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.
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SUMMARY back to top
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)
          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 clr-1C 5' 3' encoded on plus strand of chromosome II from 5,466,338 to 5,478,498 a k i b l c d e f h j g 5kb 0 183 bp exon 183 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 104 bp exon 304 bp [gt-ag] intron 5 GenBank accessions 105 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 107 bp exon 351 bp [gt-ag] intron 4 GenBank accessions 103 bp exon 183 bp [gt-ag] intron 4 GenBank accessions 333 bp exon 652 bp [gt-ag] intron 4 GenBank accessions 100 bp exon 405 bp [gt-ag] intron 5 GenBank accessions 173 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 302 bp exon 46 bp [gt-ag] intron 5 GenBank accessions 200 bp exon 57 bp [gt-ag] intron 7 GenBank accessions 384 bp exon 234 bp [gt-ag] intron 5 GenBank accessions 747 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 96 bp exon 53 bp [gt-ag] intron 3 GenBank accessions 74 bp exon 64 bp [gt-ag] intron 6 GenBank accessions 139 bp exon 45 bp [gt-ag] intron 6 GenBank accessions 691 bp exon 48 bp [gt-ag] intron 7 GenBank accessions 302 bp exon 49 bp [gt-ag] intron 11 GenBank accessions 611 bp exon 6 accessions, some from l2 (seen 3 times) l4 (once) Validated 3' end, 62 accessions 611 bp exon 168 bp exon 168 bp exon 1 accession Transpliced 5' end, 1 accession 168 bp exon 174 bp exon 174 bp exon 50 bp [gt-ag] intron 1 GenBank accession 112 bp exon 1 accession 112 bp exon 183 bp exon 183 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 104 bp exon 304 bp [gt-ag] intron 5 GenBank accessions 105 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 107 bp exon 351 bp [gt-ag] intron 4 GenBank accessions 103 bp exon 183 bp [gt-ag] intron 4 GenBank accessions 333 bp exon 652 bp [gt-ag] intron 4 GenBank accessions 100 bp exon 405 bp [gt-ag] intron 5 GenBank accessions 173 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 302 bp exon 46 bp [gt-ag] intron 5 GenBank accessions 200 bp exon 57 bp [gt-ag] intron 7 GenBank accessions 384 bp exon 234 bp [gt-ag] intron 5 GenBank accessions 747 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 89 bp exon 60 bp [gt-ag] intron 2 GenBank accessions 74 bp exon 74 bp exon 64 bp [gt-ag] intron 6 GenBank accessions 139 bp exon 45 bp [gt-ag] intron 6 GenBank accessions 691 bp exon 48 bp [gt-ag] intron 7 GenBank accessions 302 bp exon 49 bp [gt-ag] intron 11 GenBank accessions 40 accessions, some from mixed (seen 6 times) Transpliced 5' end, 1 accession Validated 3' end, 62 accessions 622 bp exon 165 bp exon 165 bp exon 1 accession Transpliced 5' end, 1 accession 165 bp exon 181 bp exon 181 bp exon 53 bp [gt-ag] intron 3 GenBank accessions 98 bp exon 304 bp [gt-ag] intron 5 GenBank accessions 105 bp exon 47 bp [gt-ag] intron 3 GenBank accessions 107 bp exon 351 bp [gt-ag] intron 4 GenBank accessions 103 bp exon 183 bp [gt-ag] intron 4 GenBank accessions 333 bp exon 652 bp [gt-ag] intron 4 GenBank accessions 100 bp exon 405 bp [gt-ag] intron 5 GenBank accessions 173 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 302 bp exon 46 bp [gt-ag] intron 5 GenBank accessions 200 bp exon 57 bp [gt-ag] intron 7 GenBank accessions 384 bp exon 234 bp [gt-ag] intron 5 GenBank accessions 747 bp exon 47 bp [gt-ag] intron 5 GenBank accessions 89 bp exon 60 bp [gt-ag] intron 2 GenBank accessions 7 bp exon 2 accessions 7 bp exon 182 bp exon 61 bp [gt-ag] intron 11 GenBank accessions 127 bp exon 148 bp [gt-ag] intron 11 GenBank accessions 131 bp exon 230 bp [gt-ag] intron 41 GenBank accessions 434 bp exon 434 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 85 bp exon 58 bp [gt-ag] intron 3 GenBank accessions 127 bp exon 298 bp [gt-ag] intron 3 GenBank accessions 886 bp exon 52 bp [gt-ag] intron 2 GenBank accessions 176 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 112 bp exon 52 bp [gt-ag] intron 5 GenBank accessions 182 bp exon 46 bp [gt-ag] intron 5 GenBank accessions 156 bp exon 44 bp [gt-ag] intron 5 GenBank accessions 470 bp exon 18 accessions, some from l1 (seen 2 times) l2 (once), mixed (once) Transpliced 5' end, 3 accessions Validated 3' end, 6 accessions 470 bp exon 333 bp exon 333 bp exon 77 bp [gt-ag] intron 1 GenBank accession 105 bp exon 470 bp [gt-ag] intron 2 GenBank accessions 100 bp exon 405 bp [gt-ag] intron 5 GenBank accessions 173 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 302 bp exon 46 bp [gt-ag] intron 5 GenBank accessions 200 bp exon 57 bp [gt-ag] intron 7 GenBank accessions 384 bp exon 3772 bp [gt-ag] intron 1 GenBank accession 182 bp exon 182 bp exon 61 bp [gt-ag] intron 11 GenBank accessions 127 bp exon 148 bp [gt-ag] intron 11 GenBank accessions 131 bp exon 230 bp [gt-ag] intron 41 GenBank accessions 8 accessions, some from mixed (seen once) Validated 3' end, 23 accessions Validated 3' end, 98 accessions 434 bp exon 695 bp exon 695 bp exon 44 bp [gt-ag] intron 1 GenBank accession 298 bp exon 1 accession 298 bp exon 96 bp exon 96 bp exon 125 bp [gt-ag] intron 1 GenBank accession 66 bp exon 214 bp [gt-ag] intron 1 GenBank accession 168 bp exon 2 accessions 168 bp exon 100 bp exon 100 bp exon 49 bp [gt-ag] intron 1 GenBank accession 1 accession 69 bp exon 182 bp exon 182 bp exon 36 bp uORF 182 bp exon 182 bp exon 61 bp [gt-ag] intron 11 GenBank accessions 127 bp exon 127 bp exon 148 bp [gt-ag] intron 11 GenBank accessions 131 bp exon 131 bp exon 230 bp [gt-ag] intron 41 GenBank accessions 180 bp exon 180 bp exon 37 accessions, some from l2 (seen 3 times) mixed (3), embryo (once) Transpliced 5' end, 3 accessions Validated 3' end, 98 accessions 180 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 4754 bp 1409 aa 109 bp 415 bp 2kb possibly including promoter 7436 bp 1kb
b 4758 bp 942 aa 109 bp 1820 bp 2kb including Promoter 7447 bp 1kb
c 2929 bp 940 aa 107 bp 2kb possibly including promoter 5418 bp 1kb
d 3068 bp 718 aa 597 bp 314 bp 33 bp 2kb including Promoter 4153 bp 1kb
e 2471 bp 536 aa 858 bp 2kb 7787 bp 1kb
f 993 bp 248 aa 245 bp 2kb 1037 bp 1kb
g 620 bp 147 aa 35 bp 141 bp 33 bp 2kb including Promoter 1059 bp 1kb
h 330 bp 109 aa 2kb 669 bp 1kb
i 286 bp 67 aa 80 bp 2kb 336 bp 1kb
j 169 bp 32 aa 69 bp 2kb 218 bp 1kb
k 168 bp 24 aa 15 bp 78 bp 2kb including Promoter 168 bp 1kb
l 165 bp 24 aa 12 bp 78 bp 2kb including Promoter 165 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
C dhs-5 C daz-1 D C I P clr-1C D C I R P 2F769 C P 2F779 C 2F781 C R P 2F783 C 2F741 C 2F770 D P 2F782 5kb 0 cex-1, 9 accessions dhs-5, 17 accessions, 4 variants daz-1, 46 accessions, 3 variants clr-1C, 118 accessions 12 variants 2F769, 39 accessions, 3 variants 2F779, 10 accessions 2F781, 11 accessions, 2 variants 2F783, 5 accessions, 2 variants 2F741, 1 accession 2F769b, 0 accession 2F770, 13 accessions, 3 variants 2F782, 2 accessions 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 these 9 articles in PubMed.
In addition we found 41 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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