Caenorhabditis elegans gene ceh-21, encoding C.Elegans Homeobox, onecut bifunctional homeodomain protein, cut class.
SUMMARY back to top
[Wormbase] ceh-21 encodes a a ONECUT class CUT homeobox protein with a single N-terminal cut domain and an OCAM domain; the cut domain may be a compact DNA-binding domain composed of alpha helices; the OCAM domain is a nematode-specific motif conserved between CEH-21, CEH-41, and T02B5.2; ceh-21 is one of three nematode-specific ONECUT genes in a cluster with ceh-39 and ceh-41; CEH-21 may be required for muscle formation and differentiation, and is expressed in muscle precursor cells and differentiated gut cells; ceh-21 has no obvious function in mass RNAi assays.
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 high level, 2.1 times the average gene in this release, mostly in embryos, and some 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 54%, L1 or L2 larvae 22%, L3 to adult 25%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 18 cDNA clones and 10 elements defined by RNA-seq, some from embryo (seen 10 times), l1 (4), mixed (2).
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces at least 5 alternatively spliced mRNAs. Variant b is transpliced to SL2, SL3, SL4. There are 2 non overlapping alternative last exons and 4 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 one intron.
Note that mRNA .e was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 3 articles specifically referring to this gene in PubMed. In addition we point below to 8 abstracts. Functionally, the gene has been proposed to participate in a process (regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (DNA binding activity, transcription factor activity) and to localize in nucleus.
Protein coding potential: The 5 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (1 complete, 3 COOH complete), some containing domains Homeodomain protein CUT, homeobox [Pfam], a second peroximal domain [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome X, links to other databases and other names
Map: This gene ceh-21 maps on chomosome X at position -16.65 (interpolated). In AceView, it covers 3.97 kb, from 1852738 to 1848772 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name XC468, in Wormbase by its cosmid.number name T26C11.6, in NextDB, the Nematode expression pattern database, as CEYK4791.
          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 ceh-21 5' 3' encoded on minus strand of chromosome X from 1,852,738 to 1,848,772 a b c d e 1 2kb 0 67 bp exon 67 bp exon 131 bp [gt-ag] intron 14 GenBank accessions 412 bp exon 115 bp [gt-ag] intron 13 GenBank accessions 97 bp exon 196 bp [gt-ag] intron 11 GenBank accessions 163 bp exon 49 bp [gt-ag] intron 6 GenBank accessions 437 bp exon 707 bp [gt-ag] intron 10 GenBank accessions 733 bp exon 2 accessions, some from embryo (seen once) 733 bp exon 60 bp exon 131 bp [gt-ag] intron 14 GenBank accessions 412 bp exon 115 bp [gt-ag] intron 13 GenBank accessions 97 bp exon 196 bp [gt-ag] intron 11 GenBank accessions 163 bp exon 49 bp [gt-ag] intron 6 GenBank accessions 437 bp exon 707 bp [gt-ag] intron 10 GenBank accessions 738 bp exon 21 accessions, some from embryo (seen 8 times) l1 (4), mixed (once) Transpliced 5' end, 5 accessions Validated 3' end, 1 accession Validated 3' end, 452 accessions 738 bp exon 412 bp exon 115 bp [gt-ag] intron 13 GenBank accessions 97 bp exon 196 bp [gt-ag] intron 11 GenBank accessions 163 bp exon 49 bp [gt-ag] intron 6 GenBank accessions 437 bp exon 707 bp [gt-ag] intron 10 GenBank accessions 1125 bp exon 1125 bp exon 174 bp [gt-ag] intron 3 GenBank accessions 1 accession from mixed 267 bp exon 55 bp exon 55 bp exon 49 bp [gt-ag] intron 6 GenBank accessions 437 bp exon 707 bp [gt-ag] intron 10 GenBank accessions 315 bp exon 984 bp [gt-ag] intron 1 GenBank accession 294 bp exon 2 accessions, some from embryo (seen once) Validated 3' end, 1 accession 294 bp exon 310 bp exon 310 bp exon 325 bp [gt-ag] intron 1 GenBank accession 485 bp exon 485 bp exon 174 bp [gt-ag] intron 3 GenBank accessions 2 accessions 285 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 Upstream sequence Transcription
Downstream sequence
a 1909 bp 495 aa 7 bp 414 bp 2kb probably including promoter 3107 bp 1kb
b 1907 bp 495 aa 419 bp 2kb including Promoter 3105 bp 1kb
c 2501 bp 475 aa 1073 bp 2kb 3742 bp 1kb
d 1101 bp 274 aa 275 bp 2kb 2841 bp 1kb
e 1080 bp 106 aa 757 bp 2kb 1579 bp 1kb

Gene neighbors and Navigator on chromosome X back to top
I P tbx-41 C XC449 XC479 XC491 XC450 C XC440 C R XC460 C I P ceh-41 C R P ceh-21 C R P ceh-39 5kb 0 XC439, 1 accession tbx-41, 1 accession XC443, 0 accession XC449, 0 accession XC479, 0 accession XC481, 2 accessions XC491, 3 accessions XC444, 5 accessions XC450, 5 accessions XC472, 0 accession XC440, 2 accessions XC460, 52 accessions, 5 variants ceh-41, 6 accessions ceh-21, 28 accessions 5 variants ceh-39, 42 accessions 5 variants 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 3 articles in PubMed.
In addition we found 8 papers for which we do not have a PubMed identifier
? 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'.

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