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

Gene ID: 10332, updated on 26-May-2016
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 HPRD:12060; MIM:605872; Vega:OTTHUMG00000182432
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]
Orthologs
Location:
19p13
Exon count:
9
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 19 NC_000019.10 (7763054..7770558)
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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • 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...
Products Interactant Other Gene Complex Source Pubs Description

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 
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 
regulation of blood coagulation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IMP
Inferred from Mutant Phenotype
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
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
Preferred Names
C-type lectin domain family 4 member M
Names
C-type lectin domain family 4, member M
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
liver/lymph node-specific ICAM-3-grabbing non-integrin
mannose binding C-type lectin DC-SIGNR

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, ENST00000334806
    Conserved Domains (2) 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)
    pfam06156
    Location:82179
    DUF972; Protein of unknown function (DUF972)
  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 (2) 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)
    pfam06156
    Location:109206
    DUF972; Protein of unknown function (DUF972)
  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, OTTHUMP00000269250, ENST00000595496, OTTHUMT00000461166
    Conserved Domains (2) 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)
    pfam10018
    Location:73121
    Med4; Vitamin-D-receptor interacting Mediator subunit 4
  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, ENST00000359059
    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
    DUF964; Protein of unknown function (DUF964)
  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, OTTHUMP00000269249, ENST00000597522, OTTHUMT00000461165
    Conserved Domains (2) summary
    cl02432
    Location:176220
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    cl19219
    Location:92172
    DUF342; Protein of unknown function (DUF342)
  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)
    pfam06156
    Location:96184
    DUF972; Protein of unknown function (DUF972)
  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 (2) 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)
    pfam06156
    Location:110207
    DUF972; Protein of unknown function (DUF972)
  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, OTTHUMP00000269247, ENST00000596363, OTTHUMT00000461162
    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, OTTHUMP00000269246, ENST00000327325, OTTHUMT00000461161
    Conserved Domains (3) 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)
    pfam06156
    Location:96184
    DUF972; Protein of unknown function (DUF972)
    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 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p2 Primary Assembly

    Range
    7763054..7770558
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722613.2XP_006722676.1  

    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:64154
    DUF342; Protein of unknown function (DUF342)
  2. XM_006722612.2XP_006722675.1  

    Related
    ENSP00000470137, OTTHUMP00000269248, ENST00000596707, OTTHUMT00000461164
    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:64154
    DUF342; Protein of unknown function (DUF342)
  3. XM_006722615.1XP_006722678.1  

    UniProtKB/Swiss-Prot
    Q9H2X3
    Related
    ENSP00000470286, OTTHUMP00000269344, ENST00000595751, OTTHUMT00000461344
    Conserved Domains (2) summary
    cl02432
    Location:268312
    CLECT; C-type lectin (CTL)/C-type lectin-like (CTLD) domain
    cl19219
    Location:92182
    DUF342; Protein of unknown function (DUF342)
  4. XM_006722611.2XP_006722674.1  

    Conserved Domains (3) 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)
    pfam06156
    Location:95183
    DUF972; Protein of unknown function (DUF972)
    cl19219
    Location:139250
    DUF342; Protein of unknown function (DUF342)
  5. XM_006722614.2XP_006722677.1  

    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:36126
    DUF342; Protein of unknown function (DUF342)

RNA

  1. XR_936147.1 RNA Sequence

  2. XR_430125.2 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018930.2 Alternate CHM1_1.1

    Range
    7827770..7834226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.