Human Gene SIGLEC1 (ENST00000344754.6_7) from GENCODE V47lift37
  Description: sialic acid binding Ig like lectin 1, transcript variant 1 (from RefSeq NM_023068.4)
Gencode Transcript: ENST00000344754.6_7
Gencode Gene: ENSG00000088827.14_9
Transcript (Including UTRs)
   Position: hg19 chr20:3,667,617-3,693,247 Size: 25,631 Total Exon Count: 22 Strand: -
Coding Region
   Position: hg19 chr20:3,669,207-3,687,775 Size: 18,569 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:3,667,617-3,693,247)mRNA (may differ from genome)Protein (1709 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SN_HUMAN
DESCRIPTION: RecName: Full=Sialoadhesin; AltName: Full=Sialic acid-binding Ig-like lectin 1; Short=Siglec-1; AltName: CD_antigen=CD169; Flags: Precursor;
FUNCTION: Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells. Preferentially binds to alpha-2,3-linked sialic acid (By similarity). Binds to SPN/CD43 on T-cells (By similarity). May play a role in hemopoiesis.
SUBCELLULAR LOCATION: Isoform 1: Cell membrane; Single-pass type I membrane protein.
SUBCELLULAR LOCATION: Isoform 2: Secreted.
TISSUE SPECIFICITY: Expressed by macrophages in various tissues. High levels are found in spleen, lymph node, perivascular macrophages in brain and lower levels in bone marrow, liver Kupffer cells and lamina propria of colon and lung. Also expressed by inflammatory macrophages in rheumatoid arthritis.
SIMILARITY: Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family.
SIMILARITY: Contains 16 Ig-like C2-type (immunoglobulin-like) domains.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=Siglec-1; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Itlect_267";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SIGLEC1
Diseases sorted by gene-association score: proliferative glomerulonephritis (11), diffuse cutaneous systemic sclerosis (7), mental retardation, x-linked, syndromic 15 (7)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.30 RPKM in Adipose - Subcutaneous
Total median expression: 126.84 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -95.70240-0.399 Picture PostScript Text
3' UTR -558.201590-0.351 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013162 - CD80_C2-set
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR013106 - Ig_V-set

Pfam Domains:
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF08205 - CD80-like C2-set immunoglobulin domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
81296 - E set domains
49265 - Fibronectin type III
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q9BZZ2
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0030246 carbohydrate binding

Biological Process:
GO:0006897 endocytosis
GO:0006954 inflammatory response
GO:0007155 cell adhesion
GO:0007160 cell-matrix adhesion
GO:0098609 cell-cell adhesion

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK057560 - Homo sapiens cDNA FLJ32998 fis, clone THYMU1000176, moderately similar to SIALOADHESIN PRECURSOR.
AL833688 - Homo sapiens mRNA; cDNA DKFZp667F058 (from clone DKFZp667F058).
AK024459 - Homo sapiens mRNA for FLJ00051 protein, partial cds.
AK024479 - Homo sapiens mRNA for FLJ00073 protein, partial cds.
AK024462 - Homo sapiens mRNA for FLJ00055 protein, partial cds.
AK122586 - Homo sapiens mRNA for FLJ00411 protein.
AF230073 - Homo sapiens sialoadhesin mRNA, complete cds.
BC141884 - Homo sapiens sialic acid binding Ig-like lectin 1, sialoadhesin, mRNA (cDNA clone IMAGE:40074414), partial cds.
AY927519 - Homo sapiens mRNA sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BZZ2 (Reactome details) participates in the following event(s):

R-HSA-5685607 Sialic acid binds SIGLEC
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000344754.1, ENST00000344754.2, ENST00000344754.3, ENST00000344754.4, ENST00000344754.5, NM_023068, Q96DL4, Q9BZZ2, Q9GZS5, Q9H1H6, Q9H1H7, Q9H7L7, SN, SN_HUMAN, uc317xbd.1, uc317xbd.2
UCSC ID: ENST00000344754.6_7
RefSeq Accession: NM_023068.4
Protein: Q9BZZ2 (aka SN_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.