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

Gene ID: 946, updated on 2-Nov-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 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)

Genotypes

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

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