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Sdc1 syndecan 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25216, updated on 4-Jan-2025

Summary

Official Symbol
Sdc1provided by RGD
Official Full Name
syndecan 1provided by RGD
Primary source
RGD:3648
See related
EnsemblRapid:ENSRNOG00000059947 AllianceGenome:RGD:3648
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
HSPG; Synd1; SYNDECA; Syndecan
Summary
Predicted to enable cargo receptor activity and identical protein binding activity. Involved in several processes, including Sertoli cell development; response to cAMP; and response to hydrogen peroxide. Part of protein-containing complex. Used to study familial hyperlipidemia. Biomarker of myocardial infarction; obesity; and proteinuria. Orthologous to human SDC1 (syndecan 1). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Lung (RPKM 457.9), Liver (RPKM 379.7) and 7 other tissues See more
Orthologs
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Genomic context

See Sdc1 in Genome Data Viewer
Location:
6q14
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (37282041..37304503)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (31562799..31585267)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (33885576..33908038)

Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene solute carrier family 7 (cationic amino acid transporter, y+ system), member 15 Neighboring gene pumilio RNA-binding family member 2 Neighboring gene ribosomal protein S21, pseudogene 6 Neighboring gene lysosomal protein transmembrane 4 alpha

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

General gene information

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables cargo receptor activity  
enables extracellular matrix binding PubMed 
enables identical protein binding  
enables protein binding PubMed 
Process Evidence Code Pubs
involved_in Sertoli cell development PubMed 
acts_upstream_of_or_within canonical Wnt signaling pathway  
involved_in cell adhesion PubMed 
involved_in cell migration  
involved_in cell-cell signaling PubMed 
involved_in myoblast development  
involved_in positive regulation of exosomal secretion  
involved_in positive regulation of extracellular exosome assembly  
involved_in receptor-mediated endocytosis  
involved_in response to cAMP PubMed 
involved_in response to calcium ion PubMed 
involved_in response to glucocorticoid PubMed 
involved_in response to hydrogen peroxide PubMed 
involved_in response to toxic substance PubMed 
involved_in striated muscle cell development  
involved_in ureteric bud development PubMed 
Component Evidence Code Pubs
is_active_in cell surface  
located_in cell surface  
located_in external side of plasma membrane  
located_in extracellular region  
is_active_in plasma membrane  
part_of protein-containing complex PubMed 

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)

  1. NM_013026.2NP_037158.1  syndecan-1 precursor

    See identical proteins and their annotated locations for NP_037158.1

    Status: PROVISIONAL

    Source sequence(s)
    BC061834
    UniProtKB/Swiss-Prot
    P26260
    UniProtKB/TrEMBL
    A6HAM5
    Related
    ENSRNOP00000104961.1, ENSRNOT00000134281.1
    Conserved Domains (1) summary
    pfam01034
    Location:248311
    Syndecan; Syndecan 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

  1. NC_086024.1 Reference GRCr8

    Range
    37282041..37304503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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