Caenorhabditis elegans essential gene cpr-3, encoding cysteine PRotease cathepsin B-like.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY
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Wormbase predicts one model, but Caenorhabditis elegans cDNA sequences in GenBank, 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 2 spliced variants.
AceView summary
Expression: According to AceView, this gene is
well expressed, 0.7 times the average gene in this release, from L2 larvae to adult [Kohara cDNAs], but not in dauers [SAGE, Jones et al, 2001]. The
sequence of this gene is defined by
9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains
3 distinct gt-ag introns. Transcription produces
2 alternatively spliced mRNAs. There are 3 validated
alternative polyadenylation sites (see the
diagram). The mRNAs appear to differ by splicing versus retention of one intron.
Protein coding potential: The 2 spliced mRNAs putatively encode
good proteins, altogether
2 different isoforms (2 complete, 1 COOH complete), some containing peptidase C1A, papain C-terminal
domain [Pfam]; 1 of the 2 complete proteins appears to be
secreted.
Isoform cpr-3.b1 is annotated using as Met a
Kozak-compatible a..ACG. start, thereby gaining 121 amino acids N-terminal to the first AUG.
Function: There are
2 articles specifically referring to this gene in PubMed. In addition we point
below to 2 abstracts. This essential gene is associated to a
phenotype (Embryonic Lethal, Up-regulated upon pathogen infection). Functionally, the gene has been proposed to participate in a
process (proteolysis and peptidolysis). Proteins are expected to have molecular
function (cysteine-type peptidase activity) and to
localize in various compartments (cytoplasm, extracellular space).
Please quote:
AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome CHROMOSOME_V, links to other databases and other names
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Map: This essential gene cpr-3 maps on chomosome V at position +7.30 (interpolated). In AceView, it covers
1.83 kb, from 15298652 to 15296822 (WS190), on the reverse strand.
Links to: WormBase,
NextDB,
RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5P778, in Wormbase by its cosmid.number name T10H4.12, in NextDB, the Nematode expression pattern database, as CEYK5601.
Closest AceView homologs in other species
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The closest human gene, according to BlastP, is the AceView gene
CTSB (e=5 10^-69).
The closest mouse gene, according to BlastP, is the AceView gene
Ctsb (e=10^-66).
The closest A.thaliana genes, according to BlastP, are the AceView genes
AT4G01610 (e=5 10^-48),
AT1G02300 (e=8 10^-46),
AT1G02305 (e=10^-44)
Complete gene on genome diagram: (in true scale, with colored introns)
This diagram was in previous releases displayed by default on the right of the screen. It shows in true scale the gene on the genome, the mRNAs and the cDNA clones. Opening may be slow for large genes. Please choose between the
zoomable GIF version., and the
Flash version
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Details on tissue of origin for each intron and exon is available from the
intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
More legend
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron.
]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron).
] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries.
]-[ Pink and
] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal,
blue flags to any single letter variant of the main . More explanations are given in the
gene help file
What is known about the gene and its neighbors on chromosome CHROMOSOME_V
ZOOM OUT
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
ZOOM IN
D:disease,
C:conserved,
I:interactions,
R:regulation,
P:publications (see the
Legend)
Annotated mRNA diagrams
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash:
.a, .b.
or in GIF:
.a, .b
Please see these
5 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
- GB:L39890_3 Submitted (28-FEB-1995) Iain L. Johnstone, Wellcome Unit of Molecular Parasitology, University of Glasgow, Anderson College, Glasgow, UK
- [wm95p328] ISOLATION AND CHARACTERISATION OF FOUR DEVELOPMENTALLY REGULATED CATHEPSIN B-LIKE CYSTEINE PROTEINASE GENES FROM C.ELEGANS.
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function and 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 and 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 all variants, their summarized annotations, 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. Merci !