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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

COLCA1 Gene

protein-coding   GIFtS: 25
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)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Colorectal Cancer Associated 11 2
C11orf921 2
Cancer Susceptibility Candidate 121
Chromosome 11 Open Reading Frame 921
CASC122

External Ids:    HGNC: 337891   Entrez Gene: 3999482   Ensembl: ENSG000001961677   UniProtKB: Q6ZS623   
ORGUL members:         
NONCODE14:n409752      

Export aliases for COLCA1 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for COLCA1 Gene: 
COLCA1 (colorectal cancer associated 1) is a protein-coding gene, and is affiliated with the lncRNA class.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for COLCA1
         Other transcription factors

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

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CK092_HUMAN, Q6ZS62 (See protein sequence)
Recommended Name: Uncharacterized protein C11orf92  
Size: 124 amino acids; 13401 Da
Subcellular location: Membrane; Single-pass membrane protein (Potential)

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

Explore proteomics data for COLCA1 at MOPED 

COLCA1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

COLCA1 Protein Expression

ENSEMBL proteins: 
 ENSP00000437253   ENSP00000347601   ENSP00000438980  

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral to membrane IEA--

COLCA1 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Animal Models:
   inGenious Targeting Laboratory - Custom generated mouse model solutions for COLCA1 
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miRNA
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In Situ Assay
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COLCA1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for COLCA1 (CK092)

Search CenterWatch for drugs/clinical trials and news about COLCA1 / CK092

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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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24/43 AceView cDNA sequences (see all 43):

AI806340 AW661751 AW573293 BX486062 NM_207429 CB241386 BX097686 CF121410 
BM795014 AI200281 BG291067 CN478733 BM853126 AW058265 AA470052 AI149706 
BX486061 CA314483 BM823942 CA437027 AI985511 BF590585 AK127703 BX486313 

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --


See COLCA1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for COLCA1
    SABiosciences Custom PCR Arrays for COLCA1
Primer
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QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COLCA1
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)
About This Section

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/185 SNPs in COLCA1 are shown (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: --
SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
  --

(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)
About This Section

PubMed articles for COLCA1 gene, integrated from 9 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 Colo rectal Tumors in a Genome-Wide Meta-analysis. (PubMed id 23266556)1 Peters U....Hsu L. (2013)
  2. Meta-analysis of new genome-wide association studies o f colorectal cancer risk. (PubMed id 21761138)1 Peters U....Casey G. (2012)
  3. Risk of genome-wide association study-identified gene tic variants for colorectal cancer in a Chinese population. (PubMed id 20530476)1 Xiong F....Lin D. (2010)
  4. Association studies on 11 published colorectal cancer risk loci. (PubMed id 20648012)1 von Holst S....Lindblom A. (2010)
  5. Susceptibility genetic variants associated with color ectal cancer risk correlate with cancer phenotype. (PubMed id 20638935)1 AbulA- A....Andreu M. (2010)
  6. Low-penetrance susceptibility variants in familial co lorectal cancer. (PubMed id 20501757)1 NiittymAoki I....Aaltonen L.A. (2010)
  7. Enrichment of low penetrance susceptibility loci in a Dutch familial colorectal cancer cohort. (PubMed id 19843678)1 Middeldorp A....van Wezel T. (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. (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. (2008)
  10. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 399948 HGNC: 33789 AceView: FLJ45803 Ensembl:ENSG00000196167 euGenes: HUgn399948
ECgene: COLCA1 H-InvDB: COLCA1

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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