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CLEC4M C-type lectin domain family 4 member M [ Homo sapiens (human) ]

Gene ID: 10332, updated on 8-Dec-2018

Summary

Official Symbol
CLEC4Mprovided by HGNC
Official Full Name
C-type lectin domain family 4 member Mprovided by HGNC
Primary source
HGNC:HGNC:13523
See related
Ensembl:ENSG00000104938 MIM:605872
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
CD299; LSIGN; CD209L; L-SIGN; DCSIGNR; HP10347; DC-SIGN2; DC-SIGNR
Summary
This gene encodes a transmembrane receptor and is often referred to as L-SIGN because of its expression in the endothelial cells of the lymph nodes and liver. The encoded protein is involved in the innate immune system and recognizes numerous evolutionarily divergent pathogens ranging from parasites to viruses, with a large impact on public health. The protein is organized into three distinct domains: an N-terminal transmembrane domain, a tandem-repeat neck domain and C-type lectin carbohydrate recognition domain. The extracellular region consisting of the C-type lectin and neck domains has a dual function as a pathogen recognition receptor and a cell adhesion receptor by binding carbohydrate ligands on the surface of microbes and endogenous cells. The neck region is important for homo-oligomerization which allows the receptor to bind multivalent ligands with high avidity. Variations in the number of 23 amino acid repeats in the neck domain of this protein are common and have a significant impact on ligand binding ability. This gene is closely related in terms of both sequence and function to a neighboring gene (GeneID 30835; often referred to as DC-SIGN or CD209). DC-SIGN and L-SIGN differ in their ligand-binding properties and distribution. Alternative splicing results in multiple variants.[provided by RefSeq, Feb 2009]
Expression
Biased expression in liver (RPKM 15.4), lymph node (RPKM 9.8) and 3 other tissues See more
Orthologs

Genomic context

See CLEC4M in Genome Data Viewer
Location:
19p13.2
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (7763052..7770559)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (7828035..7834491)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 pseudogene Neighboring gene CD209 molecule Neighboring gene ribosomal protein L21 pseudogene 129 Neighboring gene uncharacterized LOC105372263 Neighboring gene C-type lectin domain family 4 member G pseudogene 1

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Crystal structures of carbohydrate-recognition domains of DC-SIGN and of DC-SIGNR in combination with binding studies reveal that these receptors selectively recognize endogenous high-mannose oligosaccharides of HIV-1 gp120 PubMed
env HIV-1 gp120 binds to a membrane-associated mannose-binding lectin in a CD4-independent manner PubMed
env L-SIGN behaves similarly to DC-SIGN in that it has a high affinity for ICAM-3, captures HIV-1 through gp120 binding, and enhances HIV-1 infection of T cells in trans PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Measles, organism-specific biosystem (from KEGG)
    Measles, organism-specific biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Measles, conserved biosystem (from KEGG)
    Measles, conserved biosystemMeasles virus (MV) is highly contagious virus that leads infant death worldwide. Humans are the unique natural reservoir for this virus. It causes severe immunosuppression favouring secondary bacteri...
  • Phagosome, organism-specific biosystem (from KEGG)
    Phagosome, organism-specific biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • Phagosome, conserved biosystem (from KEGG)
    Phagosome, conserved biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • Tuberculosis, organism-specific biosystem (from KEGG)
    Tuberculosis, organism-specific biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Tuberculosis, conserved biosystem (from KEGG)
    Tuberculosis, conserved biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC47866, MGC129964

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ICAM-3 receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
calcium-dependent protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
carbohydrate binding NAS
Non-traceable Author Statement
more info
PubMed 
mannose binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
peptide antigen binding NAS
Non-traceable Author Statement
more info
PubMed 
signaling receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
virion binding TAS
Traceable Author Statement
more info
PubMed 
virus receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
virus receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
antigen processing and presentation NAS
Non-traceable Author Statement
more info
PubMed 
cell-cell recognition TAS
Traceable Author Statement
more info
PubMed 
endocytosis IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
intracellular signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
intracellular transport of virus TAS
Traceable Author Statement
more info
PubMed 
leukocyte cell-cell adhesion NAS
Non-traceable Author Statement
more info
PubMed 
modulation by virus of host morphology or physiology TAS
Traceable Author Statement
more info
PubMed 
peptide antigen transport NAS
Non-traceable Author Statement
more info
PubMed 
viral entry into host cell IEA
Inferred from Electronic Annotation
more info
 
viral genome replication NAS
Non-traceable Author Statement
more info
PubMed 
virion attachment to host cell TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
host cell IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
C-type lectin domain family 4 member M
Names
CD209 antigen-like protein 1
CD299 antigen
DC-SIGN-related protein
dendritic cell-specific ICAM-3-grabbing non-integrin 2
liver/lymph node-specific ICAM-3 grabbing non-integrin
mannose binding C-type lectin DC-SIGNR

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_029190.1 RefSeqGene

    Range
    5001..11457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001144904.1NP_001138376.1  C-type lectin domain family 4 member M isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon and uses an alternative splice site in the coding region and maintains the reading frame. This results in a shorter protein (isoform 2) compared to isoform 1. This isoform (2) has 6.5 repeats in the neck domain.
    Source sequence(s)
    AC008812, AK304499, BQ008265, DB048428
    UniProtKB/TrEMBL
    B4E2Z5, H7BXU4
    Related
    ENSP00000335228.5, ENST00000334806.9
    Conserved Domains (1) summary
    cd03590
    Location:217340
    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_001144905.1NP_001138377.1  C-type lectin domain family 4 member M isoform 12

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 12, which is shorter than isoform 1. The encoded isoform (12) has 6.5 repeats in the neck domain.
    Source sequence(s)
    AC008812, AK314704, BC038851, DB048428
    UniProtKB/Swiss-Prot
    Q9H2X3
    Conserved Domains (1) summary
    cd03590
    Location:244367
    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_001144906.1NP_001138378.1  C-type lectin domain family 4 member M isoform 7

    See identical proteins and their annotated locations for NP_001138378.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an exon and uses an alternate in-frame splice site in the coding region compared to variant 1. This results in a shorter protein (isoform 7) compared to isoform 1. The encoded isoform (7) lacks a transmembrane domain and has 2.5 repeats in the neck domain.
    Source sequence(s)
    AC008812, AY042240, BC038851, DB048428
    Consensus CDS
    CCDS59347.1
    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000470132.1, ENST00000595496.1
    Conserved Domains (1) summary
    cd03590
    Location:132255
    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_001144907.1NP_001138379.1  C-type lectin domain family 4 member M isoform 11

    See identical proteins and their annotated locations for NP_001138379.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 11) has a distinct C-terminus and is shorter than isoform 1. The encoded isoform (11) lacks a transmembrane domain and has 5.5 repeats in the neck domain.
    Source sequence(s)
    AY042238, BC038851, DB048428
    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000351954.5, ENST00000359059.9
    Conserved Domains (2) summary
    cd03590
    Location:201324
    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)
    cl01483
    Location:89197
    Com_YlbF; Control of competence regulator ComK, YlbF/YmcA
  5. NM_001144908.1NP_001138380.1  C-type lectin domain family 4 member M isoform 10

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 10) has a distinct C-terminus and is shorter than isoform 1. The encoded isoform (10) has 3.5 repeats in the neck domain.
    Source sequence(s)
    AC008812, AY042237, BC038851, DB048428
    Consensus CDS
    CCDS59346.1
    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000471132.1, ENST00000597522.5
    Conserved Domains (2) summary
    pfam05816
    Location:83172
    TelA; Toxic anion resistance protein (TelA)
    cl02432
    Location:176220
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
  6. NM_001144909.1NP_001138381.1  C-type lectin domain family 4 member M isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 9) compared to isoform 1. The encoded isoform (9) has 5.5 repeats in the neck domain.
    Source sequence(s)
    AC008812, AY343913, BC038851, DB048428
    UniProtKB/Swiss-Prot
    Q9H2X3
    Conserved Domains (2) summary
    cd03590
    Location:222345
    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)
    cl01234
    Location:60196
    PilO; Pilus assembly protein, PilO
  7. NM_001144910.1NP_001138382.1  C-type lectin domain family 4 member M isoform 8

    See identical proteins and their annotated locations for NP_001138382.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) uses an alternate in-frame splice site in the coding region, compared to variant 1. This results in a shorter protein (isoform 8) compared to isoform 1. The encoded isoform (8) has 6.5 repeats in the neck domain.
    Source sequence(s)
    AF290887, BC038851, DB048428
    UniProtKB/Swiss-Prot
    Q9H2X3
    Conserved Domains (1) summary
    cd03590
    Location:245368
    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)
  8. NM_001144911.1NP_001138383.1  C-type lectin domain family 4 member M isoform 3

    See identical proteins and their annotated locations for NP_001138383.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region, compared to variant 1, one of which results in a translational frameshift. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB015629, BC038851, DB048428
    Consensus CDS
    CCDS59348.1
    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000471125.1, ENST00000596363.5
    Conserved Domains (1) summary
    cl02432
    Location:240284
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
  9. NM_014257.4NP_055072.3  C-type lectin domain family 4 member M isoform 1

    See identical proteins and their annotated locations for NP_055072.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC038851, DB048428
    Consensus CDS
    CCDS12187.1
    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000316228.4, ENST00000327325.9
    Conserved Domains (2) summary
    cd03590
    Location:268391
    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)
    cl19219
    Location:140251
    DUF342; Protein of unknown function (DUF342)

RNA

  1. NR_026707.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences in the coding region, compared to variant 1. This variant 4 replaces NM_214677 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA431250, AY042235, BC038851, BX102225, DB048428
  2. NR_026708.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences in the coding region, compared to variant 1. This variant 5 replaces NM_214678 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA431250, AY042236, BC038851, BX102225, DB048428
  3. NR_026709.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences in the coding region, compared to variant 1. This variant 6 replaces NM_214679 and is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA431250, AC008812, AY042239, BC038851, BX102225

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    7763052..7770559
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722613.3XP_006722676.1  C-type lectin domain family 4 member M isoform X3

    Conserved Domains (2) summary
    cd03590
    Location:240363
    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)
    cl19219
    Location:112223
    DUF342; Protein of unknown function (DUF342)
  2. XM_006722614.3XP_006722677.1  C-type lectin domain family 4 member M isoform X4

    Conserved Domains (2) summary
    cd03590
    Location:212335
    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)
    cl19219
    Location:84195
    DUF342; Protein of unknown function (DUF342)
  3. XM_006722612.3XP_006722675.1  C-type lectin domain family 4 member M isoform X2

    Related
    ENSP00000470137.1, ENST00000596707.5
    Conserved Domains (2) summary
    cd03590
    Location:240363
    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)
    cl19219
    Location:112223
    DUF342; Protein of unknown function (DUF342)
  4. XM_006722615.2XP_006722678.1  C-type lectin domain family 4 member M isoform X5

    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000470286.1, ENST00000595751.5
    Conserved Domains (2) summary
    cl02432
    Location:268312
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    cl19219
    Location:140251
    DUF342; Protein of unknown function (DUF342)
  5. XM_006722611.2XP_006722674.1  C-type lectin domain family 4 member M isoform X1

    Conserved Domains (2) summary
    cd03590
    Location:267390
    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)
    cl19219
    Location:139250
    DUF342; Protein of unknown function (DUF342)

RNA

  1. XR_001753583.1 RNA Sequence

  2. XR_936147.2 RNA Sequence

  3. XR_430125.2 RNA Sequence

  4. XR_001753584.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_214675.1: Suppressed sequence

    Description
    NM_214675.1: This RefSeq was permanently suppressed because it is redundant.
  2. NM_214676.1: Suppressed sequence

    Description
    NM_214676.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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