Caenorhabditis elegans gene dhp-1, encoding ancestor of CRMP and dihydropyrimidinase, dihydroorotase family.
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SUMMARY back to top
Summary
[Wormbase] dhp-1 encodes a homolog of the human gene DPYS, which when mutated leads to dihydropyrimidinuria (OMIM:222748).
Wormbase predicts one model, 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 7 spliced variants
.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.1 times the average gene in this release, at all stages, except in embryos (and dauers) [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 71%, L3 to adult 26%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 13 cDNA clones and 28 elements defined by RNA-seq, some from l1 (seen 6 times), l2 (once), l4 (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 16 distinct introns (15 gt-ag, 1 gc-ag). Transcription produces at least 8 different mRNAs, 7 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1. There are 2 probable alternative promotors, 4 non overlapping alternative last exons and 4 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 a cassette exon, overlapping exons with different boundaries, splicing versus retention of one intron. 89 bp of this gene are antisense to spliced gene cpg-3, raising the possibility of regulated alternate expression.
Function: There is one article specifically referring to this gene in PubMed. In addition we point below to 4 abstracts. This gene is associated to a phenotype. Proteins are expected to have molecular function (hydrolase activity) and to localize in cytoplasm.
Protein coding potential: 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (3 complete, 1 COOH complete, 2 partial), some containing Amidohydrolase 1 domain [Pfam]. The remaining 2 mRNA variants (2 spliced; 2 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This gene dhp-1 maps on chomosome I at position +1.87 (interpolated). In AceView, it covers 5.04 kb, from 7244009 to 7238975 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1H816, in Wormbase by its cosmid.number name R06C7.3, in NextDB, the Nematode expression pattern database, as CEYK9209.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes DPYS (e= 10-148), DPYSL2 (e= 10-130).
The closest mouse genes, according to BlastP, are the AceView genes Dpys, Dpysl2, Dpysl3, Dpysl4, Dpysl5
          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 dhp-1 5' 3' encoded on minus strand of chromosome I from 7,243,987 to 7,238,975 a b e c h d f g 1 2kb 0 102 bp exon 102 bp exon 533 bp [gt-ag] intron 9 GenBank accessions 181 bp exon 585 bp [gt-ag] intron 9 GenBank accessions 178 bp exon 78 bp [gt-ag] intron 8 GenBank accessions 212 bp exon 367 bp [gt-ag] intron 6 GenBank accessions 278 bp exon 447 bp [gt-ag] intron 8 GenBank accessions 66 bp exon 51 bp [gt-ag] intron 10 GenBank accessions 247 bp exon 130 bp [gt-ag] intron 13 GenBank accessions 65 bp exon 1009 bp [gt-ag] intron 12 GenBank accessions 258 bp exon 32 accessions, some from l1 (seen 5 times) l2 (once), l4 (once) Transpliced 5' end, 5 accessions Validated 3' end, 41 accessions Validated 3' end, 1 accession 258 bp exon 60 bp exon 166 bp [gt-ag] intron 1 GenBank accession 102 bp exon 102 bp exon 533 bp [gt-ag] intron 9 GenBank accessions 181 bp exon 585 bp [gt-ag] intron 9 GenBank accessions 178 bp exon 78 bp [gt-ag] intron 8 GenBank accessions 212 bp exon 367 bp [gt-ag] intron 6 GenBank accessions 278 bp exon 447 bp [gt-ag] intron 8 GenBank accessions 66 bp exon 51 bp [gt-ag] intron 10 GenBank accessions 247 bp exon 130 bp [gt-ag] intron 13 GenBank accessions 65 bp exon 177 bp [gt-ag] intron 1 GenBank accession 156 bp exon 156 bp exon 676 bp [gt-ag] intron 1 GenBank accession 3 accessions Validated 3' end, 23 accessions 242 bp exon 106 bp exon 142 bp [gt-ag] intron 1 GenBank accession 1 accession 101 bp exon 177 bp exon 177 bp exon 148 bp [gt-ag] intron 1 GenBank accession 134 bp exon 1 accession 134 bp exon 225 bp exon 225 bp exon 74 bp [gc-ag] intron 1 GenBank accession 1 accession 120 bp exon 427 bp exon 427 bp exon 427 bp exon Sequence gap 648 bp 1 accession from l1 capped 5' end, 1 accession Validated 3' end, 24 accessions 537 bp exon 174 bp exon 41 bp [gt-ag] intron 1 GenBank accession 234 bp exon 1 accession 234 bp exon 69 bp exon 69 bp exon 100 bp [gt-ag] intron 1 GenBank accession 70 bp exon 1 accession 70 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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 1587 bp 489 aa 10 bp 107 bp 2kb including Promoter 4787 bp 1kb
b 1787 bp 452 aa 70 bp 358 bp 2kb possibly including promoter 4997 bp 1kb
c 311 bp 79 aa 69 bp 2kb 459 bp 1kb
d 1509 bp 70 aa 18 bp 1278 bp 2kb including Promoter 1612 bp 1kb
e 207 bp 69 aa 2kb 349 bp 1kb
f 408 bp 59 aa 228 bp 2kb 449 bp 1kb
g 139 bp 45 aa 2kb 239 bp 1kb
h 345 bp 38 aa 228 bp 2kb 419 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
D C I R P 1H799 C 1H803 D C I R P 1H805 C R wago-1 C I P cpg-3 C I P bub-1 D C I P ztf-15 C R P C 1H806 C P 1H810 D C P dhp-1 C 1H822 D C I R P 1H824 D C P lin-61 D C I R P myo-1 5kb 0 nhr-23, 38 accessions 7 variants 1H799, 0 accession 1H803, 81 accessions, 6 variants 1H805, 14 accessions, 5 variants wago-1, 68 accessions 2 variants cpg-3, 104 accessions 3 variants bub-1, 157 accessions ztf-15, 80 accessions 3 variants 1H806, 25 accessions, 2 variants 1H810, 7 accessions, 2 variants dhp-1, 41 accessions, 8 variants 1H822, 9 accessions, 2 variants 1H824, 48 accessions, 2 variants lin-61, 96 accessions 2 variants myo-1, 191 accessions 5 variants 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 this 1 article 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 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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