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CLEC4A C-type lectin domain family 4 member A [ Homo sapiens (human) ]

Gene ID: 50856, updated on 20-Mar-2020

Summary

Official Symbol
CLEC4Aprovided by HGNC
Official Full Name
C-type lectin domain family 4 member Aprovided by HGNC
Primary source
HGNC:HGNC:13257
See related
Ensembl:ENSG00000111729 Ensembl:ENSG00000284697 MIM:605306
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
DCIR; LLIR; CD367; DDB27; CLECSF6; HDCGC13P
Summary
This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may play a role in inflammatory and immune response. Multiple transcript variants encoding distinct isoforms have been identified for this gene. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]
Expression
Broad expression in appendix (RPKM 5.2), bone marrow (RPKM 2.2) and 20 other tissues See more
Orthologs

Genomic context

See CLEC4A in Genome Data Viewer
Location:
12p13.31
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (8102902..8138607)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (8276228..8291203)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene complement C3a receptor 1 Neighboring gene NECAP endocytosis associated 1 Neighboring gene POU class 5 homeobox 1 pseudogene 3 Neighboring gene glycine cleavage system protein H pseudogene 4 Neighboring gene zinc finger protein 705A

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 Env gp120/41 (JRFL Env in the contaxt of HIV-Gag-GFP VLP) binds to CLEC4A (DCIR) on the surface of basophils PubMed
env DCIR is less efficient than DC-SIGN in capturing a wide range of HIV-1 isolates and transferring them to target cells, and exhibits a distinct binding affinity to gp120 compared to that of DC-SIGN to gp120 PubMed
env HIV-1 gp140 trimers bind to dendritic cell immunoreceptor (DCIR) more strongly than HIV-1 gp120 proteins PubMed
Envelope surface glycoprotein gp160, precursor env HIV-1 gp140 trimers bind to dendritic cell immunoreceptor (DCIR) more strongly than HIV-1 gp120 proteins PubMed
env Soluble DCIR has a lesser binding affinity to HIV-1 gp140 than soluble DC-SIGN 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
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
carbohydrate binding IDA
Inferred from Direct Assay
more info
PubMed 
mannose binding IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane signaling receptor activity TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
C-type lectin domain family 4 member A
Names
C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6
C-type lectin DDB27
C-type lectin superfamily member 6
dendritic cell immunoreceptor
lectin-like immunoreceptor

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.

mRNA and Protein(s)

  1. NM_016184.3NP_057268.1  C-type lectin domain family 4 member A isoform 1

    See identical proteins and their annotated locations for NP_057268.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longest isoform (1).
    Source sequence(s)
    AC006511, AF067800, AI400631, AJ133532
    Consensus CDS
    CCDS8590.1
    UniProtKB/Swiss-Prot
    Q9UMR7
    Related
    ENSP00000229332.5, ENST00000229332.11
    Conserved Domains (1) summary
    cd03590
    Location:106232
    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)
  2. NM_194447.2NP_919429.2  C-type lectin domain family 4 member A isoform 3

    See identical proteins and their annotated locations for NP_919429.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as LLIRv1, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (3), that is missing the transmembrane domain compared to isoform 1.
    Source sequence(s)
    AC006511, AF067800, AI400631, AJ133532
    Consensus CDS
    CCDS41745.1
    UniProtKB/Swiss-Prot
    Q9UMR7
    Related
    ENSP00000353690.3, ENST00000360500.5
    Conserved Domains (1) summary
    cd03590
    Location:67193
    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)
  3. NM_194448.2NP_919430.1  C-type lectin domain family 4 member A isoform 4

    See identical proteins and their annotated locations for NP_919430.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), also known as LLIRv2, lacks an in-frame segment of the coding region, compared to variant 1. It encodes the shortest isoform (4), that is missing a region thought to be responsible for oligomerization, compared to isoform 1.
    Source sequence(s)
    AC006511, AF067800, AI400631, AJ133532
    Consensus CDS
    CCDS8591.1
    UniProtKB/Swiss-Prot
    Q9UMR7
    Related
    ENSP00000344646.3, ENST00000345999.9
    Conserved Domains (1) summary
    cd03590
    Location:34160
    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)
  4. NM_194450.2NP_919432.1  C-type lectin domain family 4 member A isoform 2

    See identical proteins and their annotated locations for NP_919432.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as C-type lectin DDB27 short form, lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (2), that is missing the transmembrane domain compared to isoform 1.
    Source sequence(s)
    AC006511, AF067800, AI400631, AJ133532
    Consensus CDS
    CCDS8592.1
    UniProtKB/Swiss-Prot
    Q9UMR7
    Related
    ENSP00000247243.5, ENST00000352620.9
    Conserved Domains (1) summary
    cd03590
    Location:73199
    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)

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_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    8102902..8138607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448997.1XP_024304765.1  C-type lectin domain family 4 member A isoform X2

    Conserved Domains (1) summary
    cd03590
    Location:11137
    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)
  2. XM_017019382.2XP_016874871.1  C-type lectin domain family 4 member A isoform X2

    Related
    ENST00000546339.2
    Conserved Domains (1) summary
    cd03590
    Location:11137
    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)
  3. XM_011520684.2XP_011518986.1  C-type lectin domain family 4 member A isoform X1

    Conserved Domains (1) summary
    cd03590
    Location:69195
    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)
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