Caenorhabditis elegans gene dpf-5, encoding dipeptidyl Peptidase Four (IV) family.
SUMMARY back to top
[Wormbase] dpf-5 encodes a putative acylamino-acid-releasing enzyme (AARE; EC, orthologous to human APEH, with no obvious function in mass RNAi assays.
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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.8 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 11%, L1 or L2 larvae 40%, L3 to adult 49%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 40 cDNA clones and 10 elements defined by RNA-seq, some from l1 (seen 14 times), l2 (7), mixed (7), embryo (5), l4 (4). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL1, SL2, SL3, SL4, SL7, SL8, SL5. There are 2 probable alternative promotors (see the diagram). The mRNAs appear to differ by overlapping exons with different boundaries.
Function: There is one article specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (proteolysis and peptidolysis). Proteins are expected to have molecular function (serine-type peptidase activity) and to localize in cytoplasm. These proteins appear to interact with another protein (VPS-2).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 1 COOH complete, 1 partial), some containing Peptidase S9, prolyl oligopeptidase active site region domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome IV, links to other databases and other names
Map: This gene dpf-5 maps on chomosome IV at position +1.29 (interpolated). In AceView, it covers 3.89 kb, from 4806576 to 4802691 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 4F568, in Wormbase by its cosmid.number name R11E3.8, in NextDB, the Nematode expression pattern database, as CEYK2787.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene APEH.
The closest mouse gene, according to BlastP, is the AceView gene Apeh (e= 10-108).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G14570
          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 dpf-5 5' 3' encoded on minus strand of chromosome IV from 4,806,576 to 4,802,693 a b c 1kb 0 305 bp exon 305 bp exon 588 bp [gt-ag] intron 23 GenBank accessions 316 bp exon 52 bp [gt-ag] intron 22 GenBank accessions 510 bp exon 325 bp [gt-ag] intron 8 GenBank accessions 446 bp exon 48 bp [gt-ag] intron 25 GenBank accessions 145 bp exon 465 bp [gt-ag] intron 32 GenBank accessions 404 bp exon 46 bp [gt-ag] intron 37 GenBank accessions 236 bp exon 48 accessions, some from l1 (seen 14 times) l2 (7), mixed (7), embryo (5) l4 (4) Transpliced 5' end, 16 accessions Validated 3' end, 38 accessions 236 bp exon 313 bp exon 313 bp exon 55 bp [gt-ag] intron 1 GenBank accession 505 bp exon 1 accession 505 bp exon 316 bp exon 316 bp exon 316 bp exon 38 bp [gt-ag] intron 1 GenBank accession 519 bp exon 519 bp exon 1 accession 519 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.
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
Downstream sequence
a 2362 bp 737 aa 18 bp 130 bp 2kb including Promoter 3886 bp 1kb
b 818 bp 272 aa 2kb probably including promoter 873 bp 1kb
c 835 bp 130 aa 441 bp 2kb probably including promoter 873 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
4F557 C P 4F575 D C P srw-95 C srw-94 C C R P nhr-104 D C I P eor-1 C I P dpf-7 C I P dpf-5 C 4F570 C P ubxn-6 C R 4F580 C R P 4F590 5kb 0 4F557, 12 accessions 4F575, 291 accessions 4 variants srw-95, 1 accession srw-94, 0 accession nhr-104, 89 accessions 11 variants eor-1, 113 accessions 7 variants dpf-7, 0 accession dpf-5, 50 accessions, 3 variants 4F570, 6 accessions, 2 variants ubxn-6, 59 accessions 2 variants 4F580, 33 accessions, 5 variants 4F590, 11 accessions tat-2, 73 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.
? Gene Summary Gene on genome mRNA:.a, .b, .c Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

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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