Mus musculus gene Epas1, encoding endothelial PAS domain protein 1.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Mus musculus 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 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.6 times the average gene in this release. The sequence of this gene is defined by 165 GenBank accessions from 148 cDNA clones, some from inner ear (seen 5 times), brain (3), diencephalon (3), heart (3), kidney (3), lung (3), whole embryo including extraembryonictissues at 11.5-days postcoitum (3) and 26 other tissues. We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 15 distinct gt-ag introns. Transcription produces 4 different mRNAs, 2 alternatively spliced variants and 2 unspliced forms. The mRNAs appear to differ by truncation of the 5' end, overlapping exons with different boundaries. 473 bp of this gene are antisense to spliced gene sikiro, raising the possibility of regulated alternate expression.
Function: There are 52 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (cardiovascular system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; immune system phenotype; lethality-embryonic/perinatal), proposed to participate in pathway (Renal cell carcinoma) and processes (angiogenesis, blood vessel remodeling, cardiac chronotropy, cell differentiation, cell maturation, embryonic placenta development, erythrocyte differentiation, hemopoiesis, lung development, mitochondrion organization and biogenesis, norepinephrine metabolic process, positive regulation of transcription from RNA polymerase II promoter, regulation of transcription from RNA polymerase II promoter in response to oxidative stress, response to hypoxia, surfactant homeostasis, visual perception, multicellular organismal development, regulation of transcription, DNA-dependent, signal transduction, two-component signal transduction system (phosphorelay)). Proteins are expected to have molecular functions (DNA binding, protein heterodimerization activity, transcription factor activity, transcription factor binding, protein binding, signal transducer activity, transcription regulator activity, two-component sensor activity) and to localize in various compartments (cytoplasm, nucleus, transcription factor complex).
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_109169 for in depth functional annotation of this gene.
Protein coding potential: The 2 spliced and 2 unspliced mRNAs putatively encode good proteins, altogether 4 different isoforms (2 complete, 2 partial), some containing domains basic helix-loop-helix dimerisation region bHLH, PAS fold-3 [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 17, links to other databases and other names
Map: This gene Epas1 maps on chromosome 17, at 17 E4 according to Entrez Gene. In AceView, it covers 78.01 kb, from 87153039 to 87231049 (NCBI 37a, Aug 2007), on the direct strand.
Links to: manual annotations from MGI_109169, KEGG_05211, the SNP view, gene overviews from Entrez Gene 13819, expression data from UniGene, molecular and other annotations from UCSC.
Other names: The gene is also known as Epas1, HLF, HRF, MOP2 or HIF-2alpha, LOC13819.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene EPAS1 (e=4 10-42).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene hif-1 (e=4 10-30), which may contain interesting functional annotation
          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 Epas1 5' 3' encoded on plus strand of chromosome 17 from 87,153,039 to 87,232,755 a [NM] c-u b d-u 5kb 0 610 bp exon 610 bp exon 42807 bp [gt-ag] intron 21 GenBank accessions 191 bp exon 7886 bp [gt-ag] intron 19 GenBank accessions 152 bp exon 412 bp [gt-ag] intron 16 GenBank accessions 85 bp exon 3516 bp [gt-ag] intron 12 GenBank accessions 119 bp exon 107 bp [gt-ag] intron 9 GenBank accessions 206 bp exon 8565 bp [gt-ag] intron 8 GenBank accessions 107 bp exon 5218 bp [gt-ag] intron 8 GenBank accessions 148 bp exon 579 bp [gt-ag] intron 8 GenBank accessions 215 bp exon 958 bp [gt-ag] intron 9 GenBank accessions 191 bp exon 734 bp [gt-ag] intron 9 GenBank accessions 111 bp exon 876 bp [gt-ag] intron 10 GenBank accessions 506 bp exon 692 bp [gt-ag] intron 19 GenBank accessions 127 bp exon 169 bp [gt-ag] intron 22 GenBank accessions 115 bp exon 209 bp [gt-ag] intron 25 GenBank accessions 174 bp exon 1467 bp [gt-ag] intron 19 GenBank accessions 758 bp exon 58 accessions, NM_010137 some from inner ear (seen 5 times) brain (3), diencephalon (3) heart (3), kidney (3) Validated 3' end, 5 accessions 758 bp exon 267 bp exon 267 bp exon 1 accession from retina 267 bp exon 289 bp exon 958 bp [gt-ag] intron 9 GenBank accessions 78 bp exon 1 accession 78 bp exon 1620 bp exon 1620 bp exon 97 accessions, some from mammary gland (seen 9 times) retina (9), laser-captured isthmal cells from tox176transgenic mice (8) colon epithelia progenitor cells (7) small intestinal epithelial progenitors (7) Validated 3' end, 9 accessions 1620 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
aSep07 3815 bp 874 aa 584 bp 606 bp 2kb possibly including promoter 78010 bp 1kb
bSep07 367 bp 122 aa 366 bp 2kb 1325 bp 1kb
cSep07-unspliced 267 bp 88 aa 264 bp 2kb 267 bp 1kb
dSep07-unspliced 1620 bp 73 aa 605 bp 793 bp 2kb possibly including promoter 1620 bp 1kb

Gene neighbors and Navigator on chromosome 17 E4 back to top
Prkce D C R P Epas1 D C R P 1700090G07Rik C P R R Rhoq C R P C Cript C R EG433144 C Socs5 C R P R R C R C R P Atp6v1e2 C R P Pigf C R P Mcfd2 100kb 0 Prkce, 204 accessions 12 variants Epas1, 162 accessions 4 variants 1700090G07Rik, 38 accessions larger, 1 accession parjer, 4 accessions Rhoq, 252 accessions, 7 variants rujer, 1 accession Cript, 312 accessions 7 variants EG433144, 67 accessions Socs5, 129 accessions 7 variants rohiyu, 2 accessions yuhiyu, 1 accession leyjer, 2 accessions mihiyu, 3 accessions lorjer, 1 accession loyjer, 1 accession majer, 6 accessions mehiyu, 1 accession hahiyu, 6 accessions mujer, 2 accessions mojer, 1 accession marjer, 1 accession mawjer, 1 accession huhiyu, 12 accessions meejer, 6 accessions nahiyu, 3 accessions merjer, 1 accession meyjer, 1 accession nuhiyu, 1 accession najer, 1 accession nujer, 2 accessions nojer, 2 accessions nerjer, 2 accessions neyjer, 1 accession norjer, 2 accessions pajer, 1 accession nohiyu, 2 accessions pujer, 3 accessions tahiyu, 1 accession pojer, 1 accession tehiyu, 2 accessions pawjer, 1 accession tohiyu, 2 accessions perjer, 2 accessions lawger, 21 accessions peyjer, 1 accession sihiyu, 8 accessions porjer, 1 accession poyjer, 2 accessions rajer, 1 accession ryjer, 1 accession rojer, 1 accession rarjer, 1 accession rawjer, 5 accessions reejer, 1 accession rerjer, 1 accession rorjer, 2 accessions syjer, 1 accession sawjer, 2 accessions sohiyu, 2 accessions serjer, 1 accession sorjer, 2 accessions kahiyu, 1 accession soyjer, 1 accession tyjer, 1 accession tujer, 2 accessions tarjer, 1 accession tawjer, 1 accession teejer, 1 accession terjer, 1 accession toyjer, 3 accessions, 2 variants leejer, 1 accession yahiyu, 2 accessions lerjer, 3 accessions yohiyu, 2 accessions mahiyu, 1 accession muhiyu, 2 accessions mohiyu, 4 accessions myjer, 1 accession hihiyu, 1 accession sakiro, 6 accessions nihiyu, 2 accessions morjer, 1 accession moyjer, 1 accession nyjer, 1 accession luger, 1 accession narjer, 6 accessions nawjer, 1 accession neejer, 1 accession loger, 1 accession noyjer, 1 accession pyjer, 1 accession nehiyu, 1 accession tihiyu, 2 accessions sukiro, 4 accessions tuhiyu, 2 accessions peejer, 1 accession sahiyu, 4 accessions reyjer, 1 accession royjer, 1 accession sajer, 1 accession suhiyu, 1 accession sujer, 1 accession leeger, 2 accessions sojer, 1 accession sarjer, 3 accessions, 2 variants sehiyu, 2 accessions seejer, 1 accession lerger, 2 accessions seyjer, 1 accession tajer, 1 accession kihiyu, 2 accessions tojer, 1 accession sekiro, 6 accessions teyjer, 1 accession torjer, 1 accession kuhiyu, 2 accessions kehiyu, 2 accessions lyger, 3 accessions, 2 variants hehiyu, 14 accessions hohiyu, 1 accession sikiro, 7 accessions, 4 variants Atp6v1e2, 12 accessions Pigf, 105 accessions, 2 variants Mcfd2, 414 accessions 11 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               52 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-u, .d-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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