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    SIGLEC6 sialic acid binding Ig like lectin 6 [ Homo sapiens (human) ]

    Gene ID: 946, updated on 13-Feb-2019

    Summary

    Official Symbol
    SIGLEC6provided by HGNC
    Official Full Name
    sialic acid binding Ig like lectin 6provided by HGNC
    Primary source
    HGNC:HGNC:10875
    See related
    Ensembl:ENSG00000105492 MIM:604405
    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
    CD327; CD33L; OBBP1; CD33L1; CD33L2; CDW327
    Summary
    This gene encodes a member of the SIGLEC (sialic acid binding immunoglobulin-like lectin) family of proteins. The encoded transmembrane receptor binds sialyl-TN glycans and leptin. Placental expression of the encoded protein is upregulated in preeclampsia. [provided by RefSeq, Jul 2016]
    Expression
    Biased expression in placenta (RPKM 50.1) and lung (RPKM 2.3) See more
    Orthologs

    Genomic context

    See SIGLEC6 in Genome Data Viewer
    Location:
    19q13.41
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (51517819..51531856, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (52020951..52035110, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene carcinoembryonic antigen related cell adhesion molecule 18 Neighboring gene sialic acid binding Ig like lectin 12 (gene/pseudogene) Neighboring gene sialic acid binding Ig like lectin 27, pseudogene Neighboring gene sialic acid binding Ig like lectin 28, pseudogene Neighboring gene sialic acid binding Ig like lectin 29, pseudogene

    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?

    Pathways from BioSystems

    • Adaptive Immune System, organism-specific biosystem (from REACTOME)
      Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
    • 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...
    • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
      Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    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 

    General protein information

    Preferred Names
    sialic acid-binding Ig-like lectin 6
    Names
    CD33 antigen-like 1
    obesity-binding protein 1

    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_051195.1 RefSeqGene

      Range
      5004..19041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177547.2NP_001171018.1  sialic acid-binding Ig-like lectin 6 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate, in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      AC020914, AK300170, BC035359, D86359
      Consensus CDS
      CCDS54307.1
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000410679.1, ENST00000436458.5
      Conserved Domains (3) summary
      pfam07679
      Location:202284
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28105
      Ig; Immunoglobulin domain
    2. NM_001177548.2NP_001171019.1  sialic acid-binding Ig-like lectin 6 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate, in-frame splice site and lacks an exon in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC020914, AK300182, BC035359, D86359
      Consensus CDS
      CCDS54308.1
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000353071.4, ENST00000359982.8
      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    3. NM_001177549.2NP_001171020.1  sialic acid-binding Ig-like lectin 6 isoform 6 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate, in-frame splice site and lacks two exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC020914, BC035359, BC140798, D86359
      Consensus CDS
      CCDS59417.1
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000375674.3, ENST00000391797.3
      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:243325
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:143207
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    4. NM_001245.7NP_001236.4  sialic acid-binding Ig-like lectin 6 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001236.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC020914, BC035359
      Consensus CDS
      CCDS12834.3
      UniProtKB/Swiss-Prot
      O43699
      UniProtKB/TrEMBL
      A0A024R4K4
      Related
      ENSP00000401502.2, ENST00000425629.7
      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    5. NM_198845.5NP_942142.3  sialic acid-binding Ig-like lectin 6 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC020914, BC035359, D86359
      Consensus CDS
      CCDS12835.3
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000344064.4, ENST00000346477.7
      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:238320
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    6. NM_198846.5NP_942143.3  sialic acid-binding Ig-like lectin 6 isoform 3 precursor

      See identical proteins and their annotated locations for NP_942143.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC020914, BC035359, D86359
      Consensus CDS
      CCDS12836.3
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000345907.4, ENST00000343300.8
      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain

    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
      51517819..51531856 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527536.3XP_011525838.1  sialic acid-binding Ig-like lectin 6 isoform X4

      Conserved Domains (3) summary
      pfam07679
      Location:229311
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28105
      Ig; Immunoglobulin domain
    2. XM_011527535.3XP_011525837.1  sialic acid-binding Ig-like lectin 6 isoform X3

      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:143207
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    3. XM_011527538.3XP_011525840.1  sialic acid-binding Ig-like lectin 6 isoform X6

      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    4. XM_011527533.3XP_011525835.1  sialic acid-binding Ig-like lectin 6 isoform X1

      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    5. XM_011527537.2XP_011525839.1  sialic acid-binding Ig-like lectin 6 isoform X5

      Conserved Domains (3) summary
      pfam07679
      Location:218300
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28105
      Ig; Immunoglobulin domain
    6. XM_011527539.3XP_011525841.1  sialic acid-binding Ig-like lectin 6 isoform X8

      Conserved Domains (3) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    7. XM_011527534.3XP_011525836.1  sialic acid-binding Ig-like lectin 6 isoform X2

      Conserved Domains (4) summary
      smart00410
      Location:36141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31141
      Ig; Immunoglobulin domain
    8. XM_017027511.2XP_016883000.1  sialic acid-binding Ig-like lectin 6 isoform X7

    RNA

    1. XR_935877.3 RNA Sequence

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