Caenorhabditis elegans essential complex locus clr-1C, encoding encoding in order receptor tyrosine-phosphatase isoforms, negative regulator of the Fibroblast growth factor receptor EGL-15; probable mitochondrial 28S ribosomal protein S16 and a nematode specific putative membrane protein, CLeaR, translucent appearance clr-1.TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS SUMMARY
[Wormbase] A receptor tyrosine phosphatase that negatively regulates the FGF receptorsignaling pathway; it localizes to the plasma membrane.
Wormbase predicts 5 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 10 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is expressed at very high level, 9.0 times the average gene in this release, mostly from L2 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 26%, L3 to adult 71%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 35 cDNA clones and 83 elements defined by RNA-seq, some from mixed (seen 11 times), l2 (7), l1 (2), embryo (once), l4 (once). We annotate structural defects or features in 4 cDNA clones. Alternative mRNA variants and regulation: The gene contains 38 distinct gt-ag introns. Transcription produces at least 12 different mRNAs, 10 alternatively spliced variants and 2 unspliced forms. clr-1C.b is transpliced to SL1clr-1C.d to SL1, SL1'clr-1C.g to SL1clr-1C.k to SL2clr-1C.l to SL5. There are 2 probable alternative promotors, 6 non overlapping alternative last exons and 5 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 10 cassette exons, overlapping exons with different boundaries.
Note that mRNA .b was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
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 d). Function: There are 9 articles specifically referring to this gene in PubMed. In addition we point below to 41 abstracts. This essential gene is associated to a phenotype (abnormal sex myoblast MIGration, CLeaR, translucent appearance, EGg Laying defective, embryonic lethal, partial, SLow growth, uncoordinated locomotion, sluggish). Functionally, the gene has been proposed to participate in a process (protein amino acid dephosphorylation). Proteins are expected to have molecular function (protein tyrosine phosphatase activity) and to localize in membrane. The gene interacts with 17 other genes (EGL-15, EGL-17, LET-756, MEK-2, MPK-1, PTP-3, SAX-3, SEM-5, SLT-1, SOC-1, SOC-2, SOS-1, UNC-5, UNC-34, UNC-40, VAB-1, VAB-8). Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (4 complete, 3 COOH complete, 2 partial), some containing domains fibronectin, type III, SEFIR, protein-tyrosine phosphatase, receptor/non-receptor type [Pfam], a Golgi transport domain, a vacuolar domain [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 1 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 II, links to other databases and other names Map: This essential gene clr-1C maps on chomosome II at position -1.30 (interpolated). In AceView, it covers 12.16 kb, from 5466338 to 5478498 (WS190), on the direct strand. Links to:WormBase, NextDB, RNAiDB.
as Other names: The gene is also known clr-1, in Wormgenes/AceView by its positional name 2F767, in Wormbase by its cosmid.number name F56D1.2, F56D1.3, F56D1.4, in NextDB, the Nematode expression pattern database, as CEYK71. Closest AceView homologs in other species ? The closest human genes, according to BlastP, are the AceView genes PTPRE (e=5 10-31), VPS16andPTPRA (e=9 10-31), PTPRG (e=2 10-27), PTPRF (e=8 10-27), PTPRD (e=10-26). The closest mouse genes, according to BlastP, are the AceView genes Ptpra (e=3 10-31), Ptpre (e=6 10-31), Ptprg (e=3 10-27), Ptprf (e=3 10-27). The closest A.thaliana gene, according to BlastP, is the AceView gene PTP1 (e=7 10-11)
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. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
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. Proteins supported by a single continuous cDNA sequence 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.
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
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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