Mus musculus gene Cops2, encoding COP9 (constitutive photomorphogenic) homolog, subunit 2 (Arabidopsis thaliana).
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.b), 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 7 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 4.8 times the average gene in this release. The sequence of this gene is defined by 533 GenBank accessions from 485 cDNA clones, some from mammary gland (seen 31 times), kidney (25), testis (21), head (20), mammary (18), whole body (17), lung (16) and 86 other tissues. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 19 distinct introns (18 gt-ag, 1 gc-ag). Transcription produces 11 different mRNAs, 7 alternatively spliced variants and 4 unspliced forms. There are 10 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by presence or absence of 2 cassette exons, overlapping exons with different boundaries. 80 bp of this gene are antisense to spliced gene Galk2, raising the possibility of regulated alternate expression.
Function: There are 12 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (embryogenesis phenotype; lethality-embryonic/perinatal) and proposed to participate in processes (cell proliferation, negative regulation of transcription, signal transduction, transcription from RNA polymerase II promoter). Proteins are expected to have molecular functions (protein binding, transcription corepressor activity) and to localize in various compartments (nucleus, signalosome).
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_1330276 for in depth functional annotation of this gene.
Protein coding potential: 7 spliced and 3 unspliced mRNAs putatively encode good proteins, altogether 9 different isoforms (5 complete, 1 COOH complete, 3 partial), some containing Proteasome component region PCI domain [Pfam], some transmembrane domains, a second peroximal domain [Psort2]. The remaining mRNA variant (unspliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 2, links to other databases and other names
Map: This gene Cops2 maps on chromosome 2, at 2 F1|2 70.0 cM according to Entrez Gene. In AceView, it covers 28.89 kb, from 125684922 to 125656037 (NCBI 37a, Aug 2007), on the reverse strand.
Links to: manual annotations from MGI_1330276, the SNP view, gene overviews from Gene 12848, expression data from Gene 12848, molecular and other annotations from UCSC.
Other names: The gene is also known as Cops2, Csn2, Sgn2, C85265, Trip15, AI315723 or alien-like, LOC12848.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene COPS2 (e= 10-127).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene csn-2 (e= 10-105), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene FUS12 (e=4 10-93), 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 Cops2 5' 3' encoded on minus strand of chromosome 2 from 125,684,922 to 125,656,037 a b [NM] c d e f k-u j-u g h-u i-u 1 2kb 0 127 bp exon 127 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 114 bp exon 1455 bp [gt-ag] intron 180 GenBank accessions 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2077 bp [gt-ag] intron 52 GenBank accessions 111 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 179 bp exon 104 bp [gt-ag] intron 59 GenBank accessions 53 bp exon 2909 bp [gt-ag] intron 61 GenBank accessions 98 bp exon 1305 bp [gt-ag] intron 62 GenBank accessions 83 bp exon 971 bp [gt-ag] intron 61 GenBank accessions 59 bp exon 1386 bp [gt-ag] intron 66 GenBank accessions 2036 bp exon 56 accessions, some from embryonic stem cell (seen 4 times) mammary (4), brain (3) infiltrating ductal carcinoma (3) whole embryo including extraembryonictissues at 10.5-days postcoitum (3) Validated 3' end, 4 accessions Validated 3' end, 3 accessions Validated 3' end, 2 accessions 2036 bp exon 251 bp exon 251 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 114 bp exon 1455 bp [gt-ag] intron 180 GenBank accessions 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2098 bp [gt-ag] intron 86 GenBank accessions 90 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 179 bp exon 104 bp [gt-ag] intron 59 GenBank accessions 53 bp exon 2909 bp [gt-ag] intron 61 GenBank accessions 98 bp exon 1305 bp [gt-ag] intron 62 GenBank accessions 83 bp exon 971 bp [gt-ag] intron 61 GenBank accessions 59 bp exon 1386 bp [gt-ag] intron 66 GenBank accessions 2035 bp exon 349 accessions, NM_009939 some from kidney (seen 22 times) mammary gland (19), head (17) testis (16), whole body (16) Validated 3' end, 26 accessions Validated 3' end, 3 accessions Validated 3' end, 11 accessions Validated 3' end, 10 accessions 2035 bp exon 61 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 114 bp exon 1455 bp [gt-ag] intron 180 GenBank accessions 16 bp exon 5557 bp [gt-ag] intron 5 GenBank accessions 90 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 179 bp exon 104 bp [gt-ag] intron 59 GenBank accessions 53 bp exon 2909 bp [gt-ag] intron 61 GenBank accessions 98 bp exon 1305 bp [gt-ag] intron 62 GenBank accessions 83 bp exon 971 bp [gt-ag] intron 61 GenBank accessions 59 bp exon 1386 bp [gt-ag] intron 66 GenBank accessions 2035 bp exon 15 accessions, some from mammary gland (seen 3 times) blastocyst (2), mammary (2) embryonic stem cell (once) eye (once) Validated 3' end, 2 accessions 2035 bp exon 84 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 114 bp exon 1455 bp [gt-ag] intron 180 GenBank accessions 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2050 bp [gt-ag] intron 3 GenBank accessions 138 bp exon 138 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 179 bp exon 104 bp [gt-ag] intron 59 GenBank accessions 53 bp exon 2909 bp [gt-ag] intron 61 GenBank accessions 98 bp exon 1305 bp [gt-ag] intron 62 GenBank accessions 83 bp exon 971 bp [gt-ag] intron 61 GenBank accessions 59 bp exon 1386 bp [gt-ag] intron 66 GenBank accessions 737 bp exon 58 accessions, some from mammary gland (seen 9 times) blood (5), embryo (5) lung (3), spontaneous tumor metastatic to mammary.stem cell origin (3) Validated 3' end, 5 accessions Validated 3' end, 1 accession 737 bp exon 43 bp exon 43 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 114 bp exon 1455 bp [gt-ag] intron 180 GenBank accessions 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2113 bp [gt-ag] intron 2 GenBank accessions 75 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 2 accessions, some from head (seen once) upper head (once) 179 bp exon 130 bp exon 6956 bp [gt-ag] intron 1 GenBank accession 130 bp exon 1996 bp [gt-ag] intron 1 GenBank accession 116 bp exon 1453 bp [gc-ag] intron 7 GenBank accessions 78 bp exon 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2098 bp [gt-ag] intron 86 GenBank accessions 90 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 175 bp exon 839 bp [gt-ag] intron 78 GenBank accessions 124 bp exon 5 accessions, some from pooled - molar (seen once) primary cultures of sertoli cells (once) testis (once) 124 bp exon 1113 bp exon 1113 bp exon 3 accessions, some from colon (seen once) e6.5 whole embryo (once) stomach (once) 1113 bp exon 696 bp exon 696 bp exon 2 accessions, some from mammary (seen once) tumor, gross tissue (once) 696 bp exon 62 bp exon 9082 bp [gt-ag] intron 174 GenBank accessions 116 bp exon 1453 bp [gc-ag] intron 7 GenBank accessions 78 bp exon 78 bp exon 3271 bp [gt-ag] intron 182 GenBank accessions 126 bp exon 2077 bp [gt-ag] intron 52 GenBank accessions 111 bp exon 111 bp [gt-ag] intron 133 GenBank accessions 78 bp exon 1934 bp [gt-ag] intron 114 GenBank accessions 3 accessions, some from embryonic stem cell (seen 2 times) spleen (once) 36 bp exon 431 bp exon 431 bp exon 3 accessions, some from rathke's pouches (seen 3 times) 431 bp exon 1638 bp exon 1638 bp exon 3 accessions, some from cerebellum (seen 3 times) 1638 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 3317 bp 474 aa   1891 bp 1422 bp 2kb 28761 bp 1kb
bSep07 3419 bp 443 aa 197 bp 1890 bp   2kb possibly including promoter 28884 bp 1kb
cSep07 3041 bp 319 aa 191 bp 1890 bp   2kb probably including promoter 28694 bp 1kb
dSep07 2002 bp 319 aa 450 bp 592 bp 396 bp 2kb probably including promoter 27419 bp 1kb
eSep07 868 bp 285 aa 13 bp     2kb probably including promoter 19673 bp 1kb
fSep07 1047 bp 205 aa 430 bp     2kb possibly including promoter 19705 bp 1kb
gSep07 607 bp 125 aa 232 bp     2kb probably including promoter 18535 bp 1kb
hSep07-unspliced 431 bp 116 aa 23 bp 57 bp 348 bp 2kb probably including promoter 431 bp 1kb
iSep07-unspliced 1638 bp 89 aa 867 bp 501 bp   2kb possibly including promoter 1638 bp 1kb
jSep07-unspliced 696 bp 64 aa 429 bp 72 bp   2kb possibly including promoter 696 bp 1kb
kSep07-unspliced 1113 bp 45 aa 629 bp 346 bp   2kb 1113 bp 1kb
Gene neighbors and Navigator on chromosome 2 F1|2 70.0 cM back to top
C C R Eid1 C R P Galk2 C R P C Fgf7 D C R P Dtwd1 C R D C R P Fbn1 C R P Cep152 C R P Shc4 C R P 3110001I20Rik D C R P Cops2 C R C C R P 100kb 0 reharera, 2 accessions roharera, 8 accessions Eid1, 241 accessions Galk2, 174 accessions 12 variants moharera, 2 accessions Fgf7, 62 accessions, 4 variants Dtwd1, 84 accessions, 5 variants komorera, 1 accession raharera, 1 accession leysmar, 1 accession ruharera, 1 accession fersly, 1 accession mysmar, 2 accessions mosmar, 1 accession mawsmar, 1 accession meesmar, 4 accessions meysmar, 1 accession nusmar, 1 accession yaharera, 1 accession yoharera, 2 accessions miharera, 2 accessions narsmar, 1 accession nawsmar, 2 accessions neesmar, 1 accession hiharera, 7 accessions nersmar, 3 accessions neysmar, 2 accessions heharera, 1 accession makerara, 4 accessions noysmar, 1 accession pysmar, 1 accession kemorera, 2 accessions waharera, 2 accessions riharera, 2 accessions lorsmar, 2 accessions loysmar, 1 accession masmar, 1 accession musmar, 1 accession marsmar, 1 accession mersmar, 1 accession morsmar, 1 accession moysmar, 2 accessions nasmar, 2 accessions nysmar, 2 accessions nosmar, 1 accession yuharera, 1 accession maharera, 1 accession muharera, 1 accession haharera, 4 accessions huharera, 3 accessions norsmar, 3 accessions hoharera, 3 accessions pusmar, 1 accession Fbn1, 311 accessions, 12 variants Cep152, 64 accessions 10 variants Shc4, 142 accessions, 6 variants 3110001I20Rik, 244 accessions 10 variants Cops2, 499 accessions 11 variants meharera, 1 accession feysly, 199 accessions 2 variants forsly, 1 accession yokerara, 7 accessions 2 variants pasmar, 1 accession posmar, 2 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               12 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u, .i-u, .j-u, .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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