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, 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 6 spliced variants.

AceView summary
Expression: According to AceView, this gene is expressed at high level, 2.6 times the average gene in this release, mostly from L2 larvae to adult [Kohara cDNAs]. The sequence of this gene is defined by 34 cDNA clones, some from whole animal (seen once). We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 32 distinct gt-ag introns. Transcription produces at least 6 alternatively spliced mRNAs. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by by truncation of the 5' end, truncation of the 3' end, presence or absence of 8 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).
Protein coding potential: The 6 spliced mRNAs putatively encode good proteins, altogether 7 different isoforms (4 complete, 6 COOH complete, 1 partial), some containing domains fibronectin, type III, SEFIR, protein-tyrosine phosphatase, receptor/non-receptor type [Pfam], a Golgi transport domain, a vacuolar domain [Psort2]. 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, f).
Function: There are 7 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.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12

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.

The closest human gene, according to BlastP, is the AceView gene MRPS16andDNAJC9 (e=10^-19).
The closest mouse gene, according to BlastP, is the AceView gene Mrps16 (e=2 10^-19).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G56940 (e=5 10^-11), SSR16 (e=9 10^-10)

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.
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