Caenorhabditis elegans essential gene cbp-1, encoding CBP/p300 homolog.
SUMMARY back to top
[Wormbase] cbp-1 encodes a homolog of the mammalian transcriptional cofactors CBP (OMIM:600140) and p300 (E1A-BINDING PROTEIN, 300-KD; OMIM:602700) that have been shown to possess histone acetyltransferase activity, and which, when mutated, lead to Rubinstein-Taybi syndrome (OMIM:180849) and colorectal cancer (OMIM:114500); at least one splicing form of CBP-1 exhibits histone acetyltransferase (HAT) activity in vitro and has a glutamine/asparagine-rich domain; CBP-1 is required during embryogenesis for differentiation of all non-neuronal somatic cell types; CBP-1 is expressed very early in embryogenesis, suggesting that it may interact with maternally provided transcription factors, such as SKN-1, to specific developmental fates.
Wormbase predicts 3 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 5 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 4.5 times the average gene in this release, 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 18%, L1 or L2 larvae 25%, L3 to adult (including dauer) 57%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 33 cDNA clones and 26 elements defined by RNA-seq, some from embryo (seen 7 times), mixed (7), l2 (6), l1 (3), l4 (2), dauer (once). We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 15 distinct gt-ag introns. Transcription produces at least 6 different mRNAs, 5 alternatively spliced variants and 1 unspliced form. cbp-1.a is transpliced to SL1. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 10 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 2 cassette exons, overlapping exons with different boundaries.
Function: There are 11 articles specifically referring to this gene in PubMed. In addition we point below to 15 abstracts. This essential gene is associated to a phenotype (cell determination and differentiation, Defect in cell division, Embryonic Lethal (zygotic), Sterile adult, unhealthy). Functionally, the gene has been proposed to participate in processes (regulation of transcription, regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (histone acetyltransferase activity, protein binding activity, transcription co-activator activity, transcription cofactor activity, zinc ion binding activity) and to localize in nucleus. These proteins appear to interact with other proteins (GEI-21, HIF-1). The gene interacts with 5 other genes (HDA-1, LET-60, LIN-1, PRY-1, SUR-6).
Protein coding potential: The 5 spliced and the unspliced mRNAs putatively encode good proteins, altogether 6 different isoforms (2 complete, 2 COOH complete, 2 partial), some containing domains Bromodomain, Protein of unknown function DUF902, CREBbp, Transcriptional coactivation, Coactivator CBP, KIX, Zinc finger, TAZ-type, Zinc finger, ZZ-type [Pfam], a coiled coil stretch [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This essential gene cbp-1 maps on chomosome III at position +0.83 (interpolated). In AceView, it covers 8.31 kb, from 9766415 to 9774724 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3K863, in Wormbase by its cosmid.number name R10E11.1, in NextDB, the Nematode expression pattern database, as CEYK1421.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes EP300 (e=0.0), CREBBP (e=0.0).
The closest mouse genes, according to BlastP, are the AceView genes Ep300 (e=0.0), Crebbp (e=0.0).
The closest A.thaliana genes, according to BlastP, are the AceView genes HAC1 (e=4 10-63), ATHPCAT4\/HAC5 (e=2 10-62), HAC12 (e=2 10-62)
          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 cbp-1 5' 3' encoded on plus strand of chromosome III from 9,766,415 to 9,774,724 a c b d e f 1 2kb 0 222 bp exon 222 bp exon 53 bp [gt-ag] intron 2 GenBank accessions 77 bp exon 52 bp [gt-ag] intron 2 GenBank accessions 789 bp exon 294 bp [gt-ag] intron 2 GenBank accessions 366 bp exon 52 bp [gt-ag] intron 3 GenBank accessions 127 bp exon 165 bp [gt-ag] intron 4 GenBank accessions 117 bp exon 51 bp [gt-ag] intron 4 GenBank accessions 513 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 3213 bp exon 51 bp [gt-ag] intron 6 GenBank accessions 208 bp exon 50 bp [gt-ag] intron 7 GenBank accessions 193 bp exon 172 bp [gt-ag] intron 5 GenBank accessions 303 bp exon 228 bp [gt-ag] intron 7 GenBank accessions 962 bp exon 41 accessions, some from l2 (seen 5 times) embryo (3), l1 (2), l4 (2) mixed (2) Transpliced 5' end, 3 accessions Validated 3' end, 12 accessions Validated 3' end, 9 accessions Validated 3' end, 3 accessions 962 bp exon 366 bp exon 43 bp [gt-ag] intron 1 GenBank accession 136 bp exon 165 bp [gt-ag] intron 4 GenBank accessions 117 bp exon 3 accessions 117 bp exon 925 bp exon 51 bp [gt-ag] intron 6 GenBank accessions 208 bp exon 50 bp [gt-ag] intron 7 GenBank accessions 193 bp exon 259 bp [gt-ag] intron 3 GenBank accessions 216 bp exon 228 bp [gt-ag] intron 7 GenBank accessions 964 bp exon 10 accessions, some from embryo (seen 4 times) mixed (4), l1 (once) l2 (once) Validated 3' end, 8 accessions Validated 3' end, 6 accessions Validated 3' end, 2 accessions Validated 3' end, 22 accessions 964 bp exon 457 bp exon 1 accession from dauer 457 bp exon 127 bp exon 127 bp exon 132 bp [gt-ag] intron 2 GenBank accessions 150 bp exon 51 bp [gt-ag] intron 4 GenBank accessions 513 bp exon 513 bp exon 50 bp [gt-ag] intron 4 GenBank accessions 3 accessions, some from mixed (seen once) Validated 3' end, 1 accession 2077 bp exon 193 bp exon 193 bp exon 703 bp [gt-ag] intron 1 GenBank accession 416 bp exon 1 accession Validated 3' end, 8 accessions 416 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 7090 bp 2006 aa 182 bp 887 bp 2kb including Promoter 8308 bp 1kb
b 2506 bp 538 aa 889 bp 2kb 3094 bp 1kb
c 619 bp 206 aa 2kb 827 bp 1kb
d 457 bp 152 aa 2kb 457 bp 1kb
e 2867 bp 72 aa 119 bp 2529 bp 2kb possibly including promoter 3100 bp 1kb
f 609 bp 88 aa 341 bp 2kb 1312 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
cdk-1 D C I P 3K841 C R rmd-1 D C R P cbp-1 D C I R P usp-46 D C R P vha-1 D C R P vha-2C D C R P 3K880 C R 3K840 D C I R P ech-6 D C P 3K844 C R 3K848 D C R P sqv-3 C R 3K874 5kb 0 cdk-1, 53 accessions, 2 variants 3K841, 18 accessions, 2 variants rmd-1, 251 accessions 3 variants cbp-1, 59 accessions, 6 variants usp-46, 22 accessions 4 variants vha-1, 0 accession vha-2C, 198 accessions 14 variants mcm-6, 133 accessions 2 variants 3K839, 0 accession 3K880, 7 accessions, 2 variants iff-1, 213 accessions 5 variants 3K840, 161 accessions 3 variants ech-6, 120 accessions 4 variants 3K844, 25 accessions, 2 variants 3K848, 31 accessions, 4 variants sqv-3, 12 accessions 3K874, 14 accessions, 2 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 11 articles in PubMed.
In addition we found 15 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f 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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