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Protein

Syndecan-2

Gene

SDC2

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

Functioni

Cell surface proteoglycan that bears heparan sulfate. Regulates dendritic arbor morphogenesis (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei142 – 1432Cleavage of ectodomainSequence Analysis

GO - Molecular functioni

  • PDZ domain binding Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Differentiation, Neurogenesis

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_263952. EPHB-mediated forward signaling.
REACT_267741. Defective EXT2 causes exostoses 2.
REACT_267942. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_268678. Defective B3GAT3 causes JDSSDHD.
REACT_268749. Defective B4GALT7 causes EDS, progeroid type.

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-2
Short name:
SYND2
Alternative name(s):
Fibroglycan
Heparan sulfate proteoglycan core protein
Short name:
HSPG
CD_antigen: CD362
Gene namesi
Name:SDC2
Synonyms:HSPG1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 8

Organism-specific databases

HGNCiHGNC:10659. SDC2.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini19 – 144126ExtracellularSequence AnalysisAdd
BLAST
Transmembranei145 – 16925HelicalSequence AnalysisAdd
BLAST
Topological domaini170 – 20132CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA35589.

Chemistry

DrugBankiDB00020. Sargramostim.

Polymorphism and mutation databases

BioMutaiSDC2.
DMDMi158962336.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Sequence AnalysisAdd
BLAST
Chaini19 – 201183Syndecan-2PRO_0000033503Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi41 – 411O-linked (Xyl...) (heparan sulfate)Sequence Analysis
Glycosylationi55 – 551O-linked (Xyl...) (heparan sulfate)Sequence Analysis
Glycosylationi57 – 571O-linked (Xyl...) (heparan sulfate)Sequence Analysis
Glycosylationi101 – 1011O-linked (GalNAc...)1 Publication
Modified residuei187 – 1871Phosphoserine1 Publication

Post-translational modificationi

O-glycosylated with core 1 or possibly core 8 glycans. Contains heparan sulfate.1 Publication

Keywords - PTMi

Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

Proteomic databases

PaxDbiP34741.
PRIDEiP34741.

PTM databases

PhosphoSiteiP34741.

Expressioni

Gene expression databases

BgeeiP34741.
CleanExiHS_SDC2.
ExpressionAtlasiP34741. baseline and differential.
GenevisibleiP34741. HS.

Organism-specific databases

HPAiCAB025123.
HPA044416.

Interactioni

Subunit structurei

Interacts (via cytoplasmic domain) with SARM1.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
CASKO149362EBI-1172957,EBI-1215506
NF1P213594EBI-1172957,EBI-1172917

Protein-protein interaction databases

BioGridi112285. 83 interactions.
DIPiDIP-29943N.
IntActiP34741. 13 interactions.
MINTiMINT-1536313.
STRINGi9606.ENSP00000307046.

Structurei

3D structure databases

ProteinModelPortaliP34741.
SMRiP34741. Positions 170-201.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG85596.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000263414.
HOVERGENiHBG004501.
InParanoidiP34741.
KOiK16336.
OMAiASASGSX.
OrthoDBiEOG7GJ6G5.
PhylomeDBiP34741.
TreeFamiTF320463.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[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.

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

P34741-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRRAWILLTL GLVACVSAES RAELTSDKDM YLDNSSIEEA SGVYPIDDDD
60 70 80 90 100
YASASGSGAD EDVESPELTT SRPLPKILLT SAAPKVETTT LNIQNKIPAQ
110 120 130 140 150
TKSPEETDKE KVHLSDSERK MDPAEEDTNV YTEKHSDSLF KRTEVLAAVI
160 170 180 190 200
AGGVIGFLFA IFLILLLVYR MRKKDEGSYD LGERKPSSAA YQKAPTKEFY

A
Length:201
Mass (Da):22,160
Last modified:August 21, 2007 - v2
Checksum:i7DA4159D54741054
GO

Sequence cautioni

The sequence AAA52701.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti150 – 1501I → T in BAB15150 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti59 – 591A → T.1 Publication
Corresponds to variant rs3816208 [ dbSNP | Ensembl ].
VAR_034675
Natural varianti71 – 711S → T.2 Publications
Corresponds to variant rs1042381 [ dbSNP | Ensembl ].
VAR_034676

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04621 mRNA. Translation: AAA52701.1. Different initiation.
AK025488 mRNA. Translation: BAB15150.1.
AK074530 mRNA. Translation: BAG51965.1.
AK097839 mRNA. Translation: BAG53540.1.
CH471060 Genomic DNA. Translation: EAW91755.1.
BC030133 mRNA. Translation: AAH30133.1.
BC049836 mRNA. Translation: AAH49836.1.
CCDSiCCDS6272.1.
PIRiA33880.
RefSeqiNP_002989.2. NM_002998.3.
UniGeneiHs.1501.
Hs.598247.

Genome annotation databases

EnsembliENST00000302190; ENSP00000307046; ENSG00000169439.
GeneIDi6383.
KEGGihsa:6383.
UCSCiuc003yhv.1. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J04621 mRNA. Translation: AAA52701.1. Different initiation.
AK025488 mRNA. Translation: BAB15150.1.
AK074530 mRNA. Translation: BAG51965.1.
AK097839 mRNA. Translation: BAG53540.1.
CH471060 Genomic DNA. Translation: EAW91755.1.
BC030133 mRNA. Translation: AAH30133.1.
BC049836 mRNA. Translation: AAH49836.1.
CCDSiCCDS6272.1.
PIRiA33880.
RefSeqiNP_002989.2. NM_002998.3.
UniGeneiHs.1501.
Hs.598247.

3D structure databases

ProteinModelPortaliP34741.
SMRiP34741. Positions 170-201.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112285. 83 interactions.
DIPiDIP-29943N.
IntActiP34741. 13 interactions.
MINTiMINT-1536313.
STRINGi9606.ENSP00000307046.

Chemistry

DrugBankiDB00020. Sargramostim.

PTM databases

PhosphoSiteiP34741.

Polymorphism and mutation databases

BioMutaiSDC2.
DMDMi158962336.

Proteomic databases

PaxDbiP34741.
PRIDEiP34741.

Protocols and materials databases

DNASUi6383.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000302190; ENSP00000307046; ENSG00000169439.
GeneIDi6383.
KEGGihsa:6383.
UCSCiuc003yhv.1. human.

Organism-specific databases

CTDi6383.
GeneCardsiGC08P097575.
HGNCiHGNC:10659. SDC2.
HPAiCAB025123.
HPA044416.
MIMi142460. gene.
neXtProtiNX_P34741.
PharmGKBiPA35589.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG85596.
GeneTreeiENSGT00530000063116.
HOGENOMiHOG000263414.
HOVERGENiHBG004501.
InParanoidiP34741.
KOiK16336.
OMAiASASGSX.
OrthoDBiEOG7GJ6G5.
PhylomeDBiP34741.
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_263952. EPHB-mediated forward signaling.
REACT_267741. Defective EXT2 causes exostoses 2.
REACT_267942. Defective EXT1 causes exostoses 1, TRPS2 and CHDS.
REACT_268678. Defective B3GAT3 causes JDSSDHD.
REACT_268749. Defective B4GALT7 causes EDS, progeroid type.

Miscellaneous databases

ChiTaRSiSDC2. human.
GeneWikiiSDC2.
GenomeRNAii6383.
NextBioi24788.
PROiP34741.
SOURCEiSearch...

Gene expression databases

BgeeiP34741.
CleanExiHS_SDC2.
ExpressionAtlasiP34741. baseline and differential.
GenevisibleiP34741. HS.

Family and domain databases

InterProiIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
IPR030479. Syndecan_CS.
[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. "Partial primary structure of the 48- and 90-kilodalton core proteins of cell surface-associated heparan sulfate proteoglycans of lung fibroblasts. Prediction of an integral membrane domain and evidence for multiple distinct core proteins at the cell surface of human lung fibroblasts."
    Marynen P., Zhang J., Cassiman J.-J., den Berghe H., David G.
    J. Biol. Chem. 264:7017-7024(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT THR-71.
    Tissue: Lung fibroblast.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  3. "Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries."
    Otsuki T., Ota T., Nishikawa T., Hayashi K., Suzuki Y., Yamamoto J., Wakamatsu A., Kimura K., Sakamoto K., Hatano N., Kawai Y., Ishii S., Saito K., Kojima S., Sugiyama T., Ono T., Okano K., Yoshikawa Y.
    , Aotsuka S., Sasaki N., Hattori A., Okumura K., Nagai K., Sugano S., Isogai T.
    DNA Res. 12:117-126(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT THR-59.
    Tissue: Embryo.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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], VARIANT THR-71.
    Tissue: Brain and Muscle.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD."
    Halim A., Nilsson J., Ruetschi U., Hesse C., Larson G.
    Mol. Cell. Proteomics 0:0-0(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION AT THR-101, STRUCTURE OF CARBOHYDRATES, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-187, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiSDC2_HUMAN
AccessioniPrimary (citable) accession number: P34741
Secondary accession number(s): B3KQA3, Q6PIS6, Q9H6V1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: August 21, 2007
Last modified: June 24, 2015
This is version 144 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 cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 8
    Human chromosome 8: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. 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.