Mus musculus complex locus Ctnnb1, encoding catenin (cadherin associated protein), beta 1.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Mus musculus 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at very high level, 4.7 times the average gene in this release. The sequence of this gene is defined by 1123 GenBank accessions, some from brain (seen 56 times), whole brain (55), eye (38), whole eye (37), mammary (32), embryo (23), neural retina (17) and 84 other tissues. We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 19 distinct introns (18 gt-ag, 1 gc-ag). Transcription produces 11 different mRNAs, 8 alternatively spliced variants and 3 unspliced forms. There are 5 probable alternative promotors, 3 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, splicing versus retention of one intron. 1179 bp of this gene are antisense to spliced gene Ulk4, raising the possibility of regulated alternate expression.
Function: There are 458 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (behavior/neurological phenotype; cardiovascular system phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; embryogenesis phenotype; endocrine/exocrine gland phenotype; growth/size phenotype; hearing/vestibular/ear phenotype and 15 others), proposed to participate in pathways (Adherens junction, Basal cell carcinoma, Colorectal cancer, Endometrial cancer, Focal adhesion, Leukocyte transendothelial migration, Melanogenesis, Prostate cancer, Thyroid cancer, Tight junction, Wnt signaling pathway) and processes (bone resorption, camera-type eye morphogenesis, cell differentiation, cell fate determination, cell fate specification, cell maturation, cell-cell adhesion, cellular morphogenesis during differentiation, cellular process, dorsal/ventral axis specification, dorsal/ventral pattern formation, ectoderm development, embryonic arm morphogenesis, embryonic digit morphogenesis, embryonic hindlimb morphogenesis, endoderm formation, endodermal cell fate commitment, forebrain development, gastrulation (sensu Mammalia), heart development, hemopoiesis, lung development, morphogenesis of embryonic epithelium, negative regulation of cell differentiation, negative regulation of osteoclast differentiation, negative regulation of transcription from RNA polymerase II promoter, negative regulation of transcription, DNA-dependent, odontogenesis (sensu Vertebrata), pancreas development, patterning of blood vessels, positive regulation of epithelial cell differentiation, positive regulation of osteoblast differentiation, positive regulation of transcription, positive regulation of transcription from RNA polymerase II promoter, positive regulation of transcription, DNA-dependent and 12 others). Proteins are expected to have molecular functions (alpha-catenin binding, cadherin binding, chromatin binding, DNA binding, double-stranded DNA binding, protein binding, transcription activator activity, transcription coactivator activity, transcription factor activity, transcription factor binding, structural molecule activity) and to localize in various compartments (adherens junction, apical junction complex, apical part of cell, basolateral plasma membrane and 15 others).
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_88276 for in depth functional annotation of this gene.
Protein coding potential: 7 spliced and 2 unspliced mRNAs putatively encode good proteins, altogether 8 different isoforms (4 complete, 1 COOH complete, 3 partial), some containing domains Armadillo, HEAT [Pfam], a coiled coil stretch [Psort2]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 2 partial) appear not to encode good proteins.
Isoform Ctnnb1.kSep07-unspliced is annotated using as Met a Kozak-compatible a..ACGg start, thereby gaining 69 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 9, links to other databases and other names
Map: This gene Ctnnb1 maps on chromosome 9, at 9 F4|9 72.0 cM according to Entrez Gene. In AceView, it covers 31.29 kb, from 120838334 to 120869626 (NCBI 37a, Aug 2007), on the direct strand.
Links to: manual annotations from MGI_88276, KEGG_04310, KEGG_04510, KEGG_04520, KEGG_04530, KEGG_04670, KEGG_04916, KEGG_05210, KEGG_05213, KEGG_05215, KEGG_05216, KEGG_05217, the SNP view, gene overviews from Gene 12387, expression data from Gene 12387, molecular and other annotations from UCSC.
Other names: The gene is also known as Ctnnb1, Mesc or Catnb, LOC12387.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene CTNNB1 (e=4 10-61).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene hmp-2 (e=2 10-73), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G42340 (e=5 10-04), AT5G67340 (e=0.003), AT3G54850 (e=0.004), AT2G23140 (e=0.010), which may contain interesting functional annotation
          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 Ctnnb1 5' 3' encoded on plus strand of chromosome 9 from 120,838,334 to 120,869,626 a [NM] b c d j e g f k-u h-u i-u 1 2kb 0 219 bp exon 16534 bp [gt-ag] intron 38 GenBank accessions 61 bp exon 61 bp exon 288 bp [gt-ag] intron 51 GenBank accessions 228 bp exon 144 bp [gt-ag] intron 86 GenBank accessions 254 bp exon 119 bp [gt-ag] intron 102 GenBank accessions 239 bp exon 80 bp [gt-ag] intron 91 GenBank accessions 202 bp exon 1071 bp [gt-ag] intron 86 GenBank accessions 145 bp exon 2144 bp [gt-ag] intron 91 GenBank accessions 104 bp exon 77 bp [gt-ag] intron 79 GenBank accessions 339 bp exon 146 bp [gt-ag] intron 127 GenBank accessions 159 bp exon 1134 bp [gt-ag] intron 137 GenBank accessions 120 bp exon 290 bp [gt-ag] intron 146 GenBank accessions 151 bp exon 91 bp [gt-ag] intron 148 GenBank accessions 122 bp exon 711 bp [gt-ag] intron 144 GenBank accessions 61 bp exon 656 bp [gt-ag] intron 145 GenBank accessions 1199 bp exon 45 accessions, NM_007614 some from brain (seen 6 times) whole brain (6), embryo (3) mammary (3), tumor, biopsy sample (3) Validated 3' end, 15 accessions 1199 bp exon 49 bp exon 16556 bp [gt-ag] fuzzy intron 1 GenBank accession 61 bp exon 61 bp exon 288 bp [gt-ag] intron 51 GenBank accessions 228 bp exon 144 bp [gt-ag] intron 86 GenBank accessions 254 bp exon 119 bp [gt-ag] intron 102 GenBank accessions 239 bp exon 80 bp [gt-ag] intron 91 GenBank accessions 202 bp exon 1071 bp [gt-ag] intron 86 GenBank accessions 145 bp exon 2144 bp [gt-ag] intron 91 GenBank accessions 104 bp exon 77 bp [gt-ag] intron 79 GenBank accessions 339 bp exon 146 bp [gt-ag] intron 127 GenBank accessions 159 bp exon 1134 bp [gt-ag] intron 137 GenBank accessions 120 bp exon 290 bp [gt-ag] intron 146 GenBank accessions 151 bp exon 91 bp [gt-ag] intron 148 GenBank accessions 122 bp exon 711 bp [gt-ag] intron 144 GenBank accessions 61 bp exon 656 bp [gt-ag] intron 145 GenBank accessions 1199 bp exon 301 accessions, some from brain (seen 34 times) whole brain (33), eye (30) whole eye (30), mammary (22) Validated 3' end, 45 accessions 1199 bp exon 239 bp exon 16534 bp [gt-ag] intron 38 GenBank accessions 61 bp exon 61 bp exon 288 bp [gt-ag] intron 51 GenBank accessions 228 bp exon 144 bp [gt-ag] intron 86 GenBank accessions 254 bp exon 119 bp [gt-ag] intron 102 GenBank accessions 239 bp exon 80 bp [gt-ag] intron 91 GenBank accessions 202 bp exon 1071 bp [gt-ag] intron 86 GenBank accessions 145 bp exon 2144 bp [gt-ag] intron 91 GenBank accessions 104 bp exon 77 bp [gt-ag] intron 79 GenBank accessions 339 bp exon 146 bp [gt-ag] intron 127 GenBank accessions 635 bp exon 61 accessions, some from neural retina (seen 9 times) brain (6), whole brain (6) upper head (4), thymus (3) 635 bp exon 146 bp exon 16211 bp [gt-ag] intron 4 GenBank accessions 61 bp exon 288 bp [gt-ag] intron 51 GenBank accessions 228 bp exon 144 bp [gt-ag] intron 86 GenBank accessions 254 bp exon 119 bp [gt-ag] intron 102 GenBank accessions 203 bp exon 208 bp [gt-ag] fuzzy intron 1 GenBank accession 110 bp exon 110 bp exon 1071 bp [gt-ag] intron 86 GenBank accessions 145 bp exon 2144 bp [gt-ag] intron 91 GenBank accessions 104 bp exon 77 bp [gt-ag] intron 79 GenBank accessions 339 bp exon 146 bp [gt-ag] intron 127 GenBank accessions 159 bp exon 1134 bp [gt-ag] intron 137 GenBank accessions 120 bp exon 290 bp [gt-ag] intron 146 GenBank accessions 151 bp exon 91 bp [gt-ag] intron 148 GenBank accessions 122 bp exon 711 bp [gt-ag] intron 144 GenBank accessions 1915 bp exon 55 accessions, some from brain (seen 10 times) whole brain (10), mammary (6) eye (5), whole eye (5) Validated 3' end, 1 accession 1915 bp exon 108 bp exon 739 bp [gc-ag] intron 2 GenBank accessions 81 bp exon 20029 bp [gt-ag] intron 2 GenBank accessions 61 bp exon 61 bp exon 288 bp [gt-ag] intron 51 GenBank accessions 114 bp exon 2 accessions, some from head (seen once) whole body (once) 114 bp exon 127 bp exon 127 bp exon 77 bp [gt-ag] intron 79 GenBank accessions 339 bp exon 146 bp [gt-ag] intron 127 GenBank accessions 28 bp exon 1 accession from head from upper head 28 bp exon 123 bp exon 711 bp [gt-ag] intron 144 GenBank accessions 61 bp exon 656 bp [gt-ag] intron 145 GenBank accessions 391 bp exon 1 accession from bowel 391 bp exon 360 bp exon 360 bp exon 290 bp [gt-ag] intron 146 GenBank accessions 151 bp exon 91 bp [gt-ag] intron 148 GenBank accessions 488 bp exon 5 accessions, some from whole embryo including extraembryonictissues at 11.5-days postcoitum (seen 3 times) kidney (2) 488 bp exon 296 bp exon 296 bp exon 1 accession 296 bp exon 455 bp exon 2 accessions, some from rathke's pouches (seen 2 times) 455 bp exon 647 bp exon 5 accessions, some from whole embryo including extraembryonictissues at 11.5-days postcoitum (seen once) 647 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


Click on the headers to reorder the lines
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aSep07 3603 bp 781 aa 267 bp 990 bp 2343 bp 2kb possibly including promoter 27088 bp 1kb
bSep07 3433 bp 781 aa 97 bp 990 bp 2343 bp 2kb possibly including promoter 26940 bp 1kb
cSep07 2446 bp 566 aa 287 bp 458 bp 1698 bp 2kb possibly including promoter 23049 bp 1kb
dSep07 4057 bp 434 aa 909 bp 1843 bp 870 bp 2kb possibly including promoter 26691 bp 1kb
eSep07 494 bp 164 aa     492 bp 2kb 717 bp 1kb
fSep07 999 bp 144 aa 252 bp 312 bp   2kb possibly including promoter 1380 bp 1kb
gSep07 575 bp 130 aa   182 bp 390 bp 2kb 1942 bp 1kb
hSep07-unspliced 455 bp 73 aa 236 bp     2kb possibly including promoter 455 bp 1kb
iSep07-unspliced 647 bp 59 aa   467 bp   2kb 647 bp 1kb
jSep07 364 bp 42 aa 237 bp     2kb 21420 bp 1kb
kSep07-unspliced 296 bp 73 aa 75 bp   219 bp 2kb probably including promoter 296 bp 1kb
Gene neighbors and Navigator on chromosome 9 F4|9 72.0 cM back to top
Eif1b C R Entpd3 C R P Rpl14 C R P C R R Ctnnb1 D C R P C R Trak1 D C R P C 5830454E08Rik R R R C R P Ulk4 C C C C C C C C 100kb 0 Myrip, 61 accessions, 6 variants Eif1b, 151 accessions 2 variants Entpd3, 131 accessions 2 variants Rpl14, 408 accessions 8 variants towey, 1 accession roteta, 2 accessions konane, 9 accessions, 2 variants Ctnnb1, 479 accessions 11 variants miteta, 1 accession runine, 3 accessions, 2 variants Trak1, 444 accessions 20 variants nuteta, 2 accessions ketuta, 2 accessions sawwey, 1 accession serwey, 1 accession seywey, 1 accession 5830454E08Rik, 8 accessions riteta, 2 accessions ruteta, 1 accession yateta, 1 accession poyvaw, 1 accession teewey, 1 accession yuteta, 2 accessions terwey, 1 accession toywey, 1 accession vawey, 2 accessions vywey, 3 accessions vuwey, 1 accession vowey, 1 accession meteta, 3 accessions veywey, 1 accession vorwey, 1 accession hateta, 4 accessions huteta, 1 accession ravaw, 24 accessions wuwey, 2 accessions wowey, 4 accessions neteta, 7 accessions warwey, 1 accession suwey, 1 accession sowey, 1 accession sarwey, 1 accession kotuta, 2 accessions seewey, 1 accession soywey, 1 accession tawey, 1 accession tywey, 1 accession tuwey, 1 accession wateta, 1 accession rateta, 1 accession tarwey, 1 accession reteta, 1 accession kenane, 4 accessions wanine, 1 accession tawwey, 1 accession yoteta, 2 accessions mateta, 3 accessions ranine, 2 accessions teywey, 3 accessions torwey, 1 accession muteta, 1 accession vawwey, 1 accession veewey, 1 accession hiteta, 2 accessions heteta, 1 accession voywey, 1 accession hoteta, 1 accession wawey, 6 accessions nateta, 1 accession wywey, 1 accession noteta, 1 accession wawwey, 1 accession weewey, 1 accession werwey, 5 accessions weywey, 2 accessions zawey, 1 accession kunane, 3 accessions sorwey, 2 accessions rinine, 7 accessions, 3 variants Ulk4, 240 accessions, 9 variants varwey, 1 accession verwey, 1 accession moteta, 1 accession niteta, 1 accession worwey, 2 accessions dUTPase.53, 3 accessions woywey, 1 accession tateta, 8 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               458 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u, .i-u, .j, .k-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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