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Protein

Syndecan-1

Gene

Sdc1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP.By similarity

GO - Molecular functioni

  • extracellular matrix binding Source: RGD
  • glycoprotein binding Source: Ensembl

GO - Biological processi

  • canonical Wnt signaling pathway Source: Ensembl
  • cell adhesion Source: RGD
  • cell-cell signaling Source: RGD
  • cell migration Source: GO_Central
  • inflammatory response Source: RGD
  • myoblast development Source: Ensembl
  • odontogenesis Source: RGD
  • positive regulation of exosomal secretion Source: Ensembl
  • positive regulation of extracellular exosome assembly Source: Ensembl
  • response to calcium ion Source: RGD
  • response to cAMP Source: RGD
  • response to glucocorticoid Source: RGD
  • response to hydrogen peroxide Source: RGD
  • response to organic substance Source: RGD
  • response to toxic substance Source: RGD
  • Sertoli cell development Source: RGD
  • striated muscle cell development Source: Ensembl
  • ureteric bud development Source: RGD
  • wound healing Source: RGD
Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-RNO-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-RNO-2022928. HS-GAG biosynthesis.
R-RNO-2024096. HS-GAG degradation.
R-RNO-3000170. Syndecan interactions.
R-RNO-975634. Retinoid metabolism and transport.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-1
Short name:
SYND1
Alternative name(s):
CD_antigen: CD138
Gene namesi
Name:Sdc1
Synonyms:Synd1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 6

Organism-specific databases

RGDi3648. Sdc1.

Subcellular locationi

  • Membrane Sequence analysis; Single-pass type I membrane protein Sequence analysis
  • Secreted By similarity
  • Secretedexosome By similarity

  • Note: Shedding of the ectodomain produces a soluble form.By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini23 – 257ExtracellularSequence analysisAdd BLAST235
Transmembranei258 – 278HelicalSequence analysisAdd BLAST21
Topological domaini279 – 313CytoplasmicSequence analysisAdd BLAST35

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 22Sequence analysisAdd BLAST22
ChainiPRO_000003350223 – 313Syndecan-1Add BLAST291

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi37O-linked (Xyl...) (chondroitin sulfate)By similarity1
Glycosylationi43N-linked (GlcNAc...)Sequence analysis1
Glycosylationi45O-linked (Xyl...) (heparan sulfate)By similarity1
Glycosylationi47O-linked (Xyl...) (heparan sulfate)By similarity1
Glycosylationi209O-linked (Xyl...) (chondroitin sulfate)By similarity1
Glycosylationi219O-linked (Xyl...) (chondroitin sulfate)By similarity1
Modified residuei288PhosphoserineBy similarity1

Post-translational modificationi

Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3 (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei253 – 254Cleavage of ectodomainSequence analysis2

Keywords - PTMi

Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

Proteomic databases

PaxDbiP26260.
PRIDEiP26260.

PTM databases

iPTMnetiP26260.
PhosphoSitePlusiP26260.

Expressioni

Gene expression databases

BgeeiENSRNOG00000006396.
GenevisibleiP26260. RN.

Interactioni

Subunit structurei

Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain) (By similarity).By similarity

Protein-protein interaction databases

IntActiP26260. 1 interactor.
STRINGi10116.ENSRNOP00000008582.

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IYWX. Eukaryota.
ENOG410Y2QY. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP26260.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG091G0EYV.
PhylomeDBiP26260.
TreeFamiTF320463.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR031190. Syndecan-1.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PTHR10915:SF5. PTHR10915:SF5. 1 hit.
PfamiPF01034. Syndecan. 1 hit.
[Graphical view]
SMARTiSM00294. 4.1m. 1 hit.
[Graphical view]
PROSITEiPS00964. SYNDECAN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P26260-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRRAALWLWL CALALRLQPA LPQIVTANVP PEDQDGSGDD SDNFSGSGTG
60 70 80 90 100
ALPDMTLSRQ TPSTWKDVWL LTATPTAPEP TSRDTEATLT SILPAGEKPE
110 120 130 140 150
EGEPVAHVEA EPDFTARDKE KEATTRPRET TQLPVTQQAS TAARATTAQA
160 170 180 190 200
SVTSHPHGDV QPGLHETLAP TAPGQPDHQP PSVEDGGTSV IKEVVEDETT
210 220 230 240 250
NQLPAGEGSG EQDFTFETSG ENTAVAGVEP DLRNQSPVDE GATGASQGLL
260 270 280 290 300
DRKEVLGGVI AGGLVGLIFA VCLVAFMLYR MKKKDEGSYS LEEPKQANGG
310
AYQKPTKQEE FYA
Length:313
Mass (Da):33,214
Last modified:February 1, 1994 - v2
Checksum:iC6EC50E8798A5218
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti15L → V (PubMed:1639809).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60651 mRNA. Translation: CAA43058.1.
M81785 mRNA. Translation: AAA42198.1.
S61865 mRNA. Translation: AAB26726.1.
BC061834 mRNA. Translation: AAH61834.1.
PIRiA42853.
RefSeqiNP_037158.1. NM_013026.2.
UniGeneiRn.11176.

Genome annotation databases

EnsembliENSRNOT00000086633; ENSRNOP00000072283; ENSRNOG00000059947.
GeneIDi25216.
KEGGirno:25216.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X60651 mRNA. Translation: CAA43058.1.
M81785 mRNA. Translation: AAA42198.1.
S61865 mRNA. Translation: AAB26726.1.
BC061834 mRNA. Translation: AAH61834.1.
PIRiA42853.
RefSeqiNP_037158.1. NM_013026.2.
UniGeneiRn.11176.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP26260. 1 interactor.
STRINGi10116.ENSRNOP00000008582.

PTM databases

iPTMnetiP26260.
PhosphoSitePlusiP26260.

Proteomic databases

PaxDbiP26260.
PRIDEiP26260.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000086633; ENSRNOP00000072283; ENSRNOG00000059947.
GeneIDi25216.
KEGGirno:25216.

Organism-specific databases

CTDi6382.
RGDi3648. Sdc1.

Phylogenomic databases

eggNOGiENOG410IYWX. Eukaryota.
ENOG410Y2QY. LUCA.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000133092.
HOVERGENiHBG017783.
InParanoidiP26260.
KOiK06257.
OMAiPTKQEEF.
OrthoDBiEOG091G0EYV.
PhylomeDBiP26260.
TreeFamiTF320463.

Enzyme and pathway databases

ReactomeiR-RNO-1971475. A tetrasaccharide linker sequence is required for GAG synthesis.
R-RNO-2022928. HS-GAG biosynthesis.
R-RNO-2024096. HS-GAG degradation.
R-RNO-3000170. Syndecan interactions.
R-RNO-975634. Retinoid metabolism and transport.

Miscellaneous databases

PROiP26260.

Gene expression databases

BgeeiENSRNOG00000006396.
GenevisibleiP26260. RN.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR031190. Syndecan-1.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 1 hit.
PTHR10915:SF5. PTHR10915:SF5. 1 hit.
PfamiPF01034. Syndecan. 1 hit.
[Graphical view]
SMARTiSM00294. 4.1m. 1 hit.
[Graphical view]
PROSITEiPS00964. SYNDECAN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSDC1_RAT
AccessioniPrimary (citable) accession number: P26260
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: February 1, 1994
Last modified: November 2, 2016
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.