Siglec1 sialic acid binding Ig like lectin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Siglec1provided by RGD
Official Full Name: sialic acid binding Ig like lectin 1provided by RGD
Primary source: RGD:1311953
See related: EnsemblRapid:ENSRNOG00000021243 AllianceGenome:RGD:1311953
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sn
Summary: Predicted to enable virion binding activity. Predicted to be involved in clathrin-dependent endocytosis of virus by host cell; negative regulation of phagocytosis; and negative regulation of type I interferon production. Predicted to act upstream of or within positive regulation of T cell apoptotic process and positive regulation of extrinsic apoptotic signaling pathway. Predicted to be located in endocytic vesicle. Predicted to be active in early endosome; late endosome; and plasma membrane. Orthologous to human SIGLEC1 (sialic acid binding Ig like lectin 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 104.6), Thymus (RPKM 19.5) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q36

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (138740171..138759966, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (118287988..118307125, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (123612067..123631718, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

sialoadhesin-positive macrophages were increased during the late stage of diabetes concomitantly with the increase of alpha-smooth muscle actin-positive mesangial cells, mesangial matrix area and type IV collagen.
Title: Phenotypic change of macrophages in the progression of diabetic nephropathy; sialoadhesin-positive activated macrophages are increased in diabetic kidney.
Sialoadhesin is a macrophage-restricted adhesion molecule that recognizes N-acetylneuraminylalpha2-3galactose structure. Macrophages in lymph nodes express high levels of unmasked sialoadhesin.
Title: Lymph node macrophages, but not spleen macrophages, express high levels of unmasked sialoadhesin: implication for the adhesive properties of macrophages in vivo.

Submit: New GeneRIF Correction

General gene information

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Markers

Sn (e-PCR), detects polymorphism
- UniSTS:144466

RH135254 (e-PCR)
- UniSTS:218531

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables virion binding	IBA Inferred from Biological aspect of Ancestor more info
enables virion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in clathrin-dependent endocytosis	ISO Inferred from Sequence Orthology more info
involved_in clathrin-dependent endocytosis of virus by host cell	IBA Inferred from Biological aspect of Ancestor more info
involved_in clathrin-dependent endocytosis of virus by host cell	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phagocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type I interferon production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of T cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of extrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in symbiont entry into host cell	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in early endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in late endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
NOT located_in lysosome	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
NOT located_in plasma membrane raft	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sialoadhesin

Names: sialic acid binding Ig-like lectin 1, sialoadhesin

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.

mRNA and Protein(s)

NM_001107777.1 → NP_001101247.1 sialoadhesin precursor

See identical proteins and their annotated locations for NP_001101247.1

Status: PROVISIONAL

Source sequence(s)

CH473949

UniProtKB/TrEMBL

A0A0G2K320, A6HQC1, D3ZVM6

Related

ENSRNOP00000028855.6, ENSRNOT00000028855.9

Conserved Domains (7) summary

cd00096
Location:431 → 504

Ig; Immunoglobulin domain

smart00408
Location:255 → 313

IGc2; Immunoglobulin C-2 Type

smart00409
Location:625 → 702

IG; Immunoglobulin

smart00410
Location:255 → 324

IG_like; Immunoglobulin like

pfam07679
Location:808 → 883

I-set; Immunoglobulin I-set domain

pfam13895
Location:339 → 409

Ig_2; Immunoglobulin domain

cl11960
Location:21 → 136

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086021.1 Reference GRCr8

Range

138740171..138759966 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017591747.3 → XP_017447236.1 sialoadhesin isoform X2

UniProtKB/TrEMBL

A0A0G2K320

Related

ENSRNOP00000109102.1, ENSRNOT00000139550.1
XM_006235024.5 → XP_006235086.1 sialoadhesin isoform X3

UniProtKB/TrEMBL

A0A0G2K320

Related

ENSRNOP00000072470.2, ENSRNOT00000091493.3

Conserved Domains (7) summary

cd00096
Location:431 → 504

Ig; Immunoglobulin domain

smart00408
Location:255 → 313

IGc2; Immunoglobulin C-2 Type

smart00409
Location:711 → 788

IG; Immunoglobulin

smart00410
Location:255 → 324

IG_like; Immunoglobulin like

pfam07679
Location:894 → 969

I-set; Immunoglobulin I-set domain

pfam13895
Location:515 → 595

Ig_2; Immunoglobulin domain

cl11960
Location:21 → 136

Ig; Immunoglobulin domain
XM_017591748.3 → XP_017447237.1 sialoadhesin isoform X4

UniProtKB/TrEMBL

A0A0G2K320
XM_017591746.3 → XP_017447235.1 sialoadhesin isoform X1

UniProtKB/TrEMBL

A0A0G2K320
XM_017591749.3 → XP_017447238.1 sialoadhesin isoform X5

UniProtKB/TrEMBL

A0A0G2K320