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    CLEC3A C-type lectin domain family 3 member A [ Homo sapiens (human) ]

    Gene ID: 10143, updated on 9-Dec-2024

    Summary

    Official Symbol
    CLEC3Aprovided by HGNC
    Official Full Name
    C-type lectin domain family 3 member Aprovided by HGNC
    Primary source
    HGNC:HGNC:2052
    See related
    Ensembl:ENSG00000166509 MIM:613588; AllianceGenome:HGNC:2052
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CLECSF1
    Summary
    Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in urinary bladder (RPKM 4.3), gall bladder (RPKM 1.0) and 1 other tissue See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CLEC3A in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (78022548..78032101)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (84078524..84088079)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (78056445..78065998)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene vesicle amine transport 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:77928177-77928677 Neighboring gene peptidylprolyl isomerase A pseudogene 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:77952963-77953462 Neighboring gene uncharacterized LOC105371351 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11154 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78000722-78001339 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78001340-78001958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78003196-78003813 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78025071-78026270 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026297-78026990 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:78026991-78027683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:78028377-78029069 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:78029289-78030488 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45524 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7735 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45593 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45596 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45605 Neighboring gene uncharacterized LOC107984897 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_45663 Neighboring gene leucine rich repeat containing 59 pseudogene Neighboring gene keratin 8 pseudogene 22

    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
    Gene-alcohol interactions identify several novel blood pressure loci including a promising locus near SLC16A9.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC129558, MGC129559

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in ossification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    C-type lectin domain family 3 member A
    Names
    C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)

    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_005752.6NP_005743.5  C-type lectin domain family 3 member A precursor

      Status: VALIDATED

      Source sequence(s)
      AC079414, AK313316, AY358376
      Consensus CDS
      CCDS10927.3
      UniProtKB/Swiss-Prot
      B2R8C4, O75596, Q3SX91, Q6UXF5
      UniProtKB/TrEMBL
      Q3SX92
      Related
      ENSP00000299642.5, ENST00000299642.10
      Conserved Domains (1) summary
      cd03596
      Location:68193
      CLECT_tetranectin_like; C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      78022548..78032101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      84078524..84088079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001244755.1: Suppressed sequence

      Description
      NM_001244755.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.