Caenorhabditis elegans complex locus dhs-6C, encoding DeHydrogenase, Short chain.
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SUMMARY back to top
Summary
[Wormbase] The dhs-6 locus is predicted to encode four transcripts derived from alternative splicing and alternative transcriptional initiation sites; the longest transcript is predicted to encode a member of the eukaryotic translation initiation factor family within its amino-terminal end, and is a member of both the SCP-2 sterol transfer family and short-chain dehydrogenase-reductase families within its carboxyl-terminal end; DHS-6 is predicted to be mitochondrial.
Wormbase predicts 3 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 5 spliced variants
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 5.3 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 3%, L1 or L2 larvae 45%, L3 to adult (including dauer) 53%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 46 cDNA clones and 24 elements defined by RNA-seq, some from l2 (seen 18 times), l1 (6), l4 (6), mixed (6), embryo (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 15 distinct gt-ag introns. Transcription produces at least 5 alternatively spliced mRNAs. Variant a is transpliced to SL1, b to SL1, SL2, SL3, c to SL1, SL2, SL3, SL4, SL6. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 9 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries.
Function: There are 4 articles specifically referring to this gene in PubMed. In addition we point below to one abstract. This gene is associated to a phenotype (abundant spermatogenesis enriched protein copurified with chromatin). Functionally, the gene has been proposed to participate in a process (metabolism). Proteins are expected to have molecular functions (oxidoreductase activity, sterol carrier activity). These proteins appear to interact with another protein (EIF-3.K).
Conspicuous RNA editing was observed in this gene by inspection of the cDNA sequencing traces.
Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (3 complete, 1 COOH complete, 1 partial), some containing domains short-chain dehydrogenase/reductase SDR, RNA polymerase I-associated factor PAF67, Sterol-binding [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome II, links to other databases and other names
Map: This gene dhs-6C maps on chomosome II at position -1.07 (interpolated). In AceView, it covers 5.36 kb, from 5622455 to 5617101 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known dhs-6, in Wormgenes/AceView by its positional name 2F906, in Wormbase by its cosmid.number name C17G10.8, C17G10.9, in NextDB, the Nematode expression pattern database, as CEYK3500.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes EIF3S6IP, HSDL2.
The closest mouse genes, according to BlastP, are the AceView genes Eif3eip (e=2 10-18), Eif3s6ip (e=3 10-19).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G25757, AT5G25754, AT1G63380, AT1G62610, AT5G18210, AT2G17845, AT3G55290, AT3G55310, AT3G04000
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 1889 bp 537 aa 273 bp 2kb including Promoter 2834 bp 1kb
b 2264 bp 535 aa 654 bp 2kb including Promoter 3215 bp 1kb
c 1447 bp 418 aa 39 bp 151 bp 2kb including Promoter 2191 bp 1kb
d 3129 bp 992 aa 150 bp 2kb 3640 bp 1kb
e 688 bp 228 aa 2kb 819 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
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 4 articles in PubMed.
In addition we found 1 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e 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'.

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