Caenorhabditis elegans gene dpf-4, encoding dipeptidyl Peptidase Four (IV) family.
SUMMARY back to top
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 5 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 6.3 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 16%, L1 or L2 larvae 36%, L3 to adult 49%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 23 cDNA clones and 60 elements defined by RNA-seq, some from l2 (seen 6 times), embryo (4), l1 (3), mixed (3), l4 (2). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 6 distinct introns (5 gt-ag, 1 gc-ag). Transcription produces at least 5 alternatively spliced mRNAs. Variant a is transpliced to SL2, SL6, SL7, SL3, c to SL3, SL4, SL2. There are 8 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of a cassette exon, overlapping exons with different boundaries, splicing versus retention of 2 introns. 726 bp of this gene are antisense to spliced gene 3G952, raising the possibility of regulated alternate expression.
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 b).
Function:. 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.
Protein coding potential: The 5 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 III, links to other databases and other names
Map: This gene dpf-4 maps on chomosome III at position -1.53 (interpolated). In AceView, it covers 2.86 kb, from 5859181 to 5862039 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3G951, in Wormbase by its cosmid.number name F01F1.5, in NextDB, the Nematode expression pattern database, as CEYK4399.
          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-4 5' 3' encoded on plus strand of chromosome III from 5,859,181 to 5,861,860 a b c e d 1kb 0 38 bp exon 267 bp [gc-ag] intron 11 GenBank accessions 378 bp exon 378 bp exon 57 bp [gt-ag] intron 18 GenBank accessions 499 bp exon 137 bp [gt-ag] intron 2 GenBank accessions 617 bp exon 54 bp [gt-ag] intron 19 GenBank accessions 547 bp exon 17 accessions, some from embryo (seen 4 times) l2 (3), l1 (2), l4 (2) mixed (once) Transpliced 5' end, 6 accessions Validated 3' end, 192 accessions Validated 3' end, 33 accessions 547 bp exon 762 bp exon 762 bp exon 24 bp uORF 762 bp exon 762 bp exon 57 bp [gt-ag] intron 18 GenBank accessions 499 bp exon 499 bp exon 137 bp [gt-ag] intron 2 GenBank accessions 617 bp exon 617 bp exon 54 bp [gt-ag] intron 19 GenBank accessions 733 bp exon 733 bp exon 9 accessions, some from l1 (seen once) l2 (once), mixed (once) Validated 3' end, 193 accessions Validated 3' end, 28 accessions 733 bp exon 378 bp exon 378 bp exon 57 bp [gt-ag] intron 18 GenBank accessions 499 bp exon 137 bp [gt-ag] intron 2 GenBank accessions 617 bp exon 54 bp [gt-ag] intron 19 GenBank accessions 548 bp exon 3 accessions, some from l2 (seen 2 times) Transpliced 5' end, 3 accessions Validated 3' end, 193 accessions 548 bp exon 94 bp exon 94 bp exon 209 bp [gt-ag] intron 1 GenBank accession 375 bp exon 1 accession 375 bp exon 253 bp exon 1167 bp [gt-ag] intron 1 GenBank accession 619 bp exon 53 accessions, some from mixed (seen once) Validated 3' end, 239 accessions Validated 3' end, 35 accessions 619 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 uORF Upstream sequence Transcription
Downstream sequence
a 2079 bp 643 aa 57 bp 90 bp 2kb including Promoter 2594 bp 1kb
b 2611 bp 643 aa 403 bp 276 bp 21 bp 2kb possibly including promoter 2859 bp 1kb
c 2042 bp 643 aa 19 bp 91 bp 2kb including Promoter 2290 bp 1kb
d 872 bp 127 aa 488 bp 2kb 2039 bp 1kb
e 469 bp 127 aa 86 bp 2kb probably including promoter 678 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
alh-9 C I R P dpf-4 C R rabn-5 C I P 3G971 C I R P 3G963 C 3G965 R 3G969 C R 3G973 D C P ddx-23 D C R P cct-6 C I R P 3G952 C R P eng-1 C 3G958 D C P 3G960 C 3G966 D C I R P aldo-2 C R 3G972 5kb 0 alh-9, 56 accessions, 3 variants dpf-4, 83 accessions, 5 variants rabn-5, 25 accessions 3G971, 180 accessions 12 variants 3G963, 0 accession 3G965, 0 accession 3G969, 0 accession 3G973, 9 accessions, 3 variants 3G923, 0 accession 3G920, 0 accession ddx-23, 38 accessions cct-6, 203 accessions 6 variants 3G952, 95 accessions, 4 variants eng-1, 47 accessions, 3 variants 3G958, 0 accession 3G960, 159 accessions 7 variants 3G966, 267 accessions 7 variants aldo-2, 1 accession 3G972, 4 accessions ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams 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 !