Format

Send to:

Choose Destination

COLEC12 collectin subfamily member 12 [ Homo sapiens (human) ]

Gene ID: 81035, updated on 1-Jun-2020

Summary

Official Symbol
COLEC12provided by HGNC
Official Full Name
collectin subfamily member 12provided by HGNC
Primary source
HGNC:HGNC:16016
See related
Ensembl:ENSG00000158270 MIM:607621
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLP1; NSR2; SRCL; SCARA4
Summary
This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, May 2018]
Expression
Broad expression in placenta (RPKM 63.7), lung (RPKM 26.0) and 17 other tissues See more
Orthologs

Genomic context

See COLEC12 in Genome Data Viewer
Location:
18p11.32
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (316737..500701, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (319355..500729, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371951 Neighboring gene ubiquitin specific peptidase 14 Neighboring gene THO complex 1 Neighboring gene uncharacterized LOC107985155 Neighboring gene long intergenic non-protein coding RNA 1925 Neighboring gene centrin 1

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

NHGRI GWAS Catalog

Description
Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif downregulates the expression of collectin sub-family member 12 (COLEC12) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
galactose binding NAS
Non-traceable Author Statement
more info
PubMed 
low-density lipoprotein particle binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
low-density lipoprotein particle binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
pattern recognition receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pattern recognition receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
scavenger receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
scavenger receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
carbohydrate mediated signaling NAS
Non-traceable Author Statement
more info
PubMed 
cellular response to exogenous dsRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT cellular response to exogenous dsRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
defense response TAS
Traceable Author Statement
more info
PubMed 
defense response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response TAS
Traceable Author Statement
more info
PubMed 
phagocytosis, recognition IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell adhesion molecule production IMP
Inferred from Mutant Phenotype
more info
PubMed 
receptor-mediated endocytosis TAS
Traceable Author Statement
more info
 
regulation of immune response TAS
Traceable Author Statement
more info
 
toll-like receptor 3 signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
collectin-12
Names
collectin placenta protein 1
collectin sub-family member 12
hCL-P1
nurse cell scavenger receptor 2
scavenger receptor class A, member 4
scavenger receptor with C-type lectin

NCBI Reference Sequences (RefSeq)

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_030342.1 RefSeqGene

    Range
    5001..186375
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_130386.3NP_569057.2  collectin-12

    Status: REVIEWED

    Source sequence(s)
    AP000915, AP005240
    Consensus CDS
    CCDS32782.1
    Related
    ENSP00000383115.3, ENST00000400256.5
    Conserved Domains (2) summary
    cd03590
    Location:607732
    CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    cl25732
    Location:77350
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    316737..500701 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011525741.2XP_011524043.1  collectin-12 isoform X1

    Conserved Domains (3) summary
    cd03590
    Location:590715
    CLECT_DC-SIGN_like; C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR)
    pfam05714
    Location:49171
    Borrelia_lipo_1; Borrelia burgdorferi virulent strain associated lipoprotein
    cl02193
    Location:140300
    VirB5_like; VirB5 protein family

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_030781.2: Suppressed sequence

    Description
    NM_030781.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Support Center