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CLEC12A C-type lectin domain family 12 member A [ Homo sapiens (human) ]

Gene ID: 160364, updated on 14-Oct-2018

Summary

Official Symbol
CLEC12Aprovided by HGNC
Official Full Name
C-type lectin domain family 12 member Aprovided by HGNC
Primary source
HGNC:HGNC:31713
See related
Ensembl:ENSG00000172322 MIM:612088; Vega:OTTHUMG00000168396
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
CLL1; MICL; CD371; CLL-1; DCAL-2
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 signaling, glycoprotein turnover, and roles in inflammation and immune response. The protein encoded by this gene is a negative regulator of granulocyte and monocyte function. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. This gene is closely linked to other CTL/CTLD superfamily members in the natural killer gene complex region on chromosome 12p13. [provided by RefSeq, May 2011]
Expression
Biased expression in bone marrow (RPKM 14.2), appendix (RPKM 4.4) and 7 other tissues See more
Orthologs

Genomic context

See CLEC12A in Genome Data Viewer
Location:
12p13.31
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (9951316..9995209)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10103915..10147704)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene C-type lectin domain family 2 member A Neighboring gene killer cell lectin like receptor F2 Neighboring gene long intergenic non-protein coding RNA 2470 Neighboring gene CLEC12A antisense RNA 1 Neighboring gene C-type lectin domain family 1 member B Neighboring gene uncharacterized LOC102724020 Neighboring gene uncharacterized LOC112268091 Neighboring gene C-type lectin domain family 12 member B Neighboring gene C-type lectin domain family 1 member B pseudogene Neighboring gene C-type lectin domain containing 9A

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC70602

Gene Ontology Provided by GOA

Function Evidence Code Pubs
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
neutrophil degranulation TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
specific granule membrane TAS
Traceable Author Statement
more info
 
tertiary granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
C-type lectin domain family 12 member A
Names
C-type lectin protein CLL-1
C-type lectin-like molecule-1
dendritic cell-associated lectin 2
myeloid inhibitory C-type lectin-like receptor

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.

Genomic

  1. NG_029426.1 RefSeqGene

    Range
    5001..39280
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001207010.1NP_001193939.1  C-type lectin domain family 12 member A isoform 3

    See identical proteins and their annotated locations for NP_001193939.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. This variant encodes isoform 3, which has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AY547296
    Consensus CDS
    CCDS55803.1
    UniProtKB/Swiss-Prot
    Q5QGZ9
    Related
    ENSP00000347916.4, OTTHUMP00000238691, ENST00000355690.8, OTTHUMT00000399552
    Conserved Domains (1) summary
    cd03593
    Location:143260
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  2. NM_001300730.1NP_001287659.1  C-type lectin domain family 12 member A isoform 4

    See identical proteins and their annotated locations for NP_001287659.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant 3. These differences result in distinct 5' and 3' UTRs, and cause translation initiation at a downstream start codon, compared to variant 3. The encoded isoform (4) has a shorter N-terminus, and a distinct C-terminus, compared to isoform 3.
    Source sequence(s)
    BC063424, CD642076
    Consensus CDS
    CCDS73442.1
    UniProtKB/Swiss-Prot
    Q5QGZ9
    Related
    ENSP00000405244.2, OTTHUMP00000238684, ENST00000434319.6, OTTHUMT00000399546
    Conserved Domains (1) summary
    cd03593
    Location:133212
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  3. NM_138337.5NP_612210.4  C-type lectin domain family 12 member A isoform 1

    See identical proteins and their annotated locations for NP_612210.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1, also referred to as alpha).
    Source sequence(s)
    AY547296, BC126289, CD642076
    Consensus CDS
    CCDS8608.1
    UniProtKB/Swiss-Prot
    Q5QGZ9
    Related
    ENSP00000302804.4, OTTHUMP00000238683, ENST00000304361.8, OTTHUMT00000399545
    Conserved Domains (1) summary
    cd03593
    Location:133250
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  4. NM_201623.3NP_963917.2  C-type lectin domain family 12 member A isoform 2

    See identical proteins and their annotated locations for NP_963917.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2, also referred to as beta), compared to isoform 1.
    Source sequence(s)
    AY498551, AY547296, CD642076
    Consensus CDS
    CCDS8609.1
    UniProtKB/Swiss-Prot
    Q5QGZ9
    Related
    ENSP00000345448.4, OTTHUMP00000238686, ENST00000350667.4, OTTHUMT00000399548
    Conserved Domains (1) summary
    cd03593
    Location:100217
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    9951316..9995209
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520570.1XP_011518872.1  C-type lectin domain family 12 member A isoform X2

    See identical proteins and their annotated locations for XP_011518872.1

    UniProtKB/Swiss-Prot
    Q5QGZ9
    Conserved Domains (1) summary
    cd03593
    Location:133250
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  2. XM_006719035.3XP_006719098.1  C-type lectin domain family 12 member A isoform X4

    Conserved Domains (1) summary
    cd03593
    Location:150229
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  3. XM_011520573.2XP_011518875.1  C-type lectin domain family 12 member A isoform X5

    Conserved Domains (1) summary
    cd03593
    Location:150229
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  4. XM_006719033.3XP_006719096.1  C-type lectin domain family 12 member A isoform X1

    Conserved Domains (1) summary
    cd03593
    Location:150267
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  5. XM_006719036.3XP_006719099.1  C-type lectin domain family 12 member A isoform X6

    Conserved Domains (1) summary
    cd03593
    Location:150229
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)
  6. XM_011520571.2XP_011518873.2  C-type lectin domain family 12 member A isoform X3

  7. XM_005253324.2XP_005253381.1  C-type lectin domain family 12 member A isoform X2

    See identical proteins and their annotated locations for XP_005253381.1

    UniProtKB/Swiss-Prot
    Q5QGZ9
    Conserved Domains (1) summary
    cd03593
    Location:133250
    CLECT_NK_receptors_like; C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_201625.1: Suppressed sequence

    Description
    NM_201625.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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