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

    Gene ID: 10332, updated on 20-Apr-2017
    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; 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:
    19p13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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

    • 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

    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
    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

    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, OTTHUMP00000269250, ENST00000595496.1, OTTHUMT00000461166
      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, OTTHUMP00000269249, ENST00000597522.5, OTTHUMT00000461165
      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, OTTHUMP00000269247, ENST00000596363.5, 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
      ENSP00000316228.4, OTTHUMP00000269246, ENST00000327325.9, OTTHUMT00000461161
      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 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p7 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, OTTHUMP00000269248, ENST00000596707.5, 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: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, OTTHUMP00000269344, ENST00000595751.5, OTTHUMT00000461344
      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

    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.
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