Summary
[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.
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.
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
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, .c, .d, .e.
or in GIF: .a, .b, .c, .d, .e
Please see these 3 articles in PubMed.
In addition we found 8 papers for which we do not have a PubMed identifier
GB:AJ427855_2 Submitted (11-JAN-2002) Burglin T.R., Dept. of Biosciences, Karolinska Institute, Halsovagen 7, SE-141 57 Huddinge, SWEDEN
GB:AF023470_2 Submitted (09-SEP-1997) Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, CH 4056, Switzerland
GB:AJ427855_1 Loss and gain of domains during evolution of cut superclasshomeobox genes Int. J. Dev. Biol.
GB:AF023470_1 DNA-Binding Properties of Hepatocyte Nuclear Factors-6 alpha and beta, the Prototypes of a New Cut Class of Homeodomain Proteins Unpublished
[wbg14.2p49] ceh-21 is a funny cut class homeobox gene in a cluster
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'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !
