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UniProtKB - P50605 (SDC_CAEEL)

Entry version 132 (12 Aug 2020)
Sequence version 1 (01 Oct 1996)
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Protein

Probable syndecan

Gene

sdn-1

Organism
Caenorhabditis elegans
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 (By similarity). Required for correct mitotic spindle orientation of the ABar blastomere division plane and this may be through modulation of astral microtubule array, and in association with the wnt-signaling proteins mig-5 and dsh-2 (PubMed:25344071). Involved in the migration of AQR and PQR neurons, which descend from the Q neuroblasts (PubMed:26022293). Promotes the axon guidance of D-type motor neurons (PubMed:24066155).By similarity3 Publications

<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 - Biological processi

Complete GO annotation on QuickGO ...

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-CEL-1971475, A tetrasaccharide linker sequence is required for GAG synthesis
R-CEL-2022928, HS-GAG biosynthesis
R-CEL-2024096, HS-GAG degradation
R-CEL-3000170, Syndecan interactions
R-CEL-381426, Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-CEL-3928662, EPHB-mediated forward signaling
R-CEL-8957275, Post-translational protein phosphorylation

<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%5Fand%5Ftaxonomy%5Fsection">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:
Probable syndecan
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:sdn-1Imported
ORF Names:F57C7.3Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiCaenorhabditis elegans
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri6239 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiEukaryota › Metazoa › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditina › Rhabditomorpha › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001940 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 X

Organism-specific databases

WormBase

More...WormBasei		F57C7.3a ; CE05996 ; WBGene00004749 ; sdn-1

<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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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 domaini27 – 231ExtracellularSequence analysisAdd BLAST205
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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>Transmembranei232 – 252HelicalSequence analysisAdd BLAST21
Topological domaini253 – 288CytoplasmicSequence analysisAdd BLAST36

<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

Cell junction, Cytoplasm, Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Disrupted mitotic spindle orientation of the ABar blastomere division axis, orientating parallel rather than orthogonally to the division axis of AB derived cells ABpr and ABal (PubMed:25344071). Reduced mig-5 accumulation at the cell contact sites between the ABar and C blastomere cells (PubMed:25344071). Irregular positioning of the AQR and PQR neurons in larva at the L4 stage (PubMed:26022293).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi71S → A: Reduced heperan sulfate binding; when associated with A-86 and A-214. 1 Publication1
Mutagenesisi86S → A: Reduced heperan sulfate binding; when associated with A-71 and A-214. 1 Publication1
Mutagenesisi214S → A: Reduced heperan sulfate binding; when associated with A-71 and A-86. 1 Publication1

<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 – 26Sequence analysisAdd BLAST26
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000003351427 – 288Probable syndecanAdd BLAST262

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">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>Glycosylationi69N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi71O-linked (Xyl...) (glycosaminoglycan) serine1 Publication1
Glycosylationi86O-linked (Xyl...) (glycosaminoglycan) serine1 Publication1
Glycosylationi214O-linked (Xyl...) (glycosaminoglycan) serine1 Publication1

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

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

More...PaxDbi		P50605

PeptideAtlas

More...PeptideAtlasi		P50605

PRoteomics IDEntifications database

More...PRIDEi		P50605

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		P50605

<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

<p>This subsection of the 'Expression' section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified 'at the protein level'.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Expressed from the one-cell stage of embryogenesis onwards.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		WBGene00004749, Expressed in pharyngeal muscle cell (C elegans) and 5 other tissues

ExpressionAtlas, Differential and Baseline Expression

More...ExpressionAtlasi		P50605, baseline and differential

<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

Protein-protein interaction databases

The Eukaryotic Linear Motif resource for Functional Sites in Proteins

More...ELMi		P50605

STRING: functional protein association networks

More...STRINGi		6239.F57C7.3a

<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

3D structure databases

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

More...SMRi		P50605

Database of comparative protein structure models

More...ModBasei		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

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi142 – 161Asp/Glu-rich (highly acidic)Add BLAST20
Compositional biasi175 – 181Poly-Thr7

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The cytoplasmic domain is required for correct mitotic spindle orientation and internalization of sdn-1.1 Publication

<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		ENOG502RZ6V, Eukaryota

Ensembl GeneTree

More...GeneTreei		ENSGT00940000168670

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P50605

Identification of Orthologs from Complete Genome Data

More...OMAi		DEPKQAR

Database of Orthologous Groups

More...OrthoDBi		1476863at2759

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001050, Syndecan
IPR027789, Syndecan/Neurexin_dom
IPR030479, Syndecan_CS
IPR031198, Syndecan_inverte

The PANTHER Classification System

More...PANTHERi		PTHR10915, PTHR10915, 1 hit
PTHR10915:SF1, PTHR10915:SF1, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01034, Syndecan, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

P50605-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MILKLNFCLS TYSVLILLSL STQAFAANQA KTKVVPSSTI STKSLKNGIS 
        60         70         80         90        100
EQVEGSANIP GRLADIEVNG SGYPTDDEDG DDVHGSGKPP SSATTKSDKV 
       110        120        130        140        150
TSPSHAVVTA KPTTVPTTTA SFKPPVQPKP KPAANDKEIK VEEDEDDDED 
       160        170        180        190        200
EDEDDEDDEE DFADENIHND EDFFTTTTTT TYRPIVVATT STPRSAATNP 
       210        220        230        240        250
PRQQPPMVTS TISSGPFSPF HETLANGFYA AIAGGVLVAV ITAILLVLFV 
       260        270        280 
VFRIRKKDEG SYALDEPKQA RPYASYGYTK ASTKEFYA
Length:288
Mass (Da):30,979
Last modified:October 1, 1996 - 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:i10F14F118541341F
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q8I4H9Q8I4H9_CAEEL
Syndecan
sdn-1 CELE_F57C7.3, F57C7.3
287Annotation score:

Annotation score:3 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>

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
BX284606 Genomic DNA Translation: CAA93474.1

Protein sequence database of the Protein Information Resource

More...PIRi		T22846

NCBI Reference Sequences

More...RefSeqi		NP_741894.1, NM_171972.4

Genome annotation databases

Ensembl metazoan genome annotation project

More...EnsemblMetazoai		F57C7.3a.1; F57C7.3a.1; WBGene00004749

Database of genes from NCBI RefSeq genomes

More...GeneIDi		181259

UCSC genome browser

More...UCSCi		F57C7.3a, c. elegans

<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
BX284606 Genomic DNA Translation: CAA93474.1
PIRiT22846
RefSeqiNP_741894.1, NM_171972.4

3D structure databases

SMRiP50605
ModBaseiSearch...

Protein-protein interaction databases

ELMiP50605
STRINGi6239.F57C7.3a

PTM databases

iPTMnetiP50605

Proteomic databases

PaxDbiP50605
PeptideAtlasiP50605
PRIDEiP50605

Genome annotation databases

EnsemblMetazoaiF57C7.3a.1; F57C7.3a.1; WBGene00004749
GeneIDi181259
UCSCiF57C7.3a, c. elegans

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		181259
WormBaseiF57C7.3a ; CE05996 ; WBGene00004749 ; sdn-1

Phylogenomic databases

eggNOGiENOG502RZ6V, Eukaryota
GeneTreeiENSGT00940000168670
InParanoidiP50605
OMAiDEPKQAR
OrthoDBi1476863at2759

Enzyme and pathway databases

ReactomeiR-CEL-1971475, A tetrasaccharide linker sequence is required for GAG synthesis
R-CEL-2022928, HS-GAG biosynthesis
R-CEL-2024096, HS-GAG degradation
R-CEL-3000170, Syndecan interactions
R-CEL-381426, Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-CEL-3928662, EPHB-mediated forward signaling
R-CEL-8957275, Post-translational protein phosphorylation

Miscellaneous databases

Protein Ontology

More...PROi		PR:P50605

Gene expression databases

BgeeiWBGene00004749, Expressed in pharyngeal muscle cell (C elegans) and 5 other tissues
ExpressionAtlasiP50605, baseline and differential

Family and domain databases

InterProiView protein in InterPro
IPR001050, Syndecan
IPR027789, Syndecan/Neurexin_dom
IPR030479, Syndecan_CS
IPR031198, Syndecan_inverte
PANTHERiPTHR10915, PTHR10915, 1 hit
PTHR10915:SF1, PTHR10915:SF1, 1 hit
PfamiView protein in Pfam
PF01034, Syndecan, 1 hit
PROSITEiView protein in PROSITE
PS00964, SYNDECAN, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 nameiSDC_CAEEL
<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: P50605
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: August 12, 2020
This is version 132 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 programCaenorhabditis annotation project

<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

Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families
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