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COLCA1 colorectal cancer associated 1 [ Homo sapiens (human) ]

Gene ID: 399948, updated on 22-Sep-2022

Summary

Official Symbol
COLCA1provided by HGNC
Official Full Name
colorectal cancer associated 1provided by HGNC
Primary source
HGNC:HGNC:33789
See related
Ensembl:ENSG00000196167 MIM:615693; AllianceGenome:HGNC:33789
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CASC12; C11orf92; LOH11CR1F
Summary
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]
Expression
Broad expression in stomach (RPKM 15.6), prostate (RPKM 11.1) and 14 other tissues See more
Orthologs
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Genomic context

See COLCA1 in Genome Data Viewer
Location:
11q23.1
Exon count:
6
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (111293389..111305048, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (111303576..111315229, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (111164114..111175773, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723966 Neighboring gene ribosomal protein S17 pseudogene 15 Neighboring gene POU class 2 homeobox associating factor 2 Neighboring gene POU class 2 homeobox associating factor 3 Neighboring gene uncharacterized LOC105369491 Neighboring gene uncharacterized LOC124902755

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.
EBI GWAS Catalog
Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis.
EBI GWAS Catalog
Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
EBI GWAS Catalog
Meta-analysis of new genome-wide association studies of colorectal cancer risk.
EBI GWAS Catalog

General gene information

Markers

Homology

Other Names

  • cancer susceptibility candidate 12
  • colorectal cancer-associated protein 1

Clone Names

  • FLJ45803, DKFZp781P19126

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_027686.2 RefSeqGene

    Range
    5001..16660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. NR_169237.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000669257.1
  2. NR_169241.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000532918.4
  3. NR_169242.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000355430.4
  4. NR_169243.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000540738.3
  5. NR_169244.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
  6. NR_169245.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    111293389..111305048 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    111303576..111315229 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001302644.1: Suppressed sequence

    Description
    NM_001302644.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.
  2. NM_001302645.1: Suppressed sequence

    Description
    NM_001302645.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.
  3. NM_001302646.1: Suppressed sequence

    Description
    NM_001302646.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.
  4. NM_001302647.1: Suppressed sequence

    Description
    NM_001302647.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.
  5. NM_001302648.1: Suppressed sequence

    Description
    NM_001302648.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.
  6. NM_207429.3: Suppressed sequence

    Description
    NM_207429.3: This RefSeq was removed because it is now thought that this gene does not encode a protein.