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Aliases for COLCA1 Gene

Aliases for COLCA1 Gene

  • Colorectal Cancer Associated 1 2 3 5
  • Cancer Susceptibility Candidate 12 2 3
  • C11orf92 3 4
  • Colorectal Cancer-Associated Protein 1 3
  • Chromosome 11 Open Reading Frame 92 2
  • LOH11CR1F 3
  • CASC12 3

External Ids for COLCA1 Gene

Previous HGNC Symbols for COLCA1 Gene

  • C11orf92

Previous GeneCards Identifiers for COLCA1 Gene

  • GC11M111165

Summaries for COLCA1 Gene

Entrez Gene Summary for COLCA1 Gene

  • This gene encodes a transmembrane protein that localizes to granular structures, including crystalloid eosinophilic granules and other granular organelles. This gene, along with an overlapping opposite strand gene, has been implicated as a susceptibility locus for colorectal cancer. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]

GeneCards Summary for COLCA1 Gene

COLCA1 (Colorectal Cancer Associated 1) is a Protein Coding gene. Diseases associated with COLCA1 include Colorectal Cancer.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COLCA1 Gene

Genomics for COLCA1 Gene

Regulatory Elements for COLCA1 Gene

Enhancers for COLCA1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F111352 0.6 ENCODE 26.1 -48.1 -48128 1.6 CTCF STAT1 RAD21 ZFHX2 ZNF366 POLR2A ETV6 EGR2 COLCA1 COLCA2 RNU2-60P MIR4491
GH11F111357 0.8 FANTOM5 Ensembl ENCODE 23.1 -59.9 -59857 15.7 HDGF PKNOX1 MLX WRNIP1 ZFP64 ARID4B YBX1 FEZF1 DMAP1 ZNF2 COLCA2 COLCA1 LAYN BTG4 C11orf88 MIR34B MIR34C POU2AF1 MIR4491 RNU2-60P
GH11F111375 0.4 ENCODE 22.7 -73.4 -73439 5.1 HDGF TBP PKNOX1 MXI1 WRNIP1 ZNF133 MAX BMI1 EBF1 ZBTB40 COLCA1 COLCA2 LOC644277 POU2AF1 BTG4 C11orf88 MIR34B MIR34C RNU2-60P MIR4491
GH11F111413 1.1 Ensembl ENCODE 17.7 -111.7 -111651 6.6 HDGF ELF3 TBP PKNOX1 TBL1XR1 WRNIP1 ARID4B YBX1 BMI1 RAD21 COLCA1 RNU2-60P COLCA2 BTG4 C11orf88 MIR34B MIR34C LOC100132078 BCO2 GC11M111399
GH11F111427 0.3 FANTOM5 16.9 -122.6 -122585 0.4 PKNOX1 NFIA BHLHE40 OVOL3 FEZF1 ZNF843 OSR2 GATA3 ZNF366 GATA2 COLCA1 POU2AF1 COLCA2 MIR34B MIR34C BTG4 C11orf88 RNU2-60P LAYN LOC100132078
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around COLCA1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COLCA1 Gene

Chromosome:
11
Start:
111,290,787 bp from pter
End:
111,305,048 bp from pter
Size:
14,262 bases
Orientation:
Minus strand

Genomic View for COLCA1 Gene

Genes around COLCA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COLCA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COLCA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLCA1 Gene

Proteins for COLCA1 Gene

  • Protein details for COLCA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZS62-COLC1_HUMAN
    Recommended name:
    Colorectal cancer-associated protein 1
    Protein Accession:
    Q6ZS62

    Protein attributes for COLCA1 Gene

    Size:
    124 amino acids
    Molecular mass:
    13401 Da
    Quaternary structure:
    No Data Available

neXtProt entry for COLCA1 Gene

Post-translational modifications for COLCA1 Gene

No Post-translational modifications

Other Protein References for COLCA1 Gene

No data available for DME Specific Peptides for COLCA1 Gene

Domains & Families for COLCA1 Gene

Protein Domains for COLCA1 Gene

ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with COLCA1: view

No data available for Gene Families , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for COLCA1 Gene

Function for COLCA1 Gene

genes like me logo Genes that share phenotypes with COLCA1: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for COLCA1 Gene

Localization for COLCA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COLCA1 Gene

Membrane; Single-pass membrane protein. Note=Co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages and dendritic cells.

Gene Ontology (GO) - Cellular Components for COLCA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IDA 24154973
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with COLCA1: view

No data available for Subcellular locations from COMPARTMENTS for COLCA1 Gene

Pathways & Interactions for COLCA1 Gene

SuperPathways for COLCA1 Gene

No Data Available

Interacting Proteins for COLCA1 Gene

Gene Ontology (GO) - Biological Process for COLCA1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for COLCA1 Gene

Transcripts for COLCA1 Gene

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COLCA1 Gene

No ASD Table

Relevant External Links for COLCA1 Gene

GeneLoc Exon Structure for
COLCA1
ECgene alternative splicing isoforms for
COLCA1

Expression for COLCA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COLCA1 Gene

mRNA differential expression in normal tissues according to GTEx for COLCA1 Gene

This gene is overexpressed in Stomach (x7.5), Prostate (x7.0), Bladder (x6.3), and Minor Salivary Gland (x5.3).

NURSA nuclear receptor signaling pathways regulating expression of COLCA1 Gene:

COLCA1

mRNA Expression by UniProt/SwissProt for COLCA1 Gene:

Q6ZS62-COLC1_HUMAN
Tissue specificity: Expressed in gastrointestinal and immune tissue, as well as prostate, testis and ovary. Expressed in lamina propria and eosinophils but not in epithelial cells. Expression is greater in benign adjacent tissues than in colon tumors.
genes like me logo Genes that share expression patterns with COLCA1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for COLCA1 Gene

Orthologs for COLCA1 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for COLCA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COLCA1 35
  • 96 (a)
OneToOne
Species where no ortholog for COLCA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for COLCA1 Gene

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

Paralogs for COLCA1 Gene

No data available for Paralogs for COLCA1 Gene

Variants for COLCA1 Gene

Sequence variations from dbSNP and Humsavar for COLCA1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs10244 -- 111,298,385(+) GAAAA(A/T)ACTCA upstream-variant-2KB, utr-variant-5-prime
rs1054768 -- 111,293,695(-) ACGTC(A/C)GTCTC utr-variant-3-prime
rs1054791 -- 111,303,810(+) CAAAA(A/G)AGGTG intron-variant
rs10789823 -- 111,301,678(+) ATTCC(C/T)CTTGC intron-variant, upstream-variant-2KB
rs10891244 -- 111,295,215(+) GAAAT(G/T)GAAAA utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for COLCA1 Gene

Variant ID Type Subtype PubMed ID
dgv233e214 CNV loss 21293372
esv3627732 CNV gain 21293372

Variation tolerance for COLCA1 Gene

Gene Damage Index Score: 1.19; 24.01% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COLCA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLCA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COLCA1 Gene

Disorders for COLCA1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for COLCA1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
colorectal cancer
  • colorectal cancer, somatic
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for COLCA1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COLCA1
genes like me logo Genes that share disorders with COLCA1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COLCA1 Gene

Publications for COLCA1 Gene

  1. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. (PMID: 24154973) Peltekova V.D. … Hudson T.J. (Int. J. Cancer 2013) 2 3 4 64
  2. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. (PMID: 24760461) Closa A. … Moreno V. (Carcinogenesis 2014) 2 3 64
  3. Genetic association of PLCE1, C11orf92-C11orf93, and NOC3L with colorectal cancer risk in the Han population. (PMID: 24146276) Duan X. … Chen C. (Tumour Biol. 2014) 3 64
  4. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. (PMID: 24256810) Biancolella M. … Casey G. (Hum. Mol. Genet. 2014) 3 64
  5. Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. (PMID: 24836286) Zhang B. … Zheng W. (Nat. Genet. 2014) 3 64

Products for COLCA1 Gene

Sources for COLCA1 Gene

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