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Clec4a2 C-type lectin domain family 4, member a2 [ Mus musculus (house mouse) ]

Gene ID: 26888, updated on 8-Dec-2022

Summary

Official Symbol
Clec4a2provided by MGI
Official Full Name
C-type lectin domain family 4, member a2provided by MGI
Primary source
MGI:MGI:1349412
See related
Ensembl:ENSMUSG00000030148 AllianceGenome:MGI:1349412
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
DCIR; Dcir1; Clec4a; Clecsf6
Summary
Predicted to enable calcium ion binding activity and mannose binding activity. Predicted to be involved in several processes, including antifungal innate immune response; negative regulation of tumor necrosis factor production; and plasmacytoid dendritic cell antigen processing and presentation. Predicted to act upstream of or within adaptive immune response and innate immune response. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane. Orthologous to human CLEC4A (C-type lectin domain family 4 member A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in liver E18 (RPKM 3.2), bladder adult (RPKM 1.3) and 13 other tissues See more
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Genomic context

See Clec4a2 in Genome Data Viewer
Location:
6 F2; 6 58.18 cM
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (123099649..123120958)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (123122690..123143999)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 4, member a4 Neighboring gene C-type lectin domain family 4, member b1 Neighboring gene C-type lectin domain family 4, member b2 Neighboring gene predicted gene, 22946 Neighboring gene peptidylprolyl isomerase A pseudogene 6_1344.1

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (3) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables calcium ion binding ISO
Inferred from Sequence Orthology
more info
 
enables carbohydrate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables carbohydrate binding ISO
Inferred from Sequence Orthology
more info
 
enables carbohydrate binding TAS
Traceable Author Statement
more info
PubMed 
enables mannose binding ISO
Inferred from Sequence Orthology
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
involved_in antifungal innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within innate immune response IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
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 superfamily member 6
dendritic cell immunoreceptor

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_001170332.2NP_001163803.1  C-type lectin domain family 4 member A isoform b

    See identical proteins and their annotated locations for NP_001163803.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AC164111
    Consensus CDS
    CCDS20510.1
    UniProtKB/Swiss-Prot
    Q4VA33, Q9QZ15
    Related
    ENSMUSP00000124615.2, ENSMUST00000161365.8
    Conserved Domains (1) summary
    cd03590
    Location:107233
    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_001170333.2NP_001163804.1  C-type lectin domain family 4 member A isoform a

    See identical proteins and their annotated locations for NP_001163804.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC164111
    Consensus CDS
    CCDS51894.1
    UniProtKB/Swiss-Prot
    Q9QZ15
    UniProtKB/TrEMBL
    Q923C7
    Related
    ENSMUSP00000032248.8, ENSMUST00000032248.8
    Conserved Domains (1) summary
    cd03590
    Location:131257
    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_001410583.1NP_001397512.1  C-type lectin domain family 4 member A isoform c

    Status: VALIDATED

    Source sequence(s)
    AC164111
  4. NM_001410584.1NP_001397513.1  C-type lectin domain family 4 member A isoform d

    Status: VALIDATED

    Source sequence(s)
    AC164111
  5. NM_011999.5NP_036129.1  C-type lectin domain family 4 member A isoform b

    See identical proteins and their annotated locations for NP_036129.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AC164111
    Consensus CDS
    CCDS20510.1
    UniProtKB/Swiss-Prot
    Q4VA33, Q9QZ15
    Related
    ENSMUSP00000045781.7, ENSMUST00000041779.13
    Conserved Domains (1) summary
    cd03590
    Location:107233
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    123099649..123120958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011241364.4XP_011239666.1  C-type lectin domain family 4 member A isoform X2

    Conserved Domains (1) summary
    cl02432
    Location:131177
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
  2. XM_030255403.2XP_030111263.1  C-type lectin domain family 4 member A isoform X3

    Conserved Domains (1) summary
    cl02432
    Location:107153
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
  3. XM_006506155.2XP_006506218.1  C-type lectin domain family 4 member A isoform X1

    UniProtKB/TrEMBL
    C6EQI8
    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)