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

    Gene ID: 946, updated on 10-Dec-2024

    Summary

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    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; AllianceGenome:HGNC:10875
    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
    all
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    Genomic context

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    See SIGLEC6 in Genome Data Viewer
    Location:
    19q13.41
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (51517819..51531670, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (54606444..54620306, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (52021073..52034924, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CEA cell adhesion molecule 18 Neighboring gene sialic acid binding Ig like lectin 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:52002817-52003316 Neighboring gene sialic acid binding Ig like lectin 27, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15021 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Siglec-6 mediates the uptake of extracellular vesicles through a noncanonical glycolipid binding pocket. Schmidt EN, et al. Nat Commun, 2023 Apr 22. PMID 37087495, Free PMC Article
    2. Elevated trophoblastic Siglec6 contributes to the impairment of vascular endothelial cell functions by downregulating Wnt6/β-catenin signaling in preeclampsia. Guan X, et al. Arch Biochem Biophys, 2022 Nov 15. PMID 36113626
    3. Expression and regulation of Siglec-6 (CD327) on human mast cells and basophils. Smiljkovic D, et al. J Allergy Clin Immunol, 2023 Jan. PMID 35953001
    4. Functional and Phenotypic Characterization of Siglec-6 on Human Mast Cells. Robida PA, et al. Cells, 2022 Mar 28. PMID 35406705, Free PMC Article
    5. Siglec-6 as a New Potential Immune Checkpoint for Bladder Cancer Patients. Benmerzoug S, et al. Eur Urol Focus, 2022 May. PMID 34147404

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Siglec-6 mediates the uptake of extracellular vesicles through a noncanonical glycolipid binding pocket.
      Title: Siglec-6 mediates the uptake of extracellular vesicles through a noncanonical glycolipid binding pocket.
    2. Expression and regulation of Siglec-6 (CD327) on human mast cells and basophils.
      Title: Expression and regulation of Siglec-6 (CD327) on human mast cells and basophils.
    3. Siglec-6 Signaling Uses Src Kinase Tyrosine Phosphorylation and SHP-2 Recruitment.
      Title: Siglec-6 Signaling Uses Src Kinase Tyrosine Phosphorylation and SHP-2 Recruitment.
    4. Elevated trophoblastic Siglec6 contributes to the impairment of vascular endothelial cell functions by downregulating Wnt6/beta-catenin signaling in preeclampsia.
      Title: Elevated trophoblastic Siglec6 contributes to the impairment of vascular endothelial cell functions by downregulating Wnt6/β-catenin signaling in preeclampsia.
    5. Siglec-6 as a New Potential Immune Checkpoint for Bladder Cancer Patients.
      Title: Siglec-6 as a New Potential Immune Checkpoint for Bladder Cancer Patients.
    6. Functional and Phenotypic Characterization of Siglec-6 on Human Mast Cells.
      Title: Functional and Phenotypic Characterization of Siglec-6 on Human Mast Cells.
    7. Glycosylated Siglec-6 expression in syncytiotrophoblast-derived extracellular vesicles from preeclampsia placentas.
      Title: Glycosylated Siglec-6 expression in syncytiotrophoblast-derived extracellular vesicles from preeclampsia placentas.
    8. Study findings illustrate that SIGLEC6 is a functionally inhibitory receptor on mast cells and suggest that SIGLEC6 expression may be relevant for mast cells activity in the tumor microenvironment of colorectal cancer.
      Title: Functional Inhibitory Siglec-6 Is Upregulated in Human Colorectal Cancer-Associated Mast Cells.
    9. Siglec6 and leptin play a role in the aberrant properties characteristic of gestational trophoblastic disease, namely excess proliferation and invasion.
      Title: Siglec-6 is expressed in gestational trophoblastic disease and affects proliferation, apoptosis and invasion.
    10. Siglec-6 expression is increased in preterm preeclampsia placentas.
      Title: Siglec-6 expression is increased in placentas from pregnancies complicated by preterm preeclampsia.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sialic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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

    NCBI Reference Sequences (RefSeq)

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    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
      5190..19041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001177547.3 → NP_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
      Consensus CDS
      CCDS54307.1
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000410679.1, ENST00000436458.5
      Conserved Domains (3) summary
      pfam07679
      Location:202 → 284
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111 → 182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28 → 105
      Ig; Immunoglobulin domain

    2. NM_001177548.3 → NP_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
      Consensus CDS
      CCDS54308.1
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000353071.4, ENST00000359982.8
      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265 → 347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    3. NM_001177549.3 → NP_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:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:243 → 325
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:143 → 207
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    4. NM_001245.7 → NP_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
      A8MV71, B2RTS8, C9JBE5, F8WA78, O15388, O43699, O43700
      Related
      ENSP00000401502.2, ENST00000425629.8
      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254 → 336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    5. NM_198845.6 → NP_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
      Consensus CDS
      CCDS12835.3
      UniProtKB/Swiss-Prot
      O43699
      Related
      ENSP00000344064.4, ENST00000346477.7
      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:238 → 320
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    6. NM_198846.6 → NP_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:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254 → 336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      51517819..51531670 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527537.3 → XP_011525839.1  sialic acid-binding Ig-like lectin 6 isoform X5

      Conserved Domains (3) summary
      pfam07679
      Location:218 → 300
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111 → 182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28 → 105
      Ig; Immunoglobulin domain

    2. XM_011527536.4 → XP_011525838.1  sialic acid-binding Ig-like lectin 6 isoform X4

      Conserved Domains (3) summary
      pfam07679
      Location:229 → 311
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:111 → 182
      Ig_3; Immunoglobulin domain
      cl11960
      Location:28 → 105
      Ig; Immunoglobulin domain

    3. XM_047439734.1 → XP_047295690.1  sialic acid-binding Ig-like lectin 6 isoform X3

    4. XM_011527535.4 → XP_011525837.1  sialic acid-binding Ig-like lectin 6 isoform X2

      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:254 → 336
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:143 → 207
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    5. XM_011527539.4 → XP_011525841.1  sialic acid-binding Ig-like lectin 6 isoform X10

      Conserved Domains (3) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    6. XM_047439736.1 → XP_047295692.1  sialic acid-binding Ig-like lectin 6 isoform X9

    7. XM_011527538.4 → XP_011525840.1  sialic acid-binding Ig-like lectin 6 isoform X6

      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265 → 347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    8. XM_011527533.4 → XP_011525835.1  sialic acid-binding Ig-like lectin 6 isoform X1

      Conserved Domains (4) summary
      smart00410
      Location:36 → 141
      IG_like; Immunoglobulin like
      pfam07679
      Location:265 → 347
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:147 → 218
      Ig_3; Immunoglobulin domain
      cl11960
      Location:31 → 141
      Ig; Immunoglobulin domain

    9. XM_047439735.1 → XP_047295691.1  sialic acid-binding Ig-like lectin 6 isoform X8

    10. XM_017027511.3 → XP_016883000.1  sialic acid-binding Ig-like lectin 6 isoform X7

    RNA

    1. XR_007067048.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      54606444..54620306 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322702.1 → XP_054178677.1  sialic acid-binding Ig-like lectin 6 isoform X5

    2. XM_054322701.1 → XP_054178676.1  sialic acid-binding Ig-like lectin 6 isoform X4

    3. XM_054322700.1 → XP_054178675.1  sialic acid-binding Ig-like lectin 6 isoform X3

    4. XM_054322699.1 → XP_054178674.1  sialic acid-binding Ig-like lectin 6 isoform X2

    5. XM_054322707.1 → XP_054178682.1  sialic acid-binding Ig-like lectin 6 isoform X10

    6. XM_054322706.1 → XP_054178681.1  sialic acid-binding Ig-like lectin 6 isoform X9

    7. XM_054322703.1 → XP_054178678.1  sialic acid-binding Ig-like lectin 6 isoform X6

    8. XM_054322698.1 → XP_054178673.1  sialic acid-binding Ig-like lectin 6 isoform X1

    9. XM_054322705.1 → XP_054178680.1  sialic acid-binding Ig-like lectin 6 isoform X8

    10. XM_054322704.1 → XP_054178679.1  sialic acid-binding Ig-like lectin 6 isoform X7

    RNA

    1. XR_008485224.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O43699.2 GenPept UniProtKB/Swiss-Prot:O43699

    Gene LinkOut

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