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COLCA1 Gene

protein-coding   GIFtS: 23
GCID: GC11M111165

Colorectal Cancer Associated 1

(Previous name: chromosome 11 open reading frame 92)
(Previous symbol: C11orf92)
  Search for COLCA1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Colorectal Cancer Associated 11 2
C11orf921 2 3
Cancer Susceptibility Candidate 121
Chromosome 11 Open Reading Frame 921
CASC122

External Ids:    HGNC: 337891   Entrez Gene: 3999482   Ensembl: ENSG000001961677   OMIM: 6156935   UniProtKB: Q6ZS623   

Export aliases for COLCA1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for COLCA1 Gene:
COLCA1 (colorectal cancer associated 1) is a protein-coding gene.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Search for regulatory transcription factor binding sites for COLCA1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for COLCA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COLCA1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q23.1   Ensembl cytogenetic band:  11q23.1   HGNC cytogenetic band: 11q23.1

COLCA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COLCA1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M111165:  view genomic region     (about GC identifiers)

Start:
111,164,114 bp from pter      End:
111,175,770 bp from pter
Size:
11,657 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: COLC1_HUMAN, Q6ZS62 (See protein sequence)
Recommended Name: Colorectal cancer-associated protein 1  
Size: 124 amino acids; 13401 Da

Explore the universe of human proteins at neXtProt for COLCA1: NX_Q6ZS62

Explore proteomics data for COLCA1 at MOPED


See COLCA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000437253   ENSP00000347601   ENSP00000438980  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: Q6ZS62


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
COLC1_HUMAN, Q6ZS62: Membrane; Single-pass membrane protein (Potential)

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

COLCA1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COLCA1
Interactions:

    Search GeneGlobe Interaction Network for COLCA1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for COLCA1 (COLC1)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for COLCA1 gene: 
NM_207429.2  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000532918(uc001ple.3) ENST00000355430(uc001pld.3) ENST00000526150
ENST00000540738
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat COLCA1

Selected AceView cDNA sequences (see all 43):

AI806340 NM_207429 AW661751 AW573293 BX486062 CB241386 BF590585 CA314483 
CA437027 BX486061 CN478733 AK127703 BX486313 AA470052 AI149706 BM823942 
AB096245 BG291067 AI985511 BX097686 CF121410 BM853126 AW058265 AI200281 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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COLCA1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
COLCA1 Expression
About this image

COLCA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

COLCA1 Protein Expression
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COLCA1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for COLCA1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia 2010007H06Rik5 RIKEN cDNA 2010007H06 gene   --   9 (28.04 cM) 51280295 


ENSEMBL Gene Tree for COLCA1 (if available)
TreeFam Gene Tree for COLCA1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for COLCA1 (see all 185)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1139592751,2
C--111026976(+) TATTGA/TGGCAC 1 -- ds50010--------
rs1888785651,2
--111026977(+) ATTGAC/GGCACT 1 -- ds50010--------
rs782344351,2
C--111027116(+) CAGGGG/ACATGG 1 -- ds50011Minor allele frequency- A:0.50NA 2
rs1908284941,2
--111027231(+) ACACAC/GAGTGG 1 -- ds50010--------
rs1821526621,2
--111027240(+) GGGGAA/GCATCA 1 -- ds50010--------
rs1872427971,2
--111027277(+) TGGAGA/GGGGGA 1 -- ds50010--------
rs1916921891,2
--111027278(+) GGAGGA/GGGGAG 1 -- ds50010--------
rs561600971,2
C--111027432(+) AATATC/ATTAAC 1 -- ds50014Minor allele frequency- A:0.30CSA WA NA EA 360
rs1440511041,2
--111027563(+) TTTATA/GTGTTT 1 -- nc-transcript-variant0--------
rs1846572781,2
--111027680(+) TTGCTC/TCCCAT 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for COLCA1 (111164114 - 111175770 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for COLCA1: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing COLCA1
DNA2.0 Custom Variant and Variant Library Synthesis for COLCA1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 615693    OMIM disorders: --


COLCA1 for disorders           About GeneDecksing


Export disorders for COLCA1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for COLCA1 gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with COLCA1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis. (PubMed id 23266556)1 Peters U....Hsu L. (Gastroenterology 2013)
  2. Meta-analysis of new genome-wide association studies of colorectal cancer risk. (PubMed id 21761138)1 Peters U....Casey G. (Hum. Genet. 2012)
  3. Risk of genome-wide association study-identified genetic variants for colorectal cancer in a Chinese population. (PubMed id 20530476)1 Xiong F....Lin D. (amp 2010)
  4. Association studies on 11 published colorectal cancer risk loci. (PubMed id 20648012)1 von Holst S....Lindblom A. (Br. J. Cancer 2010)
  5. Susceptibility genetic variants associated with colorectal cancer risk correlate with cancer phenotype. (PubMed id 20638935)1 AbulA- A....Andreu M. (Gastroenterology 2010)
  6. Low-penetrance susceptibility variants in familial colorectal cancer. (PubMed id 20501757)1 NiittymAoki I....Aaltonen L.A. (amp 2010)
  7. Enrichment of low penetrance susceptibility loci in a Dutch familial colorectal cancer cohort. (PubMed id 19843678)1 Middeldorp A....van Wezel T. (amp 2009)
  8. Refinement of the basis and impact of common 11q23.1 variation to the risk of developing colorectal cancer. (PubMed id 18753146)1 Pittman A.M....Houlston R.S. (Hum. Mol. Genet. 2008)
  9. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. (PubMed id 18372901)1 Tenesa A....Dunlop M.G. (Nat. Genet. 2008)
  10. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 399948 HGNC: 33789 AceView: FLJ45803 Ensembl:ENSG00000196167 euGenes: HUgn399948
ECgene: COLCA1 H-InvDB: COLCA1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for COLCA1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for COLCA1 gene:
Search GeneIP for patents involving COLCA1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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