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, ... See more...

Aliases for COLCA1 Gene

RNA type for COLCA1 Gene

lncRNA

Aliases for COLCA1 Gene

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 an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with COLCA1 include Glioma Susceptibility 1 and Colorectal Cancer.

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COLCA1 Gene

Genomics for COLCA1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COLCA1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J111304 Enhancer 0.4 ENCODE dbSUPER 250.7 +0.3 272 0.9 POLR2A COLCA1 C11orf53 COLCA2 POU2AF1
GH11J111305 Enhancer 0.3 dbSUPER 250.7 -0.6 -559 0.4 CTCF COLCA1 COLCA2 piR-50852-032 POU2AF1
GH11J111375 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 22.7 -73.0 -72989 5.1 BCLAF1 ZNF207 POLR2A IRF4 EBF1 CBFB SMARCA5 MAX TAF1 BHLHE40 POU2AF1 lnc-BTG4-3 COLCA1 COLCA2 ENSG00000255093 BTG4 HOATZ MIR34B MIR34C HSALNG0087098
GH11J111357 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 23.1 -59.6 -59552 16 BCLAF1 SP1 SSRP1 ZMYM3 KLF9 POLR2A CEBPA ATF3 CHD4 YY1 COLCA2 COLCA1 LAYN MIR34B MIR34C BTG4 HOATZ POU2AF1 HSALNG0087098 lnc-BTG4-3
GH11J111352 Enhancer 0.8 Ensembl ENCODE dbSUPER 26.1 -47.7 -47677 1.6 POLR2A ZNF366 RAD21 EGR2 YY1 ETV6 ZFHX2 HSALNG0087098 COLCA1 COLCA2 RNU2-60P MIR4491 lnc-BTG4-3 POU2AF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COLCA1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COLCA1

Genomic Locations for COLCA1 Gene

Latest Assembly
chr11:111,290,786-111,305,498
(GRCh38/hg38)
Size:
14,713 bases
Orientation:
Minus strand

Previous Assembly
chr11:111,164,114-111,175,773
(GRCh37/hg19 by Entrez Gene)
Size:
11,660 bases
Orientation:
Minus strand

chr11:111,164,114-111,175,770
(GRCh37/hg19 by Ensembl)
Size:
11,657 bases
Orientation:
Minus strand

Genomic View for COLCA1 Gene

Genes around COLCA1 on UCSC Golden Path with GeneCards custom track
COLCA1 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

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

REFSEQ proteins:

No data available for DME Specific Peptides for COLCA1 Gene

Domains & Families for COLCA1 Gene

Gene Families for COLCA1 Gene

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

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for COLCA1 Gene

Function for COLCA1 Gene

Phenotypes From GWAS Catalog for COLCA1 Gene

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

CRISPR products for research

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , 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 and Subcellular locations from the Human Protein Atlas (HPA) for COLCA1 Gene

Pathways & Interactions for COLCA1 Gene

PathCards logo

SuperPathways for COLCA1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for COLCA1 Gene

None

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

Drugs & Compounds for COLCA1 Gene

No Compound Related Data Available

Transcripts for COLCA1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for COLCA1 Gene

RNAcentral Transcript ID RNA Type Length (nts) # of Sources Source Identifiers and Annotations
URS0000AAE14C_9606 lncRNA 5368 3

RefSeq: NR_169241,

Ensembl: ENST00000532918 (view in UCSC) ,

LNCipedia: lnc-POU2AF1-1:3,

URS000076CDD1_9606 lncRNA 391 3

Ensembl: ENST00000526150 (view in UCSC) ,

LncBook: HSALNT0181010,

LNCipedia: lnc-POU2AF1-1:4,

URS0000760908_9606 lncRNA 8100 2

Ensembl: ENST00000620864 (view in UCSC) ,

LNCipedia: lnc-POU2AF1-1:2,

URS0000A89E25_9606 lncRNA 5539 2

Ensembl: ENST00000540738 (view in UCSC) ,

LNCipedia: lnc-POU2AF1-1:6,

URS0000787AA3_9606 lncRNA 5442 2

Ensembl: ENST00000355430 (view in UCSC) ,

LNCipedia: lnc-POU2AF1-1:5,

COLCA1 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for COLCA1 Gene

CRISPR products for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COLCA1

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

No ASD Table

Relevant External Links for COLCA1 Gene

GeneLoc Exon Structure 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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 for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 30
  • 96 (a)
OneToOne
Species where no ortholog for COLCA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Alliance of Genome Resources:
Additional Orthologs for COLCA1

Paralogs for COLCA1 Gene

No data available for Paralogs for COLCA1 Gene

Variants for COLCA1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COLCA1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for COLCA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLCA1
Leiden Open Variation Database (LOVD)
COLCA1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COLCA1 Gene

Disorders for COLCA1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for COLCA1 Gene - From: LNC, COP, and GCD

Disorder Aliases PubMed IDs
glioma susceptibility 1
  • glm1
colorectal cancer
  • crc
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for 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 VD … Hudson TJ (International journal of cancer 2014) 2 3 4
  2. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. (PMID: 24760461) Closa A … Moreno V (Carcinogenesis 2014) 2 3
  3. The Use of Three Long Non-Coding RNAs as Potential Prognostic Indicators of Astrocytoma. (PMID: 26252651) Zhi F … Yang Y (PloS one 2015) 72
  4. Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. (PMID: 24836286) Zhang B … Zheng W (Nature genetics 2014) 3
  5. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. (PMID: 24256810) Biancolella M … Casey G (Human molecular genetics 2014) 3

Products for COLCA1 Gene

Sources for COLCA1 Gene