Mus musculus gene Hif3a, encoding hypoxia inducible factor 3, alpha subunit.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.b), 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 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is moderately expressed, only 28.1% of the average gene in this release. The sequence of this gene is defined by 31 GenBank accessions from 28 cDNA clones, some from brain (seen 5 times), rathke's pouches (2), whole brain (2), brain, PCR rescued clones (once), branchial arches (once), whole body (once), whole embryo including extraembryonictissues at 13.5-days postcoitum (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 19 distinct gt-ag introns. Transcription produces 5 alternatively spliced mRNAs. There are 3 probable alternative promotors and 2 non overlapping alternative last exons (see the diagram). The mRNAs appear to differ by truncation of the 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries. 82 bp of this gene are antisense to spliced gene wychy, raising the possibility of regulated alternate expression.
Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (response to hypoxia, signal transduction, transcription from RNA polymerase II promoter, regulation of transcription, regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (DNA binding, signal transducer activity, transcription factor activity, transcription regulator activity) and to localize in nucleus.
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_1859778 for in depth functional annotation of this gene.
Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (1 complete, 2 COOH complete, 2 partial), some containing domains PAS fold, 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 7, links to other databases and other names
Map: This gene Hif3a maps on chromosome 7, at 7 A2 according to Entrez Gene. In AceView, it covers 27.07 kb, from 17647776 to 17620703 (NCBI 37a, Aug 2007), on the reverse strand.
Links to: manual annotations from MGI_1859778, the SNP view, gene overviews from Entrez Gene 53417, expression data from UniGene, molecular and other annotations from UCSC.
Other names: The gene is also known as Hif3a, Ipas or MOP7, LOC53417.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene HIF3A (e= 10-139).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene hif-1 (e=3 10-23), 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 Hif3a 5' 3' encoded on minus strand of chromosome 7 from 17,647,776 to 17,620,703 a b [NM] c d e 5kb 0 72 bp exon 72 bp exon 5905 bp [gt-ag] intron 10 GenBank accessions 191 bp exon 1432 bp [gt-ag] intron 14 GenBank accessions 146 bp exon 2675 bp [gt-ag] intron 11 GenBank accessions 85 bp exon 676 bp [gt-ag] intron 11 GenBank accessions 113 bp exon 375 bp [gt-ag] intron 10 GenBank accessions 209 bp exon 1442 bp [gt-ag] intron 12 GenBank accessions 107 bp exon 238 bp [gt-ag] intron 12 GenBank accessions 148 bp exon 3646 bp [gt-ag] intron 10 GenBank accessions 113 bp exon 287 bp [gt-ag] intron 9 GenBank accessions 191 bp exon 1686 bp [gt-ag] intron 7 GenBank accessions 102 bp exon 1348 bp [gt-ag] intron 6 GenBank accessions 272 bp exon 1299 bp [gt-ag] intron 6 GenBank accessions 112 bp exon 2342 bp [gt-ag] intron 8 GenBank accessions 82 bp exon 1168 bp [gt-ag] intron 9 GenBank accessions 477 bp exon 15 accessions, some from brain (seen 2 times) rathke's pouches (2) whole body (once) 477 bp exon 103 bp exon 103 bp exon 126 bp [gt-ag] intron 5 GenBank accessions 191 bp exon 1432 bp [gt-ag] intron 14 GenBank accessions 146 bp exon 2675 bp [gt-ag] intron 11 GenBank accessions 85 bp exon 676 bp [gt-ag] intron 11 GenBank accessions 113 bp exon 375 bp [gt-ag] intron 10 GenBank accessions 209 bp exon 1442 bp [gt-ag] intron 12 GenBank accessions 107 bp exon 238 bp [gt-ag] intron 12 GenBank accessions 148 bp exon 3646 bp [gt-ag] intron 10 GenBank accessions 113 bp exon 287 bp [gt-ag] intron 9 GenBank accessions 191 bp exon 1686 bp [gt-ag] intron 7 GenBank accessions 102 bp exon 1348 bp [gt-ag] intron 6 GenBank accessions 272 bp exon 1299 bp [gt-ag] intron 6 GenBank accessions 112 bp exon 2342 bp [gt-ag] intron 8 GenBank accessions 82 bp exon 1168 bp [gt-ag] intron 9 GenBank accessions 612 bp exon 10 accessions, NM_016868 some from brain (seen 3 times) whole brain (2), brain PCR rescued clones (once) whole embryo including extraembryonictissues at 13.5-days postcoitum (once) 612 bp exon 154 bp exon 1432 bp [gt-ag] intron 14 GenBank accessions 146 bp exon 2675 bp [gt-ag] intron 11 GenBank accessions 85 bp exon 676 bp [gt-ag] intron 11 GenBank accessions 113 bp exon 375 bp [gt-ag] intron 10 GenBank accessions 209 bp exon 1442 bp [gt-ag] intron 12 GenBank accessions 253 bp exon 1 accession from branchial arches 253 bp exon 111 bp exon 4154 bp [gt-ag] intron 1 GenBank accession 191 bp exon 191 bp exon 1432 bp [gt-ag] intron 14 GenBank accessions 146 bp exon 2675 bp [gt-ag] intron 11 GenBank accessions 85 bp exon 676 bp [gt-ag] intron 11 GenBank accessions 113 bp exon 375 bp [gt-ag] intron 10 GenBank accessions 209 bp exon 1442 bp [gt-ag] intron 12 GenBank accessions 107 bp exon 238 bp [gt-ag] intron 12 GenBank accessions 67 bp exon 1 accession 67 bp exon 29 bp exon 29 bp exon 5905 bp [gt-ag] intron 10 GenBank accessions 191 bp exon 1446 bp [gt-ag] intron 3 GenBank accessions 132 bp exon 868 bp [gt-ag] intron 3 GenBank accessions 56 bp exon 1751 bp [gt-ag] intron 3 GenBank accessions 58 bp exon 2 accessions 58 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.
Read more...
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 2420 bp 679 aa 379 bp 1992 bp 2kb probably including promoter 26939 bp 1kb
bSep07 2586 bp 662 aa 83 bp 514 bp 1986 bp 2kb possibly including promoter 21326 bp 1kb
cSep07 960 bp 273 aa 138 bp 819 bp 2kb 7560 bp 1kb
dSep07 1029 bp 258 aa 253 bp 2kb possibly including promoter 12021 bp 1kb
eSep07 466 bp 154 aa 462 bp 2kb probably including promoter 10436 bp 1kb

Gene neighbors and Navigator on chromosome 7 A2 back to top
R C Ceacam9 C R P Ap2s1 C R P Slc1a5 C R P C R Strn4 C R P Prkd2 C R P C R Dact3 C P Gng8 C R P Ptgir D C P EG434128 C 0710005I19Rik C R G C G C R Psg16 C R P Psg29 C P C C G C G C C C C P Ceacam15 C EG666641 G C R C R P Fkrp C R P Calm3 D C R P Ppp5c R P C R P Hif3a G C C R C C R P C 100kb 0 torete, 3 accessions, 2 variants nunete, 52 accessions Ceacam9, 68 accessions 2 variants Ap2s1, 275 accessions 10 variants Slc1a5, 234 accessions 12 variants tunete, 7 accessions sarete, 2 accessions, 2 variants Strn4, 334 accessions 13 variants Prkd2, 248 accessions 9 variants sanete, 4 accessions Dact3, 20 accessions Gng8, 21 accessions, 7 variants Ptgir, 64 accessions, 2 variants EG434128, 29 accessions 0710005I19Rik, 191 accessions 3 variants LOC100042835, 4 accessions LOC434130, 14 accessions 2 variants wychy, 2 accessions Psg16, 151 accessions 4 variants Psg29, 52 accessions swacho, 1 accession Exo_endo_phos.116, 1 accession yunete, 1 accession sloycho, 1 accession minete, 1 accession munete, 1 accession smawcho, 2 accessions monete, 7 accessions hinete, 1 accession honete, 2 accessions nanete, 1 accession smoycho, 13 accessions nonete, 3 accessions snacho, 1 accession voychy, 8 accessions tanete, 1 accession tinete, 2 accessions sneecho, 2 accessions snercho, 1 accession sneycho, 2 accessions snorcho, 1 accession snoycho, 2 accessions spacho, 2 accessions sunete, 1 accession spawcho, 30 accessions senete, 1 accession sporcho, 2 accessions spoycho, 1 accession stacho, 2 accessions stycho, 7 accessions kanete, 2 accessions stucho, 3 accessions stocho, 1 accession starcho, 1 accession kenete, 3 accessions steecho, 1 accession steycho, 1 accession storcho, 1 accession wanote, 2 accessions swucho, 1 accession ranote, 3 accessions wuchy, 1 accession yonete, 16 accessions 2 variants smacho, 1 accession smycho, 1 accession manete, 2 accessions smucho, 1 accession smocho, 1 accession smarcho, 1 accession vorchy, 1 accession menete, 2 accessions smeecho, 1 accession hunete, 1 accession henete, 1 accession smeycho, 3 accessions ninete, 1 accession smorcho, 1 accession nenete, 2 accessions snycho, 1 accession snucho, 1 accession snocho, 1 accession tenete, 6 accessions snarcho, 1 accession snawcho, 3 accessions sirete, 14 accessions 2 variants spycho, 1 accession spucho, 1 accession sinete, 5 accessions spocho, 1 accession sparcho, 1 accession wachy, 1 accession sonete, 1 accession speecho, 1 accession spercho, 2 accessions speycho, 2 accessions stawcho, 1 accession kunete, 1 accession stercho, 3 accessions swycho, 1 accession Grlf1, 446 accessions 2 variants LOC670915, 4 accessions LOC100038912, 4 accessions smercho, 1 accession hanete, 1 accession Ceacam15, 29 accessions EG666641, 7 accessions LOC434127, 149 accessions tonete, 92 accessions 2 variants Fkrp, 290 accessions, 6 variants Calm3, 469 accessions 3 variants Ppp5c, 569 accessions 10 variants kinete, 43 accessions Hif3a, 30 accessions, 5 variants LOC640145, 103 accessions konete, 1 accession stoycho, 1 accession surete, 7 accessions, 4 variants serete, 2 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               5 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !