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    COLEC10 collectin subfamily member 10 [ Homo sapiens (human) ]

    Gene ID: 10584, updated on 19-Jun-2024

    Summary

    Official Symbol
    COLEC10provided by HGNC
    Official Full Name
    collectin subfamily member 10provided by HGNC
    Primary source
    HGNC:HGNC:2220
    See related
    Ensembl:ENSG00000184374 MIM:607620; AllianceGenome:HGNC:2220
    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
    3MC3; CLL1; CL-10; CL-34
    Summary
    This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in liver (RPKM 17.0), placenta (RPKM 3.8) and 2 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COLEC10 in Genome Data Viewer
    Location:
    8q24.12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (118952263..119108455)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (120080592..120236891)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (119964502..120120694)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902008 Neighboring gene TNF receptor superfamily member 11b Neighboring gene GABA type A receptor associated protein like 2 pseudogene Neighboring gene RNA, U6 small nuclear 12, pseudogene Neighboring gene COLEC10 intron CAGE-defined low expression enhancer Neighboring gene uncharacterized LOC101927513 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:120079461-120080660 Neighboring gene Sharpr-MPRA regulatory region 7316 Neighboring gene NANOG hESC enhancer GRCh37_chr8:120136171-120136709 Neighboring gene uncharacterized LOC105375725 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:120176788-120177403 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:120181673-120182872 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:120218741-120219940 Neighboring gene MAL2 antisense RNA 1 Neighboring gene mal, T cell differentiation protein 2

    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

    Associated conditions

    Description Tests
    3MC syndrome 3
    MedGen: C0796032 OMIM: 248340 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
    EBI GWAS Catalog
    An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.
    EBI GWAS Catalog
    Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
    EBI GWAS Catalog
    Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels.
    EBI GWAS Catalog
    Multiple genetic loci for bone mineral density and fractures.
    EBI GWAS Catalog
    Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
    EBI GWAS Catalog
    Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
    EBI GWAS Catalog
    Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC118794, MGC118795

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D-mannose binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chemoattractant activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in external side of plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular space NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in multivesicular body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of serine-type endopeptidase complex NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    collectin-10
    Names
    collectin liver 1
    collectin liver protein 1
    collectin sub-family member 10 (C-type lectin)
    collectin-34

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001324095.2NP_001311024.1  collectin-10 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC080033, AC107953, AI417503, AK291791
      UniProtKB/Swiss-Prot
      Q9Y6Z7
      Conserved Domains (1) summary
      cd03591
      Location:88203
      CLECT_collectin_like; C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1)
    2. NM_006438.5NP_006429.2  collectin-10 isoform 1 precursor

      See identical proteins and their annotated locations for NP_006429.2

      Status: REVIEWED

      Source sequence(s)
      AC080033, AI417503, AK291791
      Consensus CDS
      CCDS6327.1
      UniProtKB/Swiss-Prot
      Q3SYH6, Q6UW19, Q9Y6Z7
      Related
      ENSP00000332723.2, ENST00000332843.3
      Conserved Domains (2) summary
      cd03591
      Location:157272
      CLECT_collectin_like; C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1)
      pfam01391
      Location:45111
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      118952263..119108455
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005250756.4XP_005250813.1  collectin-10 isoform X1

      See identical proteins and their annotated locations for XP_005250813.1

      Conserved Domains (1) summary
      cd03591
      Location:88203
      CLECT_collectin_like; C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      120080592..120236891
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054359588.1XP_054215563.1  collectin-10 isoform X1