Micro-first exons in GENCODE 26
Charles Plessy
knitr::opts_chunk$set(cache = TRUE)The question
I am interested in the length of first exons. To get an estimate of what to expect, I inspected the contents of GENCODE 26. I am surprised to find very small first exons, as I do not see how these could be produced by splicing: how could the spliceosome handle a donor fragment that is only a few nucleotides long ?
So my question is what do these micro-first exons repesent. Are they just bugs in processing pipelines ? Do they represent processed transcripts (in which case its short length is not in contradiction with splicing mechanisms). Or is there something else I am missing ?
Data load and preparation
This analysis is done in R. First, let’s load R libraries.
library(magrittr)
library(GenomicRanges)Then, let’s download GENCODE 26.
wget --quiet --continue ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gzThen, let’s load GENCODE 26 in R as a GenomicRanges object and select all exon features.
g <- rtracklayer::import.gff("gencode.v26.annotation.gtf.gz")
summary(g)## [1] "GRanges object with 2604486 ranges and 20 metadata columns"colnames(mcols(g))## [1] "source" "type"
## [3] "score" "phase"
## [5] "gene_id" "gene_type"
## [7] "gene_name" "level"
## [9] "havana_gene" "transcript_id"
## [11] "transcript_type" "transcript_name"
## [13] "transcript_support_level" "tag"
## [15] "havana_transcript" "exon_number"
## [17] "exon_id" "ont"
## [19] "protein_id" "ccdsid"table(g$type)##
## gene transcript exon CDS start_codon
## 58219 199324 1194547 710618 83245
## stop_codon UTR Selenocysteine
## 74994 283420 119ge <- g[g$type == "exon"]
mcols(ge) %<>% droplevelsExon lengths and number
Many transcripts have more than one exon.
tapply(ge$exon_number %>% as.numeric, ge$transcript_id, max) %>% table %>% head(50) %>%
plot(main = "Number of exons per GENCODE transcripts", sub = "Transcripts with > 50 exons were omitted.")
Exons tend to be short.
width(ge) %>% summary## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.0 88.0 129.0 249.3 198.0 205000.0width(ge) %>% table %>% head(1000) %>%
plot(main = "Length of GENCODE exons", sub = "Exons longer than 100 nt were omitted.")
Some Exons are very short; they can be microexons.
width(ge) %>% table %>% head(20) %>%
plot(main = "Length of shortest GENCODE exons", sub = "Exons longer than 20 nt were omitted.")
First exons of spliced transcripts
Let’s focus on spliced transcripts.
spliced <- tapply(ge$exon_number %>% as.numeric, ge$transcript_id, max) > 1
gs <- ge[ge$transcript_id %in% names(which(spliced))]
summary(gs)## [1] "GRanges object with 1169596 ranges and 20 metadata columns"tapply(gs$exon_number %>% as.numeric, gs$transcript_id, max) %>%
table %>% head(50) %>%
plot(main = "Number of exons per spliced transcripts", sub = "Transcripts with > 50 exons were omitted.")
width(gs) %>% table %>% head(20) %>%
plot( main = "Length of shortest GENCODE spliced exons"
, sub = "Exons longer than 20 nt were omitted.")
And within them, let’s focus on first exons. Altogether, their size distribution is not very different from all the exons together.
gs1 <- gs[gs$exon_number == 1]
width(gs1) %>% summary## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1 83 148 237 271 11370width(gs1) %>% table %>% head(1000) %>%
plot(main = "Length of spliced first exons", sub = "Exons longer than 500 nt were omitted.")
Surprisingly, even within first exons, there are microexons.
width(gs1) %>% table %>% head(20) %>%
plot(main = "Length of spliced first exons", sub = "Exons longer than 20 nt were omitted.")
Examples
Inspection in the UCSC browser suggested that many of these micro-first exons coincided with translation start sites. Indeed, it seems to happen often, but not systematically.
options(width=110)
options("showTailLines"=Inf) # http://stackoverflow.com/questions/16949545/show-all-lines-in-genomicrange-package-output
x <- g[g$transcript_id %in% gs1[width(gs1) < 4]$transcript_id]
# For display purposes, let's give names to each entry, and re-sort the names
# of the metadata's columns.
names(x) <- x$transcript_name
mcols(x) <- mcols(x)[,c("type", "transcript_type", "gene_id",
"source", "gene_type", "transcript_id", "level", "havana_gene",
"transcript_name", "transcript_support_level", "tag", "havana_transcript",
"exon_number", "exon_id", "ont", "protein_id", "ccdsid", "score", "phase",
"gene_name")]
x[x$type %in% c("start_codon", "exon") & x$exon_number == 1]## GRanges object with 101 ranges and 20 metadata columns:
## seqnames ranges strand | type transcript_type
## <Rle> <IRanges> <Rle> | <factor> <character>
## SZT2-007 chr1 [ 43437506, 43437508] + | exon processed_transcript
## TNNI1-006 chr1 [201422019, 201422021] - | exon protein_coding
## MPV17-004 chr2 [ 27323052, 27323054] - | exon protein_coding
## DQX1-004 chr2 [ 74523923, 74523925] - | exon nonsense_mediated_decay
## ST3GAL5-067 chr2 [ 85888824, 85888826] - | exon nonsense_mediated_decay
## FAP-201 chr2 [162242996, 162242998] - | exon protein_coding
## FAP-201 chr2 [162242996, 162242998] - | start_codon protein_coding
## SPEG-021 chr2 [219491867, 219491869] + | exon protein_coding
## TSEN2-008 chr3 [ 12529871, 12529873] + | exon protein_coding
## P4HTM-012 chr3 [ 49001626, 49001628] + | exon protein_coding
## ABHD14A-ACY1-022 chr3 [ 51978080, 51978082] + | exon nonsense_mediated_decay
## PXK-003 chr3 [ 58409616, 58409618] + | exon protein_coding
## GMNC-001 chr3 [190862613, 190862615] - | exon protein_coding
## GMNC-001 chr3 [190862613, 190862615] - | start_codon protein_coding
## RUBCN-004 chr3 [197701708, 197701710] - | exon protein_coding
## TGFBI-019 chr5 [136047418, 136047420] + | exon protein_coding
## TRPC7-002 chr5 [136365253, 136365254] - | exon nonsense_mediated_decay
## TRPC7-002 chr5 [136365253, 136365254] - | start_codon nonsense_mediated_decay
## TRPC7-003 chr5 [136365253, 136365254] - | exon protein_coding
## TRPC7-003 chr5 [136365253, 136365254] - | start_codon protein_coding
## TRPC7-004 chr5 [136365253, 136365254] - | exon nonsense_mediated_decay
## TRPC7-004 chr5 [136365253, 136365254] - | start_codon nonsense_mediated_decay
## TRPC7-005 chr5 [136365253, 136365254] - | exon protein_coding
## TRPC7-005 chr5 [136365253, 136365254] - | start_codon protein_coding
## TRPC7-006 chr5 [136365253, 136365254] - | exon protein_coding
## TRPC7-006 chr5 [136365253, 136365254] - | start_codon protein_coding
## OFCC1-019 chr6 [ 9908518, 9908520] - | exon nonsense_mediated_decay
## SLC17A1-003 chr6 [ 25831994, 25831996] - | exon nonsense_mediated_decay
## LST1-024 chr6 [ 31587316, 31587318] + | exon protein_coding
## KCNQ5-005 chr6 [ 73003996, 73003998] + | exon protein_coding
## FIG4-004 chr6 [109701720, 109701722] + | exon protein_coding
## FIG4-004 chr6 [109701720, 109701722] + | start_codon protein_coding
## AMD1-004 chr6 [110892825, 110892827] + | exon nonsense_mediated_decay
## MYB-004 chr6 [135186018, 135186020] + | exon protein_coding
## AC005281.1-004 chr7 [ 12504544, 12504546] + | exon protein_coding
## AC005281.1-004 chr7 [ 12504544, 12504546] + | start_codon protein_coding
## MAGI2-008 chr7 [ 78627120, 78627121] - | exon processed_transcript
## SRPK2-003 chr7 [105132791, 105132793] - | exon nonsense_mediated_decay
## SRPK2-003 chr7 [105132791, 105132793] - | start_codon nonsense_mediated_decay
## SYPL1-008 chr7 [106112140, 106112142] - | exon nonsense_mediated_decay
## SMARCA2-056 chr9 [ 2181676, 2181676] + | exon protein_coding
## KIAA2026-006 chr9 [ 5913858, 5913860] - | exon processed_transcript
## TLN1-006 chr9 [ 35706196, 35706198] - | exon retained_intron
## TRPM3-009 chr9 [ 70862908, 70862910] - | exon protein_coding
## TRPM3-009 chr9 [ 70862908, 70862910] - | start_codon protein_coding
## TRPM3-011 chr9 [ 70862908, 70862910] - | exon protein_coding
## TRPM3-011 chr9 [ 70862908, 70862910] - | start_codon protein_coding
## TRPM3-012 chr9 [ 70862908, 70862910] - | exon protein_coding
## TRPM3-012 chr9 [ 70862908, 70862910] - | start_codon protein_coding
## TRPM3-015 chr9 [ 70862908, 70862910] - | exon protein_coding
## TRPM3-015 chr9 [ 70862908, 70862910] - | start_codon protein_coding
## TRPM3-016 chr9 [ 70862908, 70862910] - | exon protein_coding
## TRPM3-016 chr9 [ 70862908, 70862910] - | start_codon protein_coding
## LRSAM1-011 chr9 [127473929, 127473931] + | exon processed_transcript
## PRRC2B-005 chr9 [131487292, 131487294] + | exon protein_coding
## GFI1B-001 chr9 [132978840, 132978841] + | exon protein_coding
## DNAJC4-012 chr11 [ 64231962, 64231964] + | exon retained_intron
## GAPDH-201 chr12 [ 6536605, 6536607] + | exon protein_coding
## GAPDH-201 chr12 [ 6536605, 6536607] + | start_codon protein_coding
## PPP1R12A-006 chr12 [ 79793863, 79793864] - | exon retained_intron
## PAH-018 chr12 [102852815, 102852817] - | exon protein_coding
## SEPT4-201 chr17 [ 58527142, 58527144] - | exon protein_coding
## SEPT4-201 chr17 [ 58527142, 58527144] - | start_codon protein_coding
## THOC1-202 chr18 [ 265534, 265536] - | exon protein_coding
## TMEM259-003 chr19 [ 1013241, 1013242] - | exon nonsense_mediated_decay
## POLR2E-014 chr19 [ 1095259, 1095261] - | exon protein_coding
## PLK5-003 chr19 [ 1526997, 1526998] + | exon protein_coding
## PLK5-003 chr19 [ 1526997, 1526998] + | start_codon protein_coding
## MKNK2-011 chr19 [ 2041840, 2041842] - | exon nonsense_mediated_decay
## NFIC-011 chr19 [ 3359683, 3359685] + | exon protein_coding
## NFIC-011 chr19 [ 3359683, 3359685] + | start_codon protein_coding
## CTB-50L17.10-003 chr19 [ 4475349, 4475351] + | exon nonsense_mediated_decay
## ILF3-004 chr19 [ 10670606, 10670608] + | exon protein_coding
## ILF3-004 chr19 [ 10670606, 10670608] + | start_codon protein_coding
## ILF3-006 chr19 [ 10670606, 10670608] + | exon protein_coding
## ILF3-006 chr19 [ 10670606, 10670608] + | start_codon protein_coding
## ILF3-005 chr19 [ 10670606, 10670608] + | exon protein_coding
## ILF3-005 chr19 [ 10670606, 10670608] + | start_codon protein_coding
## NFIX-006 chr19 [ 13024032, 13024034] + | exon protein_coding
## NFIX-006 chr19 [ 13024032, 13024034] + | start_codon protein_coding
## ZNF85-003 chr19 [ 20923401, 20923403] + | exon protein_coding
## ZNF85-003 chr19 [ 20923401, 20923403] + | start_codon protein_coding
## RP11-255H23.2-001 chr19 [ 23790772, 23790774] + | exon transcribed_unprocessed_pseudogene
## AP2S1-003 chr19 [ 46850764, 46850766] - | exon protein_coding
## AP2S1-003 chr19 [ 46850764, 46850766] - | start_codon protein_coding
## EMP3-007 chr19 [ 48325608, 48325610] + | exon protein_coding
## NELFCD-002 chr20 [ 58989019, 58989021] + | exon retained_intron
## PKNOX1-002 chr21 [ 42974662, 42974664] + | exon retained_intron
## TXNRD2-009 chr22 [ 19898039, 19898041] - | exon non_stop_decay
## PES1-011 chr22 [ 30588021, 30588023] - | exon retained_intron
## MPST-005 chr22 [ 37019772, 37019774] + | exon protein_coding
## DENND6B-005 chr22 [ 50318965, 50318967] - | exon retained_intron
## PIGA-002 chrX [ 15335501, 15335503] - | exon protein_coding
## THOC2-003 chrX [123621157, 123621159] - | exon protein_coding
## CD99L2-006 chrX [150814862, 150814864] - | exon protein_coding
## RPS4Y2-001 chrY [ 20756164, 20756166] + | exon protein_coding
## RPS4Y2-001 chrY [ 20756164, 20756166] + | start_codon protein_coding
## DAZ4-005 chrY [ 24834127, 24834129] + | exon protein_coding
## DAZ4-005 chrY [ 24834127, 24834129] + | start_codon protein_coding
## DAZ4-003 chrY [ 24834127, 24834129] + | exon protein_coding
## DAZ4-003 chrY [ 24834127, 24834129] + | start_codon protein_coding
## gene_id source gene_type transcript_id
## <character> <factor> <character> <character>
## SZT2-007 ENSG00000198198.15 HAVANA protein_coding ENST00000470897.2
## TNNI1-006 ENSG00000159173.18 HAVANA protein_coding ENST00000555948.5
## MPV17-004 ENSG00000115204.14 HAVANA protein_coding ENST00000402310.5
## DQX1-004 ENSG00000144045.13 HAVANA protein_coding ENST00000418139.5
## ST3GAL5-067 ENSG00000115525.17 HAVANA protein_coding ENST00000640222.1
## FAP-201 ENSG00000078098.13 ENSEMBL protein_coding ENST00000627638.2
## FAP-201 ENSG00000078098.13 ENSEMBL protein_coding ENST00000627638.2
## SPEG-021 ENSG00000072195.14 HAVANA protein_coding ENST00000412982.5
## TSEN2-008 ENSG00000154743.17 HAVANA protein_coding ENST00000412698.2
## P4HTM-012 ENSG00000178467.17 HAVANA protein_coding ENST00000472796.2
## ABHD14A-ACY1-022 ENSG00000114786.16 HAVANA protein_coding ENST00000636264.1
## PXK-003 ENSG00000168297.15 HAVANA protein_coding ENST00000493474.1
## GMNC-001 ENSG00000205835.8 HAVANA protein_coding ENST00000442080.5
## GMNC-001 ENSG00000205835.8 HAVANA protein_coding ENST00000442080.5
## RUBCN-004 ENSG00000145016.15 HAVANA protein_coding ENST00000415452.5
## TGFBI-019 ENSG00000120708.16 HAVANA protein_coding ENST00000604555.5
## TRPC7-002 ENSG00000069018.17 HAVANA protein_coding ENST00000503275.5
## TRPC7-002 ENSG00000069018.17 HAVANA protein_coding ENST00000503275.5
## TRPC7-003 ENSG00000069018.17 HAVANA protein_coding ENST00000352189.7
## TRPC7-003 ENSG00000069018.17 HAVANA protein_coding ENST00000352189.7
## TRPC7-004 ENSG00000069018.17 HAVANA protein_coding ENST00000514963.5
## TRPC7-004 ENSG00000069018.17 HAVANA protein_coding ENST00000514963.5
## TRPC7-005 ENSG00000069018.17 HAVANA protein_coding ENST00000378459.6
## TRPC7-005 ENSG00000069018.17 HAVANA protein_coding ENST00000378459.6
## TRPC7-006 ENSG00000069018.17 HAVANA protein_coding ENST00000502753.3
## TRPC7-006 ENSG00000069018.17 HAVANA protein_coding ENST00000502753.3
## OFCC1-019 ENSG00000181355.20 HAVANA protein_coding ENST00000469656.5
## SLC17A1-003 ENSG00000124568.10 HAVANA protein_coding ENST00000377886.6
## LST1-024 ENSG00000204482.10 HAVANA protein_coding ENST00000490742.5
## KCNQ5-005 ENSG00000185760.15 HAVANA protein_coding ENST00000443915.1
## FIG4-004 ENSG00000112367.10 HAVANA protein_coding ENST00000454215.5
## FIG4-004 ENSG00000112367.10 HAVANA protein_coding ENST00000454215.5
## AMD1-004 ENSG00000123505.15 HAVANA protein_coding ENST00000465404.2
## MYB-004 ENSG00000118513.18 HAVANA protein_coding ENST00000430686.2
## AC005281.1-004 ENSG00000226690.7 HAVANA protein_coding ENST00000636804.1
## AC005281.1-004 ENSG00000226690.7 HAVANA protein_coding ENST00000636804.1
## MAGI2-008 ENSG00000187391.19 HAVANA protein_coding ENST00000517762.2
## SRPK2-003 ENSG00000135250.16 HAVANA protein_coding ENST00000465072.5
## SRPK2-003 ENSG00000135250.16 HAVANA protein_coding ENST00000465072.5
## SYPL1-008 ENSG00000008282.8 HAVANA protein_coding ENST00000634737.1
## SMARCA2-056 ENSG00000080503.22 HAVANA protein_coding ENST00000639760.1
## KIAA2026-006 ENSG00000183354.11 HAVANA protein_coding ENST00000443149.2
## TLN1-006 ENSG00000137076.20 HAVANA protein_coding ENST00000486788.2
## TRPM3-009 ENSG00000083067.22 HAVANA protein_coding ENST00000396285.5
## TRPM3-009 ENSG00000083067.22 HAVANA protein_coding ENST00000396285.5
## TRPM3-011 ENSG00000083067.22 HAVANA protein_coding ENST00000396292.8
## TRPM3-011 ENSG00000083067.22 HAVANA protein_coding ENST00000396292.8
## TRPM3-012 ENSG00000083067.22 HAVANA protein_coding ENST00000396280.9
## TRPM3-012 ENSG00000083067.22 HAVANA protein_coding ENST00000396280.9
## TRPM3-015 ENSG00000083067.22 HAVANA protein_coding ENST00000358082.7
## TRPM3-015 ENSG00000083067.22 HAVANA protein_coding ENST00000358082.7
## TRPM3-016 ENSG00000083067.22 HAVANA protein_coding ENST00000408909.6
## TRPM3-016 ENSG00000083067.22 HAVANA protein_coding ENST00000408909.6
## LRSAM1-011 ENSG00000148356.13 HAVANA protein_coding ENST00000498513.5
## PRRC2B-005 ENSG00000130723.18 HAVANA protein_coding ENST00000320547.7
## GFI1B-001 ENSG00000165702.13 HAVANA protein_coding ENST00000372123.4
## DNAJC4-012 ENSG00000110011.13 HAVANA protein_coding ENST00000538961.1
## GAPDH-201 ENSG00000111640.14 ENSEMBL protein_coding ENST00000619601.1
## GAPDH-201 ENSG00000111640.14 ENSEMBL protein_coding ENST00000619601.1
## PPP1R12A-006 ENSG00000058272.16 HAVANA protein_coding ENST00000548908.2
## PAH-018 ENSG00000171759.9 HAVANA protein_coding ENST00000635477.1
## SEPT4-201 ENSG00000108387.14 ENSEMBL protein_coding ENST00000393086.5
## SEPT4-201 ENSG00000108387.14 ENSEMBL protein_coding ENST00000393086.5
## THOC1-202 ENSG00000079134.11 ENSEMBL protein_coding ENST00000621904.4
## TMEM259-003 ENSG00000182087.12 HAVANA protein_coding ENST00000593068.6
## POLR2E-014 ENSG00000099817.11 HAVANA protein_coding ENST00000585838.2
## PLK5-003 ENSG00000185988.11 HAVANA protein_coding ENST00000588430.2
## PLK5-003 ENSG00000185988.11 HAVANA protein_coding ENST00000588430.2
## MKNK2-011 ENSG00000099875.14 HAVANA protein_coding ENST00000589441.5
## NFIC-011 ENSG00000141905.17 HAVANA protein_coding ENST00000586919.5
## NFIC-011 ENSG00000141905.17 HAVANA protein_coding ENST00000586919.5
## CTB-50L17.10-003 ENSG00000167674.14 HAVANA protein_coding ENST00000615225.1
## ILF3-004 ENSG00000129351.17 HAVANA protein_coding ENST00000592763.5
## ILF3-004 ENSG00000129351.17 HAVANA protein_coding ENST00000592763.5
## ILF3-006 ENSG00000129351.17 HAVANA protein_coding ENST00000588657.5
## ILF3-006 ENSG00000129351.17 HAVANA protein_coding ENST00000588657.5
## ILF3-005 ENSG00000129351.17 HAVANA protein_coding ENST00000590261.5
## ILF3-005 ENSG00000129351.17 HAVANA protein_coding ENST00000590261.5
## NFIX-006 ENSG00000008441.16 HAVANA protein_coding ENST00000585575.5
## NFIX-006 ENSG00000008441.16 HAVANA protein_coding ENST00000585575.5
## ZNF85-003 ENSG00000105750.14 HAVANA protein_coding ENST00000345030.6
## ZNF85-003 ENSG00000105750.14 HAVANA protein_coding ENST00000345030.6
## RP11-255H23.2-001 ENSG00000233836.7 HAVANA transcribed_unprocessed_pseudogene ENST00000472297.2
## AP2S1-003 ENSG00000042753.11 HAVANA protein_coding ENST00000601649.1
## AP2S1-003 ENSG00000042753.11 HAVANA protein_coding ENST00000601649.1
## EMP3-007 ENSG00000142227.10 HAVANA protein_coding ENST00000593437.1
## NELFCD-002 ENSG00000101158.13 HAVANA protein_coding ENST00000474543.5
## PKNOX1-002 ENSG00000160199.14 HAVANA protein_coding ENST00000480179.1
## TXNRD2-009 ENSG00000184470.20 HAVANA protein_coding ENST00000634537.1
## PES1-011 ENSG00000100029.17 HAVANA protein_coding ENST00000477762.5
## MPST-005 ENSG00000128309.16 HAVANA protein_coding ENST00000404393.5
## DENND6B-005 ENSG00000205593.11 HAVANA protein_coding ENST00000471942.6
## PIGA-002 ENSG00000165195.15 HAVANA protein_coding ENST00000482148.6
## THOC2-003 ENSG00000125676.19 HAVANA protein_coding ENST00000448128.5
## CD99L2-006 ENSG00000102181.20 HAVANA protein_coding ENST00000634795.1
## RPS4Y2-001 ENSG00000280969.1 HAVANA protein_coding ENST00000629237.1
## RPS4Y2-001 ENSG00000280969.1 HAVANA protein_coding ENST00000629237.1
## DAZ4-005 ENSG00000205916.11 HAVANA protein_coding ENST00000634662.1
## DAZ4-005 ENSG00000205916.11 HAVANA protein_coding ENST00000634662.1
## DAZ4-003 ENSG00000205916.11 HAVANA protein_coding ENST00000382296.4
## DAZ4-003 ENSG00000205916.11 HAVANA protein_coding ENST00000382296.4
## level havana_gene transcript_name transcript_support_level
## <character> <character> <character> <character>
## SZT2-007 2 OTTHUMG00000007423.14 SZT2-007 4
## TNNI1-006 2 OTTHUMG00000035736.6 TNNI1-006 5
## MPV17-004 2 OTTHUMG00000097074.7 MPV17-004 5
## DQX1-004 2 OTTHUMG00000129965.6 DQX1-004 5
## ST3GAL5-067 2 OTTHUMG00000130171.16 ST3GAL5-067 <NA>
## FAP-201 3 OTTHUMG00000153890.8 FAP-201 5
## FAP-201 3 OTTHUMG00000153890.8 FAP-201 5
## SPEG-021 1 OTTHUMG00000058925.10 SPEG-021 5
## TSEN2-008 1 OTTHUMG00000129765.21 TSEN2-008 5
## P4HTM-012 2 OTTHUMG00000074057.5 P4HTM-012 5
## ABHD14A-ACY1-022 2 OTTHUMG00000166447.7 ABHD14A-ACY1-022 5
## PXK-003 2 OTTHUMG00000159149.4 PXK-003 5
## GMNC-001 2 OTTHUMG00000156195.1 GMNC-001 5
## GMNC-001 2 OTTHUMG00000156195.1 GMNC-001 5
## RUBCN-004 2 OTTHUMG00000155452.5 RUBCN-004 1
## TGFBI-019 2 OTTHUMG00000163213.4 TGFBI-019 2
## TRPC7-002 2 OTTHUMG00000189265.2 TRPC7-002 5
## TRPC7-002 2 OTTHUMG00000189265.2 TRPC7-002 5
## TRPC7-003 2 OTTHUMG00000189265.2 TRPC7-003 5
## TRPC7-003 2 OTTHUMG00000189265.2 TRPC7-003 5
## TRPC7-004 2 OTTHUMG00000189265.2 TRPC7-004 5
## TRPC7-004 2 OTTHUMG00000189265.2 TRPC7-004 5
## TRPC7-005 1 OTTHUMG00000189265.2 TRPC7-005 5
## TRPC7-005 1 OTTHUMG00000189265.2 TRPC7-005 5
## TRPC7-006 2 OTTHUMG00000189265.2 TRPC7-006 5
## TRPC7-006 2 OTTHUMG00000189265.2 TRPC7-006 5
## OFCC1-019 2 OTTHUMG00000159104.8 OFCC1-019 5
## SLC17A1-003 2 OTTHUMG00000016297.3 SLC17A1-003 5
## LST1-024 2 OTTHUMG00000031264.7 LST1-024 5
## KCNQ5-005 2 OTTHUMG00000015020.7 KCNQ5-005 5
## FIG4-004 2 OTTHUMG00000015352.6 FIG4-004 3
## FIG4-004 2 OTTHUMG00000015352.6 FIG4-004 3
## AMD1-004 2 OTTHUMG00000015369.5 AMD1-004 5
## MYB-004 2 OTTHUMG00000015629.10 MYB-004 5
## AC005281.1-004 2 OTTHUMG00000152383.4 AC005281.1-004 5
## AC005281.1-004 2 OTTHUMG00000152383.4 AC005281.1-004 5
## MAGI2-008 1 OTTHUMG00000130697.18 MAGI2-008 5
## SRPK2-003 2 OTTHUMG00000157405.2 SRPK2-003 5
## SRPK2-003 2 OTTHUMG00000157405.2 SRPK2-003 5
## SYPL1-008 2 OTTHUMG00000157587.2 SYPL1-008 5
## SMARCA2-056 2 OTTHUMG00000019445.12 SMARCA2-056 <NA>
## KIAA2026-006 1 OTTHUMG00000019507.6 KIAA2026-006 5
## TLN1-006 2 OTTHUMG00000019874.4 TLN1-006 5
## TRPM3-009 2 OTTHUMG00000019997.11 TRPM3-009 5
## TRPM3-009 2 OTTHUMG00000019997.11 TRPM3-009 5
## TRPM3-011 2 OTTHUMG00000019997.11 TRPM3-011 5
## TRPM3-011 2 OTTHUMG00000019997.11 TRPM3-011 5
## TRPM3-012 2 OTTHUMG00000019997.11 TRPM3-012 5
## TRPM3-012 2 OTTHUMG00000019997.11 TRPM3-012 5
## TRPM3-015 2 OTTHUMG00000019997.11 TRPM3-015 5
## TRPM3-015 2 OTTHUMG00000019997.11 TRPM3-015 5
## TRPM3-016 2 OTTHUMG00000019997.11 TRPM3-016 5
## TRPM3-016 2 OTTHUMG00000019997.11 TRPM3-016 5
## LRSAM1-011 2 OTTHUMG00000020701.2 LRSAM1-011 5
## PRRC2B-005 2 OTTHUMG00000020827.3 PRRC2B-005 2
## GFI1B-001 2 OTTHUMG00000020848.4 GFI1B-001 5
## DNAJC4-012 2 OTTHUMG00000167792.6 DNAJC4-012 5
## GAPDH-201 3 OTTHUMG00000137379.1 GAPDH-201 5
## GAPDH-201 3 OTTHUMG00000137379.1 GAPDH-201 5
## PPP1R12A-006 2 OTTHUMG00000170100.5 PPP1R12A-006 5
## PAH-018 2 OTTHUMG00000169966.4 PAH-018 5
## SEPT4-201 3 OTTHUMG00000179243.3 SEPT4-201 5
## SEPT4-201 3 OTTHUMG00000179243.3 SEPT4-201 5
## THOC1-202 3 OTTHUMG00000178051.11 THOC1-202 5
## TMEM259-003 2 OTTHUMG00000181905.6 TMEM259-003 5
## POLR2E-014 2 OTTHUMG00000181873.5 POLR2E-014 5
## PLK5-003 1 OTTHUMG00000180073.4 PLK5-003 5
## PLK5-003 1 OTTHUMG00000180073.4 PLK5-003 5
## MKNK2-011 1 OTTHUMG00000180020.6 MKNK2-011 5
## NFIC-011 2 OTTHUMG00000180731.7 NFIC-011 5
## NFIC-011 2 OTTHUMG00000180731.7 NFIC-011 5
## CTB-50L17.10-003 2 OTTHUMG00000182007.7 CTB-50L17.10-003 5
## ILF3-004 2 OTTHUMG00000180587.2 ILF3-004 5
## ILF3-004 2 OTTHUMG00000180587.2 ILF3-004 5
## ILF3-006 2 OTTHUMG00000180587.2 ILF3-006 5
## ILF3-006 2 OTTHUMG00000180587.2 ILF3-006 5
## ILF3-005 2 OTTHUMG00000180587.2 ILF3-005 5
## ILF3-005 2 OTTHUMG00000180587.2 ILF3-005 5
## NFIX-006 2 OTTHUMG00000180726.4 NFIX-006 5
## NFIX-006 2 OTTHUMG00000180726.4 NFIX-006 5
## ZNF85-003 1 OTTHUMG00000182747.5 ZNF85-003 5
## ZNF85-003 1 OTTHUMG00000182747.5 ZNF85-003 5
## RP11-255H23.2-001 1 OTTHUMG00000158123.3 RP11-255H23.2-001 NA
## AP2S1-003 2 OTTHUMG00000183437.2 AP2S1-003 3
## AP2S1-003 2 OTTHUMG00000183437.2 AP2S1-003 3
## EMP3-007 2 OTTHUMG00000183196.2 EMP3-007 5
## NELFCD-002 2 OTTHUMG00000032861.5 NELFCD-002 5
## PKNOX1-002 2 OTTHUMG00000086833.5 PKNOX1-002 2
## TXNRD2-009 2 OTTHUMG00000149975.7 TXNRD2-009 5
## PES1-011 2 OTTHUMG00000151077.5 PES1-011 5
## MPST-005 1 OTTHUMG00000150543.2 MPST-005 5
## DENND6B-005 2 OTTHUMG00000150210.6 DENND6B-005 5
## PIGA-002 2 OTTHUMG00000021174.7 PIGA-002 5
## THOC2-003 2 OTTHUMG00000022334.20 THOC2-003 5
## CD99L2-006 2 OTTHUMG00000024247.6 CD99L2-006 5
## RPS4Y2-001 2 OTTHUMG00000036540.2 RPS4Y2-001 1
## RPS4Y2-001 2 OTTHUMG00000036540.2 RPS4Y2-001 1
## DAZ4-005 2 OTTHUMG00000045100.7 DAZ4-005 5
## DAZ4-005 2 OTTHUMG00000045100.7 DAZ4-005 5
## DAZ4-003 2 OTTHUMG00000045100.7 DAZ4-003 5
## DAZ4-003 2 OTTHUMG00000045100.7 DAZ4-003 5
## tag havana_transcript exon_number exon_id ont
## <character> <character> <character> <character> <character>
## SZT2-007 <NA> OTTHUMT00000334864.6 1 ENSE00003806104.1 <NA>
## TNNI1-006 basic OTTHUMT00000411678.1 1 ENSE00002463018.1 <NA>
## MPV17-004 basic OTTHUMT00000325033.2 1 ENSE00003699088.1 <NA>
## DQX1-004 cds_start_NF OTTHUMT00000323362.1 1 ENSE00002454456.1 <NA>
## ST3GAL5-067 RNA_Seq_supported_only OTTHUMT00000491835.1 1 ENSE00003804698.1 <NA>
## FAP-201 appris_alternative_1 <NA> 1 ENSE00003766024.1 <NA>
## FAP-201 appris_alternative_1 <NA> 1 ENSE00003766024.1 <NA>
## SPEG-021 exp_conf OTTHUMT00000130261.1 1 ENSE00002525628.1 <NA>
## TSEN2-008 exp_conf OTTHUMT00000339523.3 1 ENSE00001729862.1 <NA>
## P4HTM-012 cds_start_NF OTTHUMT00000345523.2 1 ENSE00003705080.1 <NA>
## ABHD14A-ACY1-022 readthrough_transcript OTTHUMT00000489140.1 1 ENSE00003794443.1 <NA>
## PXK-003 cds_start_NF OTTHUMT00000353501.1 1 ENSE00002408401.1 <NA>
## GMNC-001 CCDS OTTHUMT00000343364.1 1 ENSE00002503205.1 <NA>
## GMNC-001 CCDS OTTHUMT00000343364.1 1 ENSE00002503205.1 <NA>
## RUBCN-004 cds_start_NF OTTHUMT00000340177.1 1 ENSE00002491913.1 <NA>
## TGFBI-019 cds_start_NF OTTHUMT00000470116.1 1 ENSE00003658068.1 <NA>
## TRPC7-002 <NA> OTTHUMT00000366976.2 1 ENSE00002322790.2 <NA>
## TRPC7-002 <NA> OTTHUMT00000366976.2 1 ENSE00002322790.2 <NA>
## TRPC7-003 CCDS OTTHUMT00000366977.3 1 ENSE00002322790.2 <NA>
## TRPC7-003 CCDS OTTHUMT00000366977.3 1 ENSE00002322790.2 <NA>
## TRPC7-004 <NA> OTTHUMT00000366978.2 1 ENSE00002322790.2 <NA>
## TRPC7-004 <NA> OTTHUMT00000366978.2 1 ENSE00002322790.2 <NA>
## TRPC7-005 CCDS OTTHUMT00000366979.2 1 ENSE00002322790.2 <NA>
## TRPC7-005 CCDS OTTHUMT00000366979.2 1 ENSE00002322790.2 <NA>
## TRPC7-006 basic OTTHUMT00000366980.3 1 ENSE00002322790.2 <NA>
## TRPC7-006 basic OTTHUMT00000366980.3 1 ENSE00002322790.2 <NA>
## OFCC1-019 cds_start_NF OTTHUMT00000353453.1 1 ENSE00001988765.1 <NA>
## SLC17A1-003 <NA> OTTHUMT00000353947.1 1 ENSE00001989113.1 <NA>
## LST1-024 cds_start_NF OTTHUMT00000355079.1 1 ENSE00001920584.1 <NA>
## KCNQ5-005 cds_start_NF OTTHUMT00000316123.1 1 ENSE00002525647.1 <NA>
## FIG4-004 cds_end_NF OTTHUMT00000041771.6 1 ENSE00002459604.1 <NA>
## FIG4-004 cds_end_NF OTTHUMT00000041771.6 1 ENSE00002459604.1 <NA>
## AMD1-004 cds_start_NF OTTHUMT00000041819.4 1 ENSE00003283317.1 <NA>
## MYB-004 cds_start_NF OTTHUMT00000042350.2 1 ENSE00002462030.1 <NA>
## AC005281.1-004 appris_principal_5 OTTHUMT00000491044.1 1 ENSE00003796958.1 <NA>
## AC005281.1-004 appris_principal_5 OTTHUMT00000491044.1 1 ENSE00003796958.1 <NA>
## MAGI2-008 exp_conf OTTHUMT00000344257.3 1 ENSE00003773007.1 <NA>
## SRPK2-003 <NA> OTTHUMT00000348718.1 1 ENSE00002527397.1 <NA>
## SRPK2-003 <NA> OTTHUMT00000348718.1 1 ENSE00002527397.1 <NA>
## SYPL1-008 cds_start_NF OTTHUMT00000488185.1 1 ENSE00003789042.1 <NA>
## SMARCA2-056 RNA_Seq_supported_partial OTTHUMT00000490252.2 1 ENSE00003804220.1 <NA>
## KIAA2026-006 exp_conf OTTHUMT00000051649.3 1 ENSE00003493435.1 <NA>
## TLN1-006 <NA> OTTHUMT00000052358.2 1 ENSE00003471102.1 <NA>
## TRPM3-009 appris_alternative_2 OTTHUMT00000214159.3 1 ENSE00001643540.1 <NA>
## TRPM3-009 appris_alternative_2 OTTHUMT00000214159.3 1 ENSE00001643540.1 <NA>
## TRPM3-011 CCDS OTTHUMT00000214161.2 1 ENSE00001643540.1 <NA>
## TRPM3-011 CCDS OTTHUMT00000214161.2 1 ENSE00001643540.1 <NA>
## TRPM3-012 CCDS OTTHUMT00000214162.3 1 ENSE00001643540.1 <NA>
## TRPM3-012 CCDS OTTHUMT00000214162.3 1 ENSE00001643540.1 <NA>
## TRPM3-015 CCDS OTTHUMT00000214164.2 1 ENSE00001643540.1 <NA>
## TRPM3-015 CCDS OTTHUMT00000214164.2 1 ENSE00001643540.1 <NA>
## TRPM3-016 CCDS OTTHUMT00000356082.1 1 ENSE00001643540.1 <NA>
## TRPM3-016 CCDS OTTHUMT00000356082.1 1 ENSE00001643540.1 <NA>
## LRSAM1-011 <NA> OTTHUMT00000054171.1 1 ENSE00001860145.1 <NA>
## PRRC2B-005 cds_start_NF OTTHUMT00000054755.2 1 ENSE00001742991.1 <NA>
## GFI1B-001 CCDS OTTHUMT00000054809.3 1 ENSE00003763989.1 <NA>
## DNAJC4-012 <NA> OTTHUMT00000397044.1 1 ENSE00002500255.1 <NA>
## GAPDH-201 basic <NA> 1 ENSE00003718373.1 <NA>
## GAPDH-201 basic <NA> 1 ENSE00003718373.1 <NA>
## PPP1R12A-006 <NA> OTTHUMT00000407323.2 1 ENSE00002347749.2 <NA>
## PAH-018 cds_end_NF OTTHUMT00000488030.2 1 ENSE00003786850.1 <NA>
## SEPT4-201 appris_alternative_2 <NA> 1 ENSE00002449440.1 <NA>
## SEPT4-201 appris_alternative_2 <NA> 1 ENSE00002449440.1 <NA>
## THOC1-202 basic <NA> 1 ENSE00003724837.1 <NA>
## TMEM259-003 cds_start_NF OTTHUMT00000474031.2 1 ENSE00003732965.1 <NA>
## POLR2E-014 cds_start_NF OTTHUMT00000474115.1 1 ENSE00003735483.1 <NA>
## PLK5-003 exp_conf OTTHUMT00000449629.3 1 ENSE00003740607.1 <NA>
## PLK5-003 exp_conf OTTHUMT00000449629.3 1 ENSE00003740607.1 <NA>
## MKNK2-011 exp_conf OTTHUMT00000458356.2 1 ENSE00003672430.2 <NA>
## NFIC-011 basic OTTHUMT00000458320.2 1 ENSE00002849759.1 <NA>
## NFIC-011 basic OTTHUMT00000458320.2 1 ENSE00002849759.1 <NA>
## CTB-50L17.10-003 cds_start_NF OTTHUMT00000458644.2 1 ENSE00003745482.1 <NA>
## ILF3-004 basic OTTHUMT00000452072.1 1 ENSE00002869201.1 <NA>
## ILF3-004 basic OTTHUMT00000452072.1 1 ENSE00002869201.1 <NA>
## ILF3-006 CCDS OTTHUMT00000452073.2 1 ENSE00002869201.1 <NA>
## ILF3-006 CCDS OTTHUMT00000452073.2 1 ENSE00002869201.1 <NA>
## ILF3-005 CCDS OTTHUMT00000452074.1 1 ENSE00002869201.1 <NA>
## ILF3-005 CCDS OTTHUMT00000452074.1 1 ENSE00002869201.1 <NA>
## NFIX-006 appris_alternative_2 OTTHUMT00000452767.1 1 ENSE00002852064.1 <NA>
## NFIX-006 appris_alternative_2 OTTHUMT00000452767.1 1 ENSE00002852064.1 <NA>
## ZNF85-003 exp_conf OTTHUMT00000463432.2 1 ENSE00003150682.1 <NA>
## ZNF85-003 exp_conf OTTHUMT00000463432.2 1 ENSE00003150682.1 <NA>
## RP11-255H23.2-001 basic OTTHUMT00000350241.2 1 ENSE00002316016.1 PGO:0000019
## AP2S1-003 CCDS OTTHUMT00000466647.2 1 ENSE00003104628.1 <NA>
## AP2S1-003 CCDS OTTHUMT00000466647.2 1 ENSE00003104628.1 <NA>
## EMP3-007 cds_end_NF OTTHUMT00000465619.2 1 ENSE00003046076.1 <NA>
## NELFCD-002 <NA> OTTHUMT00000079906.4 1 ENSE00001943342.1 <NA>
## PKNOX1-002 <NA> OTTHUMT00000195521.2 1 ENSE00002508807.1 <NA>
## TXNRD2-009 seleno OTTHUMT00000488469.1 1 ENSE00003788934.1 <NA>
## PES1-011 <NA> OTTHUMT00000321255.1 1 ENSE00001915655.1 <NA>
## MPST-005 exp_conf OTTHUMT00000318831.1 1 ENSE00001666837.1 <NA>
## DENND6B-005 <NA> OTTHUMT00000316857.2 1 ENSE00003520427.1 <NA>
## PIGA-002 basic OTTHUMT00000055855.2 1 ENSE00003787914.1 <NA>
## THOC2-003 cds_start_NF OTTHUMT00000058156.4 1 ENSE00001762175.1 <NA>
## CD99L2-006 appris_alternative_2 OTTHUMT00000488174.1 1 ENSE00003788707.1 <NA>
## RPS4Y2-001 CCDS OTTHUMT00000088873.2 1 ENSE00003773208.1 <NA>
## RPS4Y2-001 CCDS OTTHUMT00000088873.2 1 ENSE00003773208.1 <NA>
## DAZ4-005 appris_alternative_2 OTTHUMT00000488635.1 1 ENSE00003756390.1 <NA>
## DAZ4-005 appris_alternative_2 OTTHUMT00000488635.1 1 ENSE00003756390.1 <NA>
## DAZ4-003 appris_principal_5 OTTHUMT00000104780.4 1 ENSE00003756390.1 <NA>
## DAZ4-003 appris_principal_5 OTTHUMT00000104780.4 1 ENSE00003756390.1 <NA>
## protein_id ccdsid score phase gene_name
## <character> <character> <numeric> <integer> <character>
## SZT2-007 <NA> <NA> <NA> <NA> SZT2
## TNNI1-006 ENSP00000451307.1 <NA> <NA> <NA> TNNI1
## MPV17-004 ENSP00000383955.1 <NA> <NA> <NA> MPV17
## DQX1-004 ENSP00000389196.1 <NA> <NA> <NA> DQX1
## ST3GAL5-067 ENSP00000492035.1 <NA> <NA> <NA> ST3GAL5
## FAP-201 ENSP00000485844.1 <NA> <NA> <NA> FAP
## FAP-201 ENSP00000485844.1 <NA> <NA> 0 FAP
## SPEG-021 ENSP00000390353.1 <NA> <NA> <NA> SPEG
## TSEN2-008 ENSP00000408528.2 <NA> <NA> <NA> TSEN2
## P4HTM-012 ENSP00000476858.1 <NA> <NA> <NA> P4HTM
## ABHD14A-ACY1-022 ENSP00000490680.1 <NA> <NA> <NA> ABHD14A-ACY1
## PXK-003 ENSP00000418836.1 <NA> <NA> <NA> PXK
## GMNC-001 ENSP00000406164.1 CCDS54697.1 <NA> <NA> GMNC
## GMNC-001 ENSP00000406164.1 CCDS54697.1 <NA> 0 GMNC
## RUBCN-004 ENSP00000409618.1 <NA> <NA> <NA> RUBCN
## TGFBI-019 ENSP00000474155.1 <NA> <NA> <NA> TGFBI
## TRPC7-002 ENSP00000421571.2 <NA> <NA> <NA> TRPC7
## TRPC7-002 ENSP00000421571.2 <NA> <NA> 0 TRPC7
## TRPC7-003 ENSP00000330322.5 CCDS54905.1 <NA> <NA> TRPC7
## TRPC7-003 ENSP00000330322.5 CCDS54905.1 <NA> 0 TRPC7
## TRPC7-004 ENSP00000426870.2 <NA> <NA> <NA> TRPC7
## TRPC7-004 ENSP00000426870.2 <NA> <NA> 0 TRPC7
## TRPC7-005 ENSP00000367720.3 CCDS54906.1 <NA> <NA> TRPC7
## TRPC7-005 ENSP00000367720.3 CCDS54906.1 <NA> 0 TRPC7
## TRPC7-006 ENSP00000424854.3 <NA> <NA> <NA> TRPC7
## TRPC7-006 ENSP00000424854.3 <NA> <NA> 0 TRPC7
## OFCC1-019 ENSP00000420421.1 <NA> <NA> <NA> OFCC1
## SLC17A1-003 ENSP00000367118.2 <NA> <NA> <NA> SLC17A1
## LST1-024 ENSP00000418578.1 <NA> <NA> <NA> LST1
## KCNQ5-005 ENSP00000414829.1 <NA> <NA> <NA> KCNQ5
## FIG4-004 ENSP00000412156.1 <NA> <NA> <NA> FIG4
## FIG4-004 ENSP00000412156.1 <NA> <NA> 0 FIG4
## AMD1-004 ENSP00000433396.2 <NA> <NA> <NA> AMD1
## MYB-004 ENSP00000390460.2 <NA> <NA> <NA> MYB
## AC005281.1-004 ENSP00000490444.1 <NA> <NA> <NA> AC005281.1
## AC005281.1-004 ENSP00000490444.1 <NA> <NA> 0 AC005281.1
## MAGI2-008 <NA> <NA> <NA> <NA> MAGI2
## SRPK2-003 ENSP00000417946.1 <NA> <NA> <NA> SRPK2
## SRPK2-003 ENSP00000417946.1 <NA> <NA> 0 SRPK2
## SYPL1-008 ENSP00000489167.1 <NA> <NA> <NA> SYPL1
## SMARCA2-056 ENSP00000492585.1 <NA> <NA> <NA> SMARCA2
## KIAA2026-006 <NA> <NA> <NA> <NA> KIAA2026
## TLN1-006 <NA> <NA> <NA> <NA> TLN1
## TRPM3-009 ENSP00000379581.1 <NA> <NA> <NA> TRPM3
## TRPM3-009 ENSP00000379581.1 <NA> <NA> 0 TRPM3
## TRPM3-011 ENSP00000379587.4 CCDS6635.1 <NA> <NA> TRPM3
## TRPM3-011 ENSP00000379587.4 CCDS6635.1 <NA> 0 TRPM3
## TRPM3-012 ENSP00000379576.5 CCDS65064.1 <NA> <NA> TRPM3
## TRPM3-012 ENSP00000379576.5 CCDS65064.1 <NA> 0 TRPM3
## TRPM3-015 ENSP00000350791.3 CCDS6636.1 <NA> <NA> TRPM3
## TRPM3-015 ENSP00000350791.3 CCDS6636.1 <NA> 0 TRPM3
## TRPM3-016 ENSP00000386127.2 CCDS6634.1 <NA> <NA> TRPM3
## TRPM3-016 ENSP00000386127.2 CCDS6634.1 <NA> 0 TRPM3
## LRSAM1-011 <NA> <NA> <NA> <NA> LRSAM1
## PRRC2B-005 ENSP00000326101.7 <NA> <NA> <NA> PRRC2B
## GFI1B-001 ENSP00000361196.1 CCDS48049.1 <NA> <NA> GFI1B
## DNAJC4-012 <NA> <NA> <NA> <NA> DNAJC4
## GAPDH-201 ENSP00000478864.1 <NA> <NA> <NA> GAPDH
## GAPDH-201 ENSP00000478864.1 <NA> <NA> 0 GAPDH
## PPP1R12A-006 <NA> <NA> <NA> <NA> PPP1R12A
## PAH-018 ENSP00000489230.1 <NA> <NA> <NA> PAH
## SEPT4-201 ENSP00000376801.1 <NA> <NA> <NA> SEPT4
## SEPT4-201 ENSP00000376801.1 <NA> <NA> 0 SEPT4
## THOC1-202 ENSP00000481599.1 <NA> <NA> <NA> THOC1
## TMEM259-003 ENSP00000475704.2 <NA> <NA> <NA> TMEM259
## POLR2E-014 ENSP00000480562.1 <NA> <NA> <NA> POLR2E
## PLK5-003 ENSP00000465896.2 <NA> <NA> <NA> PLK5
## PLK5-003 ENSP00000465896.2 <NA> <NA> 0 PLK5
## MKNK2-011 ENSP00000466594.2 <NA> <NA> <NA> MKNK2
## NFIC-011 ENSP00000465177.1 <NA> <NA> <NA> NFIC
## NFIC-011 ENSP00000465177.1 <NA> <NA> 0 NFIC
## CTB-50L17.10-003 ENSP00000477592.1 <NA> <NA> <NA> CTB-50L17.10
## ILF3-004 ENSP00000465515.1 <NA> <NA> <NA> ILF3
## ILF3-004 ENSP00000465515.1 <NA> <NA> 0 ILF3
## ILF3-006 ENSP00000468181.1 CCDS45965.1 <NA> <NA> ILF3
## ILF3-006 ENSP00000468181.1 CCDS45965.1 <NA> 0 ILF3
## ILF3-005 ENSP00000468156.1 CCDS12246.1 <NA> <NA> ILF3
## ILF3-005 ENSP00000468156.1 CCDS12246.1 <NA> 0 ILF3
## NFIX-006 ENSP00000468794.1 <NA> <NA> <NA> NFIX
## NFIX-006 ENSP00000468794.1 <NA> <NA> 0 NFIX
## ZNF85-003 ENSP00000342340.5 <NA> <NA> <NA> ZNF85
## ZNF85-003 ENSP00000342340.5 <NA> <NA> 0 ZNF85
## RP11-255H23.2-001 <NA> <NA> <NA> <NA> RP11-255H23.2
## AP2S1-003 ENSP00000470898.1 CCDS12693.1 <NA> <NA> AP2S1
## AP2S1-003 ENSP00000470898.1 CCDS12693.1 <NA> 0 AP2S1
## EMP3-007 ENSP00000469275.1 <NA> <NA> <NA> EMP3
## NELFCD-002 <NA> <NA> <NA> <NA> NELFCD
## PKNOX1-002 <NA> <NA> <NA> <NA> PKNOX1
## TXNRD2-009 ENSP00000489208.1 <NA> <NA> <NA> TXNRD2
## PES1-011 <NA> <NA> <NA> <NA> PES1
## MPST-005 ENSP00000385062.1 <NA> <NA> <NA> MPST
## DENND6B-005 <NA> <NA> <NA> <NA> DENND6B
## PIGA-002 ENSP00000489528.1 <NA> <NA> <NA> PIGA
## THOC2-003 ENSP00000397317.1 <NA> <NA> <NA> THOC2
## CD99L2-006 ENSP00000489166.1 <NA> <NA> <NA> CD99L2
## RPS4Y2-001 ENSP00000486252.1 CCDS44028.1 <NA> <NA> RPS4Y2
## RPS4Y2-001 ENSP00000486252.1 CCDS44028.1 <NA> 0 RPS4Y2
## DAZ4-005 ENSP00000489430.1 <NA> <NA> <NA> DAZ4
## DAZ4-005 ENSP00000489430.1 <NA> <NA> 0 DAZ4
## DAZ4-003 ENSP00000371733.3 <NA> <NA> <NA> DAZ4
## DAZ4-003 ENSP00000371733.3 <NA> <NA> 0 DAZ4
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengthsoptions("showTailLines"=NULL)