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Protein

Syndecan-4

Gene

Sdc4

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP.By similarity

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-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-202733 Cell surface interactions at the vascular wall
R-RNO-3000170 Syndecan interactions
R-RNO-975634 Retinoid metabolism and transport

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Syndecan-4
Short name:
SYND4
Alternative name(s):
Ryudocan core protein
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Sdc4
Synonyms:Synd4
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 3

Organism-specific databases

Rat genome database

More...
RGDi
3650 Sdc4

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini24 – 149ExtracellularSequence analysisAdd BLAST126
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei150 – 174HelicalSequence analysisAdd BLAST25
Topological domaini175 – 202CytoplasmicSequence analysisAdd BLAST28

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywords - Cellular componenti

Membrane, Secreted

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 23Sequence analysisAdd BLAST23
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000003351324 – 202Syndecan-4Add BLAST179

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section specifies the position and type of each covalently attached glycan group (mono-, di-, or polysaccharide).<p><a href='/help/carbohyd' target='_top'>More...</a></p>Glycosylationi44O-linked (Xyl...) (heparan sulfate) serineCurated1
Glycosylationi65O-linked (Xyl...) (heparan sulfate) serineSequence analysis1
Glycosylationi67O-linked (Xyl...) (heparan sulfate) serineSequence analysis1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>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

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P34901

PRoteomics IDEntifications database

More...
PRIDEi
P34901

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P34901

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
P34901

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSRNOG00000014297 Expressed in 9 organ(s), highest expression level in adult mammalian kidney

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
P34901 RN

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer. Interacts with CDCP1 and SDCBP. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity).By similarity

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
246895, 2 interactors

Protein interaction database and analysis system

More...
IntActi
P34901, 4 interactors

Molecular INTeraction database

More...
MINTi
P34901

STRING: functional protein association networks

More...
STRINGi
10116.ENSRNOP00000019386

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1202
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
P34901

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P34901

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410IXIG Eukaryota
ENOG4111QSA LUCA

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000160663

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000263414

The HOVERGEN Database of Homologous Vertebrate Genes

More...
HOVERGENi
HBG004501

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P34901

KEGG Orthology (KO)

More...
KOi
K16338

Identification of Orthologs from Complete Genome Data

More...
OMAi
QEPDDFE

Database of Orthologous Groups

More...
OrthoDBi
EOG091G0OOE

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P34901

TreeFam database of animal gene trees

More...
TreeFami
TF320463

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003585 Neurexin-like
IPR001050 Syndecan
IPR027789 Syndecan/Neurexin_dom
IPR030479 Syndecan_CS

The PANTHER Classification System

More...
PANTHERi
PTHR10915 PTHR10915, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01034 Syndecan, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00294 4.1m, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00964 SYNDECAN, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P34901-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAPVCLFAPL LLLLLGGFPV APGESIRETE VIDPQDLLEG RYFSGALPDD
60 70 80 90 100
EDAGGLEQDS DFELSGSGDL DDTEEPRTFP EVISPLVPLD NHIPENAQPG
110 120 130 140 150
IRVPSEPKEL EENEVIPKRV PSDVGDDDVS NKVSMSSTSQ GSNIFERTEV
160 170 180 190 200
LAALIVGGVV GILFAVFLIL LLVYRMKKKD EGSYDLGKKP IYKKAPTNEF

YA
Length:202
Mass (Da):21,962
Last modified:February 1, 1994 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i5D9C8B3BF4C0D58A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M81786 mRNA Translation: AAA73167.1
S61868 mRNA Translation: AAB26725.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A42410

NCBI Reference Sequences

More...
RefSeqi
NP_036781.1, NM_012649.2

UniGene gene-oriented nucleotide sequence clusters

More...
UniGenei
Rn.2029

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSRNOT00000019386; ENSRNOP00000019386; ENSRNOG00000014297

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
24771

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:24771

UCSC genome browser

More...
UCSCi
RGD:3650 rat

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M81786 mRNA Translation: AAA73167.1
S61868 mRNA Translation: AAB26725.1
PIRiA42410
RefSeqiNP_036781.1, NM_012649.2
UniGeneiRn.2029

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5A2PX-ray2.50E/F/G/H195-202[»]
5G1DX-ray2.81C/D195-202[»]
ProteinModelPortaliP34901
SMRiP34901
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246895, 2 interactors
IntActiP34901, 4 interactors
MINTiP34901
STRINGi10116.ENSRNOP00000019386

PTM databases

iPTMnetiP34901
PhosphoSitePlusiP34901

Proteomic databases

PaxDbiP34901
PRIDEiP34901

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000019386; ENSRNOP00000019386; ENSRNOG00000014297
GeneIDi24771
KEGGirno:24771
UCSCiRGD:3650 rat

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
6385
RGDi3650 Sdc4

Phylogenomic databases

eggNOGiENOG410IXIG Eukaryota
ENOG4111QSA LUCA
GeneTreeiENSGT00940000160663
HOGENOMiHOG000263414
HOVERGENiHBG004501
InParanoidiP34901
KOiK16338
OMAiQEPDDFE
OrthoDBiEOG091G0OOE
PhylomeDBiP34901
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-202733 Cell surface interactions at the vascular wall
R-RNO-3000170 Syndecan interactions
R-RNO-975634 Retinoid metabolism and transport

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P34901

Gene expression databases

BgeeiENSRNOG00000014297 Expressed in 9 organ(s), highest expression level in adult mammalian kidney
GenevisibleiP34901 RN

Family and domain databases

InterProiView protein in InterPro
IPR003585 Neurexin-like
IPR001050 Syndecan
IPR027789 Syndecan/Neurexin_dom
IPR030479 Syndecan_CS
PANTHERiPTHR10915 PTHR10915, 1 hit
PfamiView protein in Pfam
PF01034 Syndecan, 1 hit
SMARTiView protein in SMART
SM00294 4.1m, 1 hit
PROSITEiView protein in PROSITE
PS00964 SYNDECAN, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSDC4_RAT
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P34901
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: December 5, 2018
This is version 138 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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