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Protein

Syndecan-3

Gene

SDC3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cell surface proteoglycan that may bear heparan sulfate (By similarity). May have a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism.By similarity1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei383 – 3842Cleavage of ectodomainSequence Analysis

GO - Biological processi

  1. carbohydrate metabolic process Source: Reactome
  2. chondroitin sulfate metabolic process Source: Reactome
  3. extracellular matrix organization Source: Reactome
  4. glycosaminoglycan biosynthetic process Source: Reactome
  5. glycosaminoglycan catabolic process Source: Reactome
  6. glycosaminoglycan metabolic process Source: Reactome
  7. phototransduction, visible light Source: Reactome
  8. retinoid metabolic process Source: Reactome
  9. small molecule metabolic process Source: Reactome
Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_120752. HS-GAG degradation.
REACT_121248. HS-GAG biosynthesis.
REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
REACT_163942. Syndecan interactions.
REACT_24968. Retinoid metabolism and transport.
REACT_267654. Defective EXT2 causes exostoses 2.
REACT_267659. Defective B3GAT3 causes JDSSDHD.
REACT_267674. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_267711. Defective B4GALT7 causes EDS, progeroid type.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-3
Short name:
SYND3
Gene namesi
Name:SDC3
Synonyms:KIAA0468
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:10660. SDC3.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 387387ExtracellularSequence AnalysisAdd
BLAST
Transmembranei388 – 40821HelicalSequence AnalysisAdd
BLAST
Topological domaini409 – 44234CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. Golgi lumen Source: Reactome
  2. integral component of membrane Source: UniProtKB-KW
  3. lysosomal lumen Source: Reactome
  4. membrane Source: UniProtKB
  5. plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35590.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 442442Syndecan-3PRO_0000183989Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi80 – 801O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Glycosylationi82 – 821O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Glycosylationi84 – 841O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Glycosylationi91 – 911O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Glycosylationi314 – 3141O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Glycosylationi367 – 3671O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
Modified residuei409 – 4091Phosphotyrosine1 Publication
Modified residuei419 – 4191Phosphotyrosine1 Publication
Modified residuei431 – 4311Phosphotyrosine1 Publication
Modified residuei441 – 4411Phosphotyrosine1 Publication

Post-translational modificationi

O-glycosylated within the Thr/Ser-rich region which could interact with lectin domains on other molecules.Curated

Keywords - PTMi

Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

Proteomic databases

MaxQBiO75056.
PaxDbiO75056.
PRIDEiO75056.

PTM databases

PhosphoSiteiO75056.

Expressioni

Tissue specificityi

Expressed in the nervous system, the adrenal gland, and the spleen.1 Publication

Gene expression databases

BgeeiO75056.
CleanExiHS_SDC3.
ExpressionAtlasiO75056. baseline and differential.
GenevestigatoriO75056.

Organism-specific databases

HPAiCAB025786.
HPA017087.

Interactioni

Subunit structurei

Interacts with TIAM1.1 Publication

Protein-protein interaction databases

BioGridi115027. 11 interactions.
DIPiDIP-29944N.
IntActiO75056. 2 interactions.
MINTiMINT-3057059.
STRINGi9606.ENSP00000344468.

Structurei

3D structure databases

ProteinModelPortaliO75056.
SMRiO75056. Positions 410-442.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi115 – 302188Ser/Thr-rich (mucin-like)Add
BLAST

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG85596.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000049151.
HOVERGENiHBG004144.
InParanoidiO75056.
KOiK16337.
OMAiTQEPDIP.
PhylomeDBiO75056.
TreeFamiTF320463.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
[Graphical view]
PANTHERiPTHR10915. PTHR10915. 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.

O75056-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKPGPPHRAG AAHGAGAGAG AAAGPGARGL LLPPLLLLLL AGRAAGAQRW
60 70 80 90 100
RSENFERPVD LEGSGDDDSF PDDELDDLYS GSGSGYFEQE SGIETAMRFS
110 120 130 140 150
PDVALAVSTT PAVLPTTNIQ PVGTPFEELP SERPTLEPAT SPLVVTEVPE
160 170 180 190 200
EPSQRATTVS TTMATTAATS TGDPTVATVP ATVATATPST PAAPPFTATT
210 220 230 240 250
AVIRTTGVRR LLPLPLTTVA TARATTPEAP SPPTTAAVLD TEAPTPRLVS
260 270 280 290 300
TATSRPRALP RPATTQEPDI PERSTLPLGT TAPGPTEVAQ TPTPETFLTT
310 320 330 340 350
IRDEPEVPVS GGPSGDFELP EEETTQPDTA NEVVAVGGAA AKASSPPGTL
360 370 380 390 400
PKGARPGPGL LDNAIDSGSS AAQLPQKSIL ERKEVLVAVI VGGVVGALFA
410 420 430 440
AFLVTLLIYR MKKKDEGSYT LEEPKQASVT YQKPDKQEEF YA
Length:442
Mass (Da):45,497
Last modified:September 5, 2006 - v2
Checksum:iD4C284CBC36A92E2
GO

Sequence cautioni

The sequence BAA32313.2 differs from that shown.Intron retention.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti208 – 2081V → I.
Corresponds to variant rs2491132 [ dbSNP | Ensembl ].
VAR_027251
Natural varianti303 – 3031D → N.1 Publication
Corresponds to variant rs4949184 [ dbSNP | Ensembl ].
VAR_027252
Natural varianti329 – 3291T → I.
Corresponds to variant rs2282440 [ dbSNP | Ensembl ].
VAR_027253

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF248634 mRNA. Translation: AAK39969.1.
AB007937 mRNA. Translation: BAA32313.2. Sequence problems.
AL445235 Genomic DNA. Translation: CAI22245.1.
AL445235 Genomic DNA. Translation: CAI22250.1.
BC013974 mRNA. No translation available.
CCDSiCCDS30661.1.
RefSeqiNP_055469.3. NM_014654.3.
UniGeneiHs.158287.

Genome annotation databases

EnsembliENST00000339394; ENSP00000344468; ENSG00000162512.
GeneIDi9672.
KEGGihsa:9672.
UCSCiuc001bse.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF248634 mRNA. Translation: AAK39969.1.
AB007937 mRNA. Translation: BAA32313.2. Sequence problems.
AL445235 Genomic DNA. Translation: CAI22245.1.
AL445235 Genomic DNA. Translation: CAI22250.1.
BC013974 mRNA. No translation available.
CCDSiCCDS30661.1.
RefSeqiNP_055469.3. NM_014654.3.
UniGeneiHs.158287.

3D structure databases

ProteinModelPortaliO75056.
SMRiO75056. Positions 410-442.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115027. 11 interactions.
DIPiDIP-29944N.
IntActiO75056. 2 interactions.
MINTiMINT-3057059.
STRINGi9606.ENSP00000344468.

PTM databases

PhosphoSiteiO75056.

Proteomic databases

MaxQBiO75056.
PaxDbiO75056.
PRIDEiO75056.

Protocols and materials databases

DNASUi9672.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000339394; ENSP00000344468; ENSG00000162512.
GeneIDi9672.
KEGGihsa:9672.
UCSCiuc001bse.2. human.

Organism-specific databases

CTDi9672.
GeneCardsiGC01M031342.
H-InvDBHIX0000348.
HGNCiHGNC:10660. SDC3.
HPAiCAB025786.
HPA017087.
MIMi186357. gene.
neXtProtiNX_O75056.
PharmGKBiPA35590.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG85596.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000049151.
HOVERGENiHBG004144.
InParanoidiO75056.
KOiK16337.
OMAiTQEPDIP.
PhylomeDBiO75056.
TreeFamiTF320463.

Enzyme and pathway databases

ReactomeiREACT_120752. HS-GAG degradation.
REACT_121248. HS-GAG biosynthesis.
REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
REACT_163942. Syndecan interactions.
REACT_24968. Retinoid metabolism and transport.
REACT_267654. Defective EXT2 causes exostoses 2.
REACT_267659. Defective B3GAT3 causes JDSSDHD.
REACT_267674. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_267711. Defective B4GALT7 causes EDS, progeroid type.

Miscellaneous databases

ChiTaRSiSDC3. human.
GeneWikiiSDC3.
GenomeRNAii9672.
NextBioi36319.
PROiO75056.
SOURCEiSearch...

Gene expression databases

BgeeiO75056.
CleanExiHS_SDC3.
ExpressionAtlasiO75056. baseline and differential.
GenevestigatoriO75056.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, VARIANT ASN-303.
  2. "Characterization of cDNA clones in size-fractionated cDNA libraries from human brain."
    Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D., Nomura N., Ohara O.
    DNA Res. 4:345-349(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  3. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Muscle.
  5. "Phosphorylation of recombinant N-syndecan (syndecan 3) core protein."
    Asundi V.K., Carey D.J.
    Biochem. Biophys. Res. Commun. 240:502-506(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT TYR-409; TYR-419; TYR-431 AND TYR-441.
  6. "The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics."
    Liu X., Shepherd T.R., Murray A.M., Xu Z., Fuentes E.J.
    Structure 21:342-354(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TIAM1.

Entry informationi

Entry nameiSDC3_HUMAN
AccessioniPrimary (citable) accession number: O75056
Secondary accession number(s): Q5T1Z6
, Q5T1Z7, Q96CT3, Q96PR8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: September 5, 2006
Last modified: February 4, 2015
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.