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CLEC3B C-type lectin domain family 3 member B [ Homo sapiens (human) ]

Gene ID: 7123, updated on 13-Aug-2022

Summary

Official Symbol
CLEC3Bprovided by HGNC
Official Full Name
C-type lectin domain family 3 member Bprovided by HGNC
Primary source
HGNC:HGNC:11891
See related
Ensembl:ENSG00000163815 MIM:187520; AllianceGenome:HGNC:11891
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
TN; TNA; MCDR4
Summary
Enables calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in bone mineralization and cellular response to transforming growth factor beta stimulus. Located in cytoplasm; extracellular space; and granular component. Part of collagen-containing extracellular matrix. Implicated in osteoarthritis. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in spleen (RPKM 63.9), fat (RPKM 63.1) and 20 other tissues See more
Orthologs
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Genomic context

See CLEC3B in Genome Data Viewer
Location:
3p21.31
Exon count:
4
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45026303..45036071)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45042041..45051809)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45067795..45077563)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type palmitoyltransferase 3 Neighboring gene ribosomal protein L12 pseudogene 44 Neighboring gene exosome component 7 Neighboring gene RNA, U5B small nuclear 3, pseudogene Neighboring gene uncharacterized LOC124906233 Neighboring gene CUB domain containing protein 1 Neighboring gene Sharpr-MPRA regulatory region 12576

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
Macular dystrophy, retinal, 4
MedGen: CN315822 OMIM: 619977 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686H17246

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
enables carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
enables heparin binding IDA
Inferred from Direct Assay
more info
PubMed 
enables kringle domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in bone mineralization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in bone mineralization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in bone mineralization IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to organic substance IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in cellular response to transforming growth factor beta stimulus IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in ossification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in ossification IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in positive regulation of plasminogen activation ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
tetranectin
Names
plasminogen kringle 4-binding protein
tetranectin (plasminogen-binding protein)

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.

mRNA and Protein(s)

  1. NM_001308394.2NP_001295323.1  tetranectin isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks a 5' exon and contains an alternate 5' terminal exon, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    BI826174, BI826652, BM669340, CD616729
    Consensus CDS
    CCDS77730.1
    UniProtKB/TrEMBL
    E9PHK0
    Related
    ENSP00000396013.1, ENST00000428034.1
    Conserved Domains (1) summary
    cd03596
    Location:29157
    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)
  2. NM_003278.3NP_003269.2  tetranectin isoform 1precursor

    See identical proteins and their annotated locations for NP_003269.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC104165, BC011024, BI837909
    Consensus CDS
    CCDS2726.1
    UniProtKB/Swiss-Prot
    P05452, Q6FGX6
    UniProtKB/TrEMBL
    A0A024R2Q7
    Related
    ENSP00000296130.4, ENST00000296130.5
    Conserved Domains (1) summary
    cd03596
    Location:71199
    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: 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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    45026303..45036071
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007116.2XP_016862605.1  tetranectin isoform X1

    Conserved Domains (1) summary
    cd03596
    Location:38166
    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)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    45042041..45051809
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)