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Aliases for COLCA1 Gene

Subcategory (RNA class) for COLCA1 Gene

non-coding RNA

Quality Score for this RNA gene is

3

Aliases for COLCA1 Gene

  • Colorectal Cancer Associated 1 2 3
  • 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 an RNA Gene, and is affiliated with the non-coding RNA class. 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for COLCA1 Gene

Start:
111,290,787 bp from pter
End:
111,305,045 bp from pter
Size:
14,259 bases
Orientation:
Minus strand

Genomic View for COLCA1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COLCA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLCA1 Gene

No data available for Regulatory Elements 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
    Secondary Accessions:

    Protein attributes for COLCA1 Gene

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

neXtProt entry for COLCA1 Gene

Proteomics data for COLCA1 Gene at MOPED

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 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

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting 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 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 for COLCA1 Gene

Transcripts for COLCA1 Gene

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COLCA1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for COLCA1
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

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 for COLCA1 Gene

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

This gene is overexpressed in Stomach (7.5), Prostate (7.0), Bladder (6.3), and Minor Salivary Gland (5.3).

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 expressions with COLCA1: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Protein expression for COLCA1 Gene

Orthologs for COLCA1 Gene

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

Orthologs for COLCA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia COLCA1 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 2010007H06Rik 16
Species with no ortholog for COLCA1:
  • 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)
  • 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 MAF
rs1054768 -- 111,293,695(-) ACGTC(A/C)GTCTC nc-transcript-variant
rs4512891 -- 111,295,548(+) aaaaa(C/T)acaaa nc-transcript-variant
rs5794737 -- 111,296,482(+) AAAAA(-/A)TAGAA nc-transcript-variant
rs7103178 -- 111,294,284(+) TTCTT(C/T)AGAGT nc-transcript-variant
rs10891244 -- 111,295,215(+) GAAAT(G/T)GAAAA nc-transcript-variant

Relevant External Links for COLCA1 Gene

HapMap Linkage Disequilibrium report
COLCA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for COLCA1 Gene

Disorders for COLCA1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for COLCA1 Gene including...

Search for COLCA1 Gene in MalaCards »
genes like me logo Genes that share disorders with COLCA1: view

No data available for UniProtKB/Swiss-Prot 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
  2. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. (PMID: 24760461) Closa A. … Moreno V. (Carcinogenesis 2014) 2 3
  3. 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
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 4
  5. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor T.D. … Sakaki Y. (Nature 2006) 4

Products for COLCA1 Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate COLCA1
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for COLCA1
    • Block miRNA regulation of COLCA1 using miScript Target Protectors

    Sources for COLCA1 Gene

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