predicted gene 5274
3	gene	47.20063	47.20076	positive	MGI_C57BL6J_5453668	Gm23891	ENSEMBL:ENSMUSG00000088739	MGI:5453668	snoRNA gene	predicted gene, 23891
3	pseudogene	47.23050	47.23100	negative	MGI_C57BL6J_3643228	Rpl23a-ps5	NCBI_Gene:383850,ENSEMBL:ENSMUSG00000102220	MGI:3643228	pseudogene	ribosomal protein L23A, pseudogene 5
3	gene	47.26308	47.26580	negative	MGI_C57BL6J_3809922	Gm10730	ENSEMBL:ENSMUSG00000103491	MGI:3809922	unclassified gene	predicted gene 10730
3	pseudogene	47.45961	47.46034	negative	MGI_C57BL6J_3780399	Gm2229	NCBI_Gene:100039426,ENSEMBL:ENSMUSG00000103798	MGI:3780399	pseudogene	predicted gene 2229
3	pseudogene	48.02601	48.02676	negative	MGI_C57BL6J_3648898	Gm7977	NCBI_Gene:666202,ENSEMBL:ENSMUSG00000103257	MGI:3648898	pseudogene	predicted gene 7977
3	gene	48.07834	48.07845	positive	MGI_C57BL6J_5610523	Gm37295	ENSEMBL:ENSMUSG00000104110	MGI:5610523	unclassified gene	predicted gene, 37295
3	gene	48.54642	48.57947	positive	MGI_C57BL6J_5826472	Gm46835	NCBI_Gene:108168915	MGI:5826472	lncRNA gene	predicted gene, 46835
3	gene	48.60573	48.60910	negative	MGI_C57BL6J_1913582	1700018B24Rik	NCBI_Gene:66332,ENSEMBL:ENSMUSG00000037910	MGI:1913582	lncRNA gene	RIKEN cDNA 1700018B24 gene

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] abind_1.4-5       qtl2_0.22         reshape2_1.4.4    ggplot2_3.3.5    
 [5] tibble_3.1.2      psych_2.0.7       readxl_1.3.1      cluster_2.1.0    
 [9] dplyr_0.8.5       optparse_1.6.6    rhdf5_2.28.1      mclust_5.4.6     
[13] tidyr_1.0.2       data.table_1.14.0 knitr_1.33        kableExtra_1.1.0 
[17] workflowr_1.6.2  

loaded via a namespace (and not attached):
 [1] httr_1.4.1        bit64_4.0.5       viridisLite_0.4.0 assertthat_0.2.1 
 [5] highr_0.9         blob_1.2.1        cellranger_1.1.0  yaml_2.2.1       
 [9] pillar_1.6.1      RSQLite_2.2.7     backports_1.2.1   lattice_0.20-38  
[13] glue_1.4.2        digest_0.6.27     promises_1.1.0    rvest_0.3.5      
[17] colorspace_2.0-2  htmltools_0.5.1.1 httpuv_1.5.2      plyr_1.8.6       
[21] pkgconfig_2.0.3   purrr_0.3.4       scales_1.1.1      webshot_0.5.2    
[25] whisker_0.4       getopt_1.20.3     later_1.0.0       git2r_0.26.1     
[29] ellipsis_0.3.2    cachem_1.0.5      withr_2.4.2       mnormt_1.5-7     
[33] magrittr_2.0.1    crayon_1.4.1      memoise_2.0.0     evaluate_0.14    
[37] fs_1.4.1          fansi_0.5.0       nlme_3.1-142      xml2_1.3.1       
[41] tools_3.6.2       hms_0.5.3         lifecycle_1.0.0   stringr_1.4.0    
[45] Rhdf5lib_1.6.3    munsell_0.5.0     compiler_3.6.2    rlang_0.4.11     
[49] grid_3.6.2        rstudioapi_0.13   rmarkdown_2.1     gtable_0.3.0     
[53] DBI_1.1.1         R6_2.5.0          fastmap_1.1.0     bit_4.0.4        
[57] utf8_1.2.1        rprojroot_1.3-2   readr_1.3.1       stringi_1.7.2    
[61] parallel_3.6.2    Rcpp_1.0.7        vctrs_0.3.8       tidyselect_1.0.0 
[65] xfun_0.24

QTL Analysis - binary [ICI vs EOI]

Belinda Cornes

2022-02-11

Loading Data

Genome-wide scan

LOD peaks

QTL effects