Caenorhabditis elegans gene hif-1, hypoxia Inducible Factor, encoding mammalian Hypoxia Inducible Factor homolog, Helix Loop Helix containing protein.
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SUMMARY back to top
Summary
[Wormbase] hif-1 encodes an ortholog of the mammalian hypoxia-induced factor HIF-1, and is required for survival in hypoxic environments (1% oxygen) that have no effect on wild-type C. elegans.
Wormbase predicts 4 models, but Caenorhabditis elegans 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 9.3 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 5%, L1 or L2 larvae 34%, L3 to adult 62%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 103 cDNA clones and 20 elements defined by RNA-seq, some from mixed (seen 35 times), l1 (34), l2 (14), embryo (5), l4 (5), whole animal (once). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 17 distinct gt-ag introns. Transcription produces at least 8 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2. There are 4 probable alternative promotors, 2 non overlapping alternative last exons and 3 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 4 cassette exons, overlapping exons with different boundaries.
Note that mRNA .d was found in vivo, although it is a predicted target 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 c).
Function: There are 20 articles specifically referring to this gene in PubMed. In addition we point below to 4 abstracts. This gene is associated to a phenotype (adaptation to hypoxia, Hypoxia Inducible Factor, reduced susceptibility to pathogens). Functionally, the gene has been proposed to participate in a process (regulation of transcription). Proteins are expected to have molecular function (transcription regulator activity) and to localize in nucleus. These proteins appear to interact with other proteins (AHA-1, CBP-1, EGL-9, LIN-2, VHL-1). The gene interacts with MTSS-1.
Protein coding potential: The 8 spliced mRNAs putatively encode good proteins, altogether 8 different isoforms (3 complete, 1 COOH complete, 4 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 V, links to other databases and other names
Map: This gene hif-1 maps on chomosome V at position +29.88 (interpolated). In AceView, it covers 4.88 kb, from 20775801 to 20780680 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5V253, in Wormbase by its cosmid.number name F38A6.3, in NextDB, the Nematode expression pattern database, as CEYK179.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene HIF3A (e=10-11).
The closest mouse genes, according to BlastP, are the AceView genes Hif3a (e=3 10-39), Epas1 (e=2 10-35)
          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 hif-1 5' 3' encoded on plus strand of chromosome V from 20,775,801 to 20,780,658 a b c d g e f h 1 2kb 0 109 bp exon 109 bp exon 793 bp [gt-ag] intron 34 GenBank accessions 191 bp exon 126 bp [gt-ag] intron 47 GenBank accessions 155 bp exon 45 bp [gt-ag] intron 54 GenBank accessions 315 bp exon 517 bp [gt-ag] intron 48 GenBank accessions 559 bp exon 515 bp [gt-ag] intron 28 GenBank accessions 328 bp exon 76 bp [gt-ag] intron 14 GenBank accessions 251 bp exon 80 bp [gt-ag] intron 56 GenBank accessions 173 bp exon 48 bp [gt-ag] intron 72 GenBank accessions 599 bp exon 107 accessions, some from mixed (seen 33 times) l1 (30), l2 (13), embryo (5) l4 (5) Transpliced 5' end, 28 accessions Validated 3' end, 111 accessions 599 bp exon 109 bp exon 109 bp exon 793 bp [gt-ag] intron 34 GenBank accessions 191 bp exon 126 bp [gt-ag] intron 47 GenBank accessions 155 bp exon 45 bp [gt-ag] intron 54 GenBank accessions 315 bp exon 517 bp [gt-ag] intron 48 GenBank accessions 559 bp exon 103 bp [gt-ag] intron 4 GenBank accessions 203 bp exon 209 bp [gt-ag] intron 2 GenBank accessions 328 bp exon 76 bp [gt-ag] intron 14 GenBank accessions 251 bp exon 251 bp exon 80 bp [gt-ag] intron 56 GenBank accessions 173 bp exon 48 bp [gt-ag] intron 72 GenBank accessions 1 accession from l1 559 bp exon 97 bp exon 97 bp exon 39 bp uORF 97 bp exon 97 bp exon 95 bp [gt-ag] intron 3 GenBank accessions 559 bp exon 559 bp exon 515 bp [gt-ag] intron 28 GenBank accessions 328 bp exon 328 bp exon 70 bp [gt-ag] intron 3 GenBank accessions 257 bp exon 257 bp exon 80 bp [gt-ag] intron 56 GenBank accessions 173 bp exon 173 bp exon 48 bp [gt-ag] intron 72 GenBank accessions 564 bp exon 564 bp exon 6 accessions, some from l1 (seen 3 times) mixed (once) capped 5' end, 2 accessions 564 bp exon 243 bp exon 576 bp [gt-ag] intron 1 GenBank accession 559 bp exon 559 bp exon 103 bp [gt-ag] intron 4 GenBank accessions 203 bp exon 209 bp [gt-ag] intron 2 GenBank accessions 328 bp exon 76 bp [gt-ag] intron 14 GenBank accessions 251 bp exon 251 bp exon 80 bp [gt-ag] intron 56 GenBank accessions 173 bp exon 48 bp [gt-ag] intron 72 GenBank accessions 5 accessions, some from l2 (seen once) mixed (once) 554 bp exon 302 bp exon 302 bp exon 332 bp [gt-ag] intron 1 GenBank accession 83 bp exon 1 accession 83 bp exon 414 bp exon 414 bp exon 199 bp [gt-ag] intron 1 GenBank accession 100 bp exon 1 accession 100 bp exon 414 bp exon 414 bp exon 223 bp [gt-ag] intron 1 GenBank accession 76 bp exon 1 accession 76 bp exon 47 bp exon 47 bp exon 47 bp exon 344 bp [gt-ag] intron 1 GenBank accession 94 bp exon 94 bp exon 1 accession 94 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
a 2680 bp 719 aa 89 bp 431 bp 2kb including Promoter 4880 bp 1kb
b 2843 bp 694 aa 756 bp 2kb probably including promoter 4840 bp 1kb
c 1978 bp 505 aa 64 bp 396 bp 36 bp 2kb including Promoter 2786 bp 1kb
d 2311 bp 433 aa 258 bp 751 bp 2kb probably including promoter 3403 bp 1kb
e 514 bp 170 aa 2kb 713 bp 1kb
f 490 bp 162 aa 2kb 713 bp 1kb
g 385 bp 107 aa 62 bp 2kb probably including promoter 717 bp 1kb
h 141 bp 46 aa 2kb 485 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
hif-1 D C I R P 5V259 C sdf-9 D C I P 5V254 C R P elp-1 C 5V244 C R 5V256 C 5V272 5kb 0 pha-4, 84 accessions, 4 variants hif-1, 123 accessions 8 variants 5V259, 12 accessions sdf-9, 6 accessions 5V242, 0 accession 5V254, 3 accessions, 2 variants elp-1, 76 accessions, 9 variants 5V244, 0 accession 5V256, 40 accessions, 6 variants 5V272, 0 accession ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 20 articles in PubMed.
In addition we found 4 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h 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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