Homo sapiens complex locus RALY, encoding RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse)).
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SUMMARY back to top
RefSeq summary
[RALY] In infectious mononucleosis, anti-EBNA-1 antibodies are produced which cross-react with multiple normal human proteins. The cross-reactivity is due to anti-gly/ala antibodies that cross-react with host proteins containing configurations like those in the EBNA-1 repeat. One such antigen is RALY which is a member of the heterogeneous nuclear ribonucleoprotein gene family. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .d and .e), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 21 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at very high level, 5.1 times the average gene in this release. The sequence of this gene is defined by 648 GenBank accessions, some from brain (seen 44 times), lung (29), stomach (29), skin (25), eye (22), testis (21), ovary (18) and 157 other tissues. We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 26 distinct introns (25 gt-ag, 1 gc-ag). Transcription produces 23 different mRNAs, 21 alternatively spliced variants and 2 unspliced forms. There are 8 probable alternative promotors, 7 non overlapping alternative last exons and 10 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 17 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
3 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant eAug10, kAug10).
Function: There are 6 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Infectious Mononucleosis) and proposed to participate in processes (mRNA processing, RNA splicing). Proteins are expected to have molecular functions (nucleotide binding, RNA binding) and to localize in various compartments (heterogeneous nuclear ribonucleoprotein complex, nucleus, spliceosomal complex). Putative protein interactors have been described (PCBP1, PIK3CD, SPG7, USP45, WDR62).
Protein coding potential: 14 spliced mRNAs putatively encode good proteins, altogether 11 different isoforms (7 complete, 1 COOH complete, 3 partial), some containing RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) [Pfam], a coiled coil stretch [Psort2]. The remaining 9 mRNA variants (7 spliced, 2 unspliced; 4 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by acetylation; phosphorylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 20, links to other databases and other names
Map: This gene RALY maps on chromosome 20, at 20q11.21-q11.23 according to Entrez Gene. In AceView, it covers 134.94 kb, from 32581466 to 32716409 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 22913, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as RALY, RP1-64K7.1, P542, HNRPCL2 or MGC117312, LOC22913. It has been described as RNA-binding protein Raly, autoantigen p542, OTTHUMP00000030678, hnRNP core protein C-like 2, RNA-binding protein (autoantigenic), heterogeneous nuclear ribonucleoprotein C-like 2, hnRNP associated with lethal yellow protein homolog, RNA binding protein (autoantigenic, hnRNP-associated with lethal yellow), RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow).
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Raly (e= 10-101).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes ztf-4 (e=8 10-07), psf-1 (e=8 10-06), rsp-1 (e=2 10-05), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes RSZ32 (e=10-06), RSZ33 (e=5 10-06), ATRSP31 (e=5 10-06), AT2G46610 (e=3 10-05), UBP1B (e=3 10-05), UBP1A (e=6 10-05), AT3G14100 (e=8 10-05), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RALY Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 43.2 24.8 37.6 14.3 57.1 35.1 46.3 57.1 35.1 28.5 26.6 16.4 30.6 23.2 30.6 14.3 37.6 46.3 32.8 28.5 46.3 43.2 40.3 10.8 12.4 10.1 20.2 26.6 24.8 37.6 24.8 21.6 24.8 13.3 14.3 26.6 53.2 53.2 53.2 70.2 32.8 28.5 80.7 70.2 43.2 40.3 65.5 65.5 53.2 30.6 32.8 28.5 61.1 49.7 46.3 23.2 53.2 70.2 61.1 24.8 15.3 43.2 99.3 23.2 35.1 49.7 32.8 26.6 28.5 49.7 40.3 57.1 35.1 65.5 53.2 53.2 80.7 53.2 28.5 49.7 37.6 30.6 65.5 53.2 32.8 57.1 70.2 57.1 37.6 23.2 30.6 65.5 53.2 40.3 32.8 40.3 49.7 37.6 53.2 65.5 24.8 57.1 43.2 70.2 37.6 61.1 40.3 49.7 70.2 46.3 32.8 46.3 37.6 49.7 26.6 24.8 40.3 53.2 46.3 57.1 21.6 57.1 46.3 24.8 37.6 43.2 21.6 30.6 57.1 57.1 86.5 32.8 57.1 49.7 30.6 43.2 21.6 13.3 26.6 21.6 11.6 26.6 20.2 16.4 30.6 18.8 28.5 35.1 14.3 13.3 10.1 28.5 20.2 40.3 15.3 53.2 40.3 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
Read more...
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene RALY 5' 3' encoded on plus strand of chromosome 20 from 32,581,466 to 32,716,409 14312 257718 152049 323259 224559 a p-u 211336 4952 6423 257718 152049 323259 224559 336502 324524 b 211336 279782 257718 152049 323259 224559 336502 1288 c 211336 279782 257718 152049 323259 224559 336502 324524 d [NM] 211336 279782 257718 71016 323259 224559 336502 324524 e [NM] va-u 211336 279782 257718 152049 52 224559 336502 324524 f 211336 279782 30 152049 323259 224559 g 211336 279782 257718 71016 52 224559 h 147 279782 257718 71016 52 224559 i 211336 279782 257718 j 323259 224559 336502 324524 k 279 279782 257718 t 2 l 1 638 r 336502 324524 m 1 323259 224559 n o 336502 220 q 87 s 211336 987 u 336502 14 vb 5kb 0 442 bp exon 442 bp exon 77934 bp [gt-ag] intron 22 GenBank accessions 14290 RNA-seq supporting reads 3125 UHR pooled cells 1308 Brain 585 Blood 9209 Neuroblastoma 63 Other (also 1482 Primates bodymap) 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 574 bp exon 24 accessions, some from melanotic melanoma (seen 4 times) skin (4), brain (2), neuroblastoma (2) adipose (once) 574 bp exon 525 bp exon 525 bp exon 5 accessions, some from carcinoid (seen once) liver and spleen (once) lung (once), marrow (once) poorly differentiated adenocarcinoma withsignet ring cell features (once) Validated 3' end, 1 accession 525 bp exon 452 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 33439 bp [gt-ag] intron 13 GenBank accessions 4939 RNA-seq supporting reads 1996 UHR pooled cells 147 Brain 627 Blood 2157 Neuroblastoma 12 Other (also 60 Primates bodymap) 117 bp exon 6905 bp [gt-ag] intron 16 GenBank accessions 6407 RNA-seq supporting reads 2716 UHR pooled cells 193 Brain 818 Blood 2660 Neuroblastoma 20 Other (also 99 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 16 accessions, some from muscle (seen 3 times) rhabdomyosarcoma (3) brain (2), testis (2) adenocarcinoma (once) 202 bp exon 206 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 6107 bp [gt-ag] intron 9 GenBank accessions 1279 RNA-seq supporting reads 860 UHR pooled cells 40 Brain 75 Blood 304 Neuroblastoma 132 accessions, some from stomach (seen 18 times) lymph node (10), brain (8) epidermoid carcinoma cell line (7), ovary (7) capped 5' end, 6 accessions Validated 3' end, 2 accessions 224 bp exon 466 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 162 accessions, NM_016732.1 some from brain (seen 15 times) placenta cot 25-normalized (10) skin (10), eye (8), lung (7) Validated 3' end, 16 accessions 352 bp exon 472 bp exon 472 bp exon 294 bp uORF 472 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 73 bp exon 2238 bp [gt-ag] intron 65 GenBank accessions 70951 RNA-seq supporting reads 12157 UHR pooled cells 5379 Brain 4005 Blood 49114 Neuroblastoma 296 Other (also 7490 Primates bodymap) 167 bp exon 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 88 accessions, NM_007367.2 some from brain (seen 11 times) adenocarcinoma (5), placenta cot 25-normalized (5) liver (4), colon (3) capped 5' end, 5 accessions Validated 3' end, 7 accessions 1000 bp exon 373 bp exon 373 bp exon 1 accession from testis normal 373 bp exon 206 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 165 bp exon 663 bp [gt-ag] intron 5 GenBank accessions 47 RNA-seq supporting reads 14 UHR pooled cells 2 Brain 1 Blood 30 Neuroblastoma (also 5 Primates bodymap) 114 bp exon 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 4 accessions, some from B cells (ramos cell line) cot 25-normalized (seen once) chondrosarcoma grade II (once) eye (once), left pelvis (once) lens (once) Validated 3' end, 3 accessions 350 bp exon 179 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 140 bp exon 140 bp exon 1613 bp [gt-ag] intron 1 GenBank accession 29 RNA-seq supporting reads 17 UHR pooled cells 1 Brain 1 Blood 10 Neuroblastoma (also 1 Primates bodymap) 48 bp exon 2007 bp [gt-ag] intron 187 GenBank accessions 151862 RNA-seq supporting reads 35599 UHR pooled cells 11728 Brain 16370 Blood 87573 Neuroblastoma 592 Other (also 11482 Primates bodymap) 167 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 1 accession from ovary from teratocarcinoma cell line 83 bp exon 48 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 2238 bp [gt-ag] intron 65 GenBank accessions 70951 RNA-seq supporting reads 12157 UHR pooled cells 5379 Brain 4005 Blood 49114 Neuroblastoma 296 Other (also 7490 Primates bodymap) 165 bp exon 663 bp [gt-ag] intron 5 GenBank accessions 47 RNA-seq supporting reads 14 UHR pooled cells 2 Brain 1 Blood 30 Neuroblastoma (also 5 Primates bodymap) 114 bp exon 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 1 accession from adenocarcinoma cell line from colon 51 bp exon 67 bp exon 1594 bp [gt-ag] intron 1 GenBank accession 146 RNA-seq supporting reads 41 UHR pooled cells 79 Blood 26 Neuroblastoma 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 2238 bp [gt-ag] intron 65 GenBank accessions 70951 RNA-seq supporting reads 12157 UHR pooled cells 5379 Brain 4005 Blood 49114 Neuroblastoma 296 Other (also 7490 Primates bodymap) 165 bp exon 663 bp [gt-ag] intron 5 GenBank accessions 47 RNA-seq supporting reads 14 UHR pooled cells 2 Brain 1 Blood 30 Neuroblastoma (also 5 Primates bodymap) 114 bp exon 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 1 accession from adenocarcinoma cell line from ovary 103 bp exon 221 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 73 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 217 bp exon 1 accession from brain 217 bp exon 351 bp exon 351 bp exon 138 bp uORF 351 bp exon 351 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 218 bp exon 218 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 88 accessions, some from lung (seen 12 times) epidermoid carcinoma cell line (7), head neck (5) colon (4), eye (4) Validated 3' end, 26 accessions Validated 3' end, 5 accessions 361 bp exon 43 bp exon 8806 bp [gt-ag] intron 1 GenBank accession 278 RNA-seq supporting reads 34 UHR pooled cells 5 Brain 76 Blood 161 Neuroblastoma 2 Other (also 2 Primates bodymap) 83 bp exon 40461 bp [gt-ag] intron 261 GenBank accessions 279521 RNA-seq supporting reads 65138 UHR pooled cells 22298 Brain 24434 Blood 165971 Neuroblastoma 1680 Other (also 25178 Primates bodymap) 265 bp exon 265 bp exon 1232 bp [gt-ag] intron 263 GenBank accessions 257455 RNA-seq supporting reads 59520 UHR pooled cells 20891 Brain 22452 Blood 153299 Neuroblastoma 1293 Other (also 23616 Primates bodymap) 1 accession from adipose 23 bp exon 19 bp exon 19 bp exon 3153 bp [gc-ag] intron 2 GenBank accessions 313 bp exon 2 accessions, some from pooled germ cell tumors (seen once) 313 bp exon 61 bp exon 13493 bp [gt-ag] intron 1 GenBank accession 83 bp exon 83 bp exon 27588 bp [gt-ag] intron 1 GenBank accession 637 RNA-seq supporting reads 336 UHR pooled cells 19 Brain 7 Blood 273 Neuroblastoma 2 Other (also 36 Primates bodymap) 1 accession from testis 276 bp exon 2553 bp exon 2553 bp exon 33 bp uORF 2553 bp exon Sequence gap 1468 bp 123 bp exon 123 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 49 bp exon 1356 bp [gt-ag] intron 174 GenBank accessions 324350 RNA-seq supporting reads 67271 UHR pooled cells 25941 Brain 19692 Blood 210895 Neuroblastoma 551 Other (also 21393 Primates bodymap) 350 bp exon 350 bp exon 12 accessions, some from brain (seen once) breast (once), cerebellum (once) embryonic stem cells cell lines H1, H7, andh9 (once) eye (once) 350 bp exon 36 bp exon 36 bp exon 2276 bp [gt-ag] intron 1 GenBank accession 129 bp exon 661 bp [gt-ag] intron 194 GenBank accessions 323065 RNA-seq supporting reads 78591 UHR pooled cells 27891 Brain 25131 Blood 190289 Neuroblastoma 1163 Other (also 25555 Primates bodymap) 114 bp exon 212 bp [gt-ag] intron 183 GenBank accessions 224376 RNA-seq supporting reads 51051 UHR pooled cells 17784 Brain 18213 Blood 136463 Neuroblastoma 865 Other (also 16084 Primates bodymap) 37 bp exon 1 accession from brain 37 bp exon 356 bp exon 356 bp exon 183 bp [gt-ag] intron 188 GenBank accessions 167082 RNA-seq supporting reads 41824 UHR pooled cells 13577 Brain 16539 Blood 94297 Neuroblastoma 845 Other (also 13629 Primates bodymap) 202 bp exon 1 accession from thalamus capped 5' end, 1 accession 202 bp exon 109 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 1364 bp [gt-ag] intron 1 GenBank accession 219 RNA-seq supporting reads 20 UHR pooled cells 23 Brain 9 Blood 167 Neuroblastoma (also 3 Primates bodymap) 342 bp exon 1 accession from alveolar macrophage from lung Validated 3' end, 1 accession 342 bp exon 64 bp exon 48305 bp [gt-ag] intron 1 GenBank accession 86 RNA-seq supporting reads 5 UHR pooled cells 16 Brain 2 Blood 63 Neuroblastoma 352 bp exon 352 bp exon 11 accessions, some from pancreas (seen 3 times) brain (2), adenocarcinoma (once) carcinoid (once), epithelioid carcinoma (once) Validated 3' end, 5 accessions 352 bp exon 165 bp exon 37390 bp [gt-ag] intron 252 GenBank accessions 211084 RNA-seq supporting reads 44301 UHR pooled cells 16097 Brain 12064 Blood 137657 Neuroblastoma 965 Other (also 17723 Primates bodymap) 83 bp exon 83 bp exon 96869 bp [gt-ag] intron 1 GenBank accession 986 RNA-seq supporting reads 33 UHR pooled cells 114 Brain 4 Blood 828 Neuroblastoma 7 Other 1 accession from embryonic stem cells embryoid bodiesderived from H1 H7 and H9 cells 130 bp exon 33 bp exon 1259 bp [gt-ag] intron 182 GenBank accessions 336320 RNA-seq supporting reads 74411 UHR pooled cells 27766 Brain 20365 Blood 213148 Neuroblastoma 630 Other (also 22478 Primates bodymap) 49 bp exon 49 bp exon 29610 bp [gt-ag] intron 1 GenBank accession 13 RNA-seq supporting reads 8 UHR pooled cells 5 Neuroblastoma 145 bp exon 1 accession from bone marrow from stem cell 34+/38+ Validated 3' end, 1 accession 145 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 1683 bp 468 aa 275 bp 2kb 83912 bp 1kb
bAug10 1788 bp 306 aa 661 bp 206 bp 2kb possibly including promoter 86432 bp 1kb
cAug10 1447 bp 306 aa 298 bp 228 bp 2kb including Promoter 90959 bp 1kb
dAug10 1835 bp 306 aa 558 bp 356 bp 2kb possibly including promoter 86596 bp 1kb
eAug10 2441 bp 290 aa 564 bp 1004 bp 291 bp 2kb including Promoter 87250 bp 1kb
fAug10 1571 bp 184 aa 298 bp 718 bp 2kb probably including promoter 86334 bp 1kb
gAug10 814 bp 181 aa 271 bp 2kb probably including promoter 83158 bp 1kb
hAug10 799 bp 168 aa 140 bp 152 bp 2kb possibly including promoter 82995 bp 1kb
iAug10 870 bp 168 aa 159 bp 204 bp 2kb possibly including promoter 47270 bp 1kb
jAug10 859 bp 126 aa 313 bp 165 bp 2kb probably including promoter 80125 bp 1kb
kAug10 1093 bp 126 aa 347 bp 365 bp 135 bp 2kb possibly including promoter 4581 bp 1kb
lAug10 332 bp 110 aa 2kb 3485 bp 1kb
mAug10 3785 bp 106 aa 3411 bp 53 bp 30 bp 2kb possibly including promoter 7158 bp 1kb
nAug10 316 bp 93 aa 35 bp 2kb possibly including promoter 3465 bp 1kb
oAug10 558 bp 38 aa 291 bp 150 bp 2kb including Promoter 741 bp 1kb
pAug10-unspliced 525 bp 56 aa 132 bp 222 bp 2kb 525 bp 1kb
qAug10 500 bp 69 aa 134 bp 156 bp 2kb 3123 bp 1kb
rAug10 420 bp 33 aa 318 bp 2kb 41501 bp 1kb
sAug10 416 bp 73 aa 139 bp 55 bp 2kb 48721 bp 1kb
tAug10 414 bp 93 aa 135 bp 2kb 50913 bp 1kb
uAug10 378 bp 65 aa 180 bp 2kb 134637 bp 1kb
vaAug10-unspliced 373 bp 36 aa 261 bp 2kb 373 bp 1kb
vbAug10 227 bp 10 aa 58 bp 136 bp 2kb 31096 bp 1kb

Gene neighbors and Navigator on chromosome 20q11.21-q11.23 back to top
C20orf144 R P C20orf134 C P R ZNF341 C I R P CHMP4B D C I R P RALY D C I R P ASIP D C I R P ITCH D C I R P C DYNLRB1 D C I R P MAP1LC3A RPL31P2 XPOTP1 C I R P PXMP4andNECAB3 D C I R P E2F1 R C R C R R C I R P EIF2S2 D C I R P AHCY C P FDX1P1 R 100kb 0 CBFA2T2, 471 accessions 25 variants C20orf144, 20 accessions C20orf134, 42 accessions latar, 6 accessions ZNF341, 97 accessions 9 variants CHMP4B, 413 accessions 2 variants RALY, 557 accessions, 23 variants ASIP, 12 accessions, 2 variants ITCH, 316 accessions, 23 variants bylee, 2 accessions DYNLRB1, 354 accessions 16 variants plorzar, 1 accession reelaw, 1 accession slozar, 1 accession wutu, 2 accessions hetori, 2 accessions, 2 variants fysarbo, 1 accession snuzar, 1 accession minuru, 2 accessions snarzar, 1 accession blawsawbu, 3 accessions wartu, 1 accession bleesawbu, 1 accession snawzar, 3 accessions blersawbu, 1 accession sneezar, 2 accessions spazar, 2 accessions spawzar, 2 accessions sweezar, 1 accession boyzaw, 1 accession glatu, 1 accession bloysawbu, 2 accessions steyvor, 1 accession forzaw, 1 accession gawzaw, 1 accession geezaw, 2 accessions gorzaw, 3 accessions flosawbu, 1 accession storvor, 1 accession leyzaw, 1 accession shorlaw, 4 accessions mazaw, 1 accession klartu, 1 accession noyzaw, 2 accessions klortu, 1 accession flersawbu, 5 accessions porzaw, 1 accession peegee, 1 accession poyzaw, 1 accession skatu, 2 accessions reezaw, 1 accession syzaw, 1 accession serzaw, 1 accession skawtu, 1 accession tozaw, 1 accession tawzaw, 1 accession teezaw, 1 accession glusawbu, 1 accession swervor, 6 accessions skoytu, 1 accession smatu, 1 accession swoyvor, 5 accessions makura, 3 accessions, 2 variants wozaw, 1 accession wawzaw, 1 accession chuzaw, 2 accessions bavoy, 2 accessions klalaw, 13 accessions 2 variants poygee, 3 accessions smertu, 1 accession cherzaw, 2 accessions choyzaw, 2 accessions snatu, 1 accession ragee, 1 accession spawtu, 1 accession byvoy, 10 accessions barto, 2 accessions shorzaw, 1 accession blyzaw, 1 accession berto, 1 accession bleyzaw, 1 accession rugee, 1 accession gleesawbu, 4 accessions glersawbu, 1 accession bloyzaw, 1 accession lortar, 1 accession rogee, 1 accession nisara, 2 accessions florzaw, 1 accession sygee, 1 accession gleezaw, 1 accession pyto, 4 accessions kleesawbu, 1 accession klyzaw, 1 accession klozaw, 1 accession werto, 1 accession bawvoy, 1 accession fawsarbo, 2 accessions sorgee, 1 accession chuto, 2 accessions slozaw, 1 accession hesari, 1 accession smeezaw, 1 accession smerzaw, 2 accessions smorzaw, 3 accessions snozaw, 1 accession plarsawbu, 1 accession snawzaw, 1 accession togee, 8 accessions glorto, 1 accession berlee, 1 accession mortar, 4 accessions spozaw, 2 accessions speezaw, 1 accession sporzaw, 1 accession stozaw, 1 accession pleyto, 1 accession starzaw, 2 accessions plawsawbu, 2 accessions 2 variants plorsawbu, 1 accession dolee, 1 accession vytaw, 20 accessions vugee, 1 accession skyto, 2 accessions steezaw, 1 accession steyzaw, 1 accession storzaw, 2 accessions zugee, 1 accession feetar, 1 accession gartar, 1 accession skarsawbu, 1 accession skersawbu, 1 accession keytar, 1 accession swyzaw, 1 accession sweyzaw, 2 accessions bazee, 1 accession reytu, 1 accession fasarbo, 1 accession sawtu, 7 accessions snazar, 1 accession snozar, 1 accession rokura, 1 accession zeebee, 3 accessions blawtu, 1 accession neegee, 1 accession sperzar, 5 accessions nitori, 2 accessions, 2 variants stuvor, 3 accessions swazar, 1 accession bleysawbu, 2 accessions flortu, 2 accessions zeybee, 3 accessions darzaw, 3 accessions stervor, 2 accessions fuzaw, 2 accessions RPL31P2, 1 accession feyzaw, 1 accession flasawbu, 11 accessions gerzaw, 1 accession juzaw, 1 accession stoyvor, 2 accessions gleetu, 1 accession swavor, 1 accession swyvor, 3 accessions flawsawbu, 2 accessions jerzaw, 2 accessions muzaw, 1 accession pyzaw, 1 accession pleytu, 1 accession lartar, 4 accessions fleysawbu, 1 accession perzaw, 2 accessions sweevor, 1 accession fleylaw, 1 accession leetar, 2 accessions royzaw, 1 accession seezaw, 3 accessions fusarbo, 1 accession sorzaw, 1 accession glysawbu, 1 accession sweyvor, 6 accessions sworvor, 5 accessions vozaw, 1 accession verzaw, 1 accession weyzaw, 1 accession woyzaw, 1 accession smytu, 1 accession charzaw, 2 accessions smutu, 1 accession cheezaw, 1 accession leytar, 3 accessions sharzaw, 2 accessions snartu, 3 accessions speytu, 4 accessions mikura, 1 accession bleezaw, 1 accession gleysawbu, 1 accession XPOTP1, 1 accession gloysawbu, 9 accessions klysawbu, 2 accessions floyzaw, 6 accessions klosawbu, 1 accession neyto, 1 accession gluzaw, 1 accession glawzaw, 3 accessions glorzaw, 4 accessions gloyzaw, 2 accessions barvoy, 2 accessions farsarbo, 1 accession klawsawbu, 1 accession poto, 1 accession loytar, 15 accessions klersawbu, 1 accession matar, 14 accessions spulaw, 7 accessions klazaw, 1 accession seygee, 1 accession plarzaw, 1 accession swolaw, 2 accessions slyzaw, 3 accessions slarzaw, 2 accessions tygee, 1 accession flato, 1 accession smyzaw, 1 accession smarzaw, 1 accession floyto, 1 accession snuzaw, 1 accession doyroybu, 3 accessions snorzaw, 1 accession boylee, 3 accessions sperzaw, 1 accession speyzaw, 1 accession kleyto, 1 accession stawzaw, 1 accession vygee, 1 accession dawlee, 2 accessions fersarbo, 1 accession zygee, 1 accession skoyto, 1 accession dortar, 1 accession doytar, 1 accession zergee, 2 accessions skysawbu, 1 accession skosawbu, 1 accession keetar, 2 accessions skawsawbu, 1 accession skeesawbu, 5 accessions borvoy, 15 accessions skeysawbu, 1 accession lutar, 5 accessions golee, 2 accessions dozee, 4 accessions chugee, 1 accession dawzee, 1 accession PXMP4andNECAB3, 408 accessions 34 variants E2F1, 157 accessions, 5 variants lytar, 2 accessions weeku, 13 accessions, 5 variants lotar, 24 accessions, 2 variants kogar, 12 accessions, 2 variants EIF2S2, 482 accessions 17 variants AHCY, 475 accessions, 12 variants sluzaw, 1 accession FDX1P1, 2 accessions munuru, 11 accessions 2 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               6 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p-u, .q, .r, .s, .t, .u, .va-u, .vb Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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