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UniProtKB - Q04887 (SOX9_MOUSE)

Protein

Transcription factor SOX-9

Gene

Sox9

Organism
Mus musculus (Mouse)
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

Transcriptional regulator that plays a role in chondrocytes differentiation and skeletal development (PubMed:20940257, PubMed:28263186). Binds to the COL2A1 promoter and activates COL2A1 expression, as part of a complex with ZNF219 (PubMed:20940257).2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi105 – 173HMG boxPROSITE-ProRule annotationAdd BLAST69

<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

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

<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>Keywordsi

Molecular functionDNA-binding
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-MMU-3769402 Deactivation of the beta-catenin transactivating complex
R-MMU-8878166 Transcriptional regulation by RUNX2

<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:
Transcription factor SOX-9
<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:Sox9
Synonyms:Sox-9
<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>OrganismiMus musculus (Mouse)
<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 identifieri10090 [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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
<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
  • UP000000589 <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 11

Organism-specific databases

Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

More...MGIi		MGI:98371 Sox9

<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

Keywords - Cellular componenti

Nucleus

<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 describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000487411 – 507Transcription factor SOX-9Add BLAST507

<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

Ubiquitinated. Ubiquitination leads to proteasomal degradation and is negatively regulated by DDRGK1.By similarity

Keywords - PTMi

Ubl conjugation

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		Q04887

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

More...PaxDbi		Q04887

PeptideAtlas

More...PeptideAtlasi		Q04887

PRoteomics IDEntifications database

More...PRIDEi		Q04887

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...iPTMneti		Q04887

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

More...PhosphoSitePlusi		Q04887

<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		ENSMUSG00000000567 Expressed in 465 organ(s), highest expression level in humerus cartilage element

CleanEx database of gene expression profiles

More...CleanExi		MM_SOX9

Genevisible search portal to normalized and curated expression data from Genevestigator

More...Genevisiblei		Q04887 MM

<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

Interacts (via C-terminus) with ZNF219 (PubMed:20940257). Interacts with DDRGK1 (By similarity).By similarity1 Publication

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		203413, 6 interactors

Protein interaction database and analysis system

More...IntActi		Q04887, 1 interactor

STRING: functional protein association networks

More...STRINGi		10090.ENSMUSP00000000579

<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

1507
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		Q04887

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

More...SMRi		Q04887

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

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 biasi339 – 415Gln/Pro-richAdd BLAST77
Compositional biasi342 – 346Poly-Pro5

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG0527 Eukaryota
ENOG410XT0K LUCA

Ensembl GeneTree

More...GeneTreei		ENSGT00940000158269

The HOVERGEN Database of Homologous Vertebrate Genes

More...HOVERGENi		HBG002061

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q04887

KEGG Orthology (KO)

More...KOi		K18435

Identification of Orthologs from Complete Genome Data

More...OMAi		IAYSPFS

Database of Orthologous Groups

More...OrthoDBi		EOG091G0EKD

TreeFam database of animal gene trees

More...TreeFami		TF351735

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		1.10.30.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
IPR029548 SOX-9
IPR022151 Sox_N

The PANTHER Classification System

More...PANTHERi		PTHR10270:SF212 PTHR10270:SF212, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00505 HMG_box, 1 hit
PF12444 Sox_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00398 HMG, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47095 SSF47095, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50118 HMG_BOX_2, 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.

Q04887-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNLLDPFMKM TDEQEKGLSG APSPTMSEDS AGSPCPSGSG SDTENTRPQE 
        60         70         80         90        100
NTFPKGEPDL KKESEEDKFP VCIREAVSQV LKGYDWTLVP MPVRVNGSSK 
       110        120        130        140        150
NKPHVKRPMN AFMVWAQAAR RKLADQYPHL HNAELSKTLG KLWRLLNESE 
       160        170        180        190        200
KRPFVEEAER LRVQHKKDHP DYKYQPRRRK SVKNGQAEAE EATEQTHISP 
       210        220        230        240        250
NAIFKALQAD SPHSSSGMSE VHSPGEHSGQ SQGPPTPPTT PKTDVQAGKV 
       260        270        280        290        300
DLKREGRPLA EGGRQPPIDF RDVDIGELSS DVISNIETFD VNEFDQYLPP 
       310        320        330        340        350
NGHPGVPATH GQVTYTGSYG ISSTAPTPAT AGHVWMSKQQ APPPPPQQPP 
       360        370        380        390        400
QAPQAPQAPP QQQAPPQQPQ APQQQQAHTL TTLSSEPGQS QRTHIKTEQL 
       410        420        430        440        450
SPSHYSEQQQ HSPQQISYSP FNLPHYSPSY PPITRSQYDY ADHQNSGSYY 
       460        470        480        490        500
SHAAGQGSGL YSTFTYMNPA QRPMYTPIAD TSGVPSIPQT HSPQHWEQPV 

YTQLTRP
Length:507
Mass (Da):56,077
Last modified:May 10, 2004 - v2
<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:i01FC3B54FF329BDA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti62K → R in BAC34018 (PubMed:16141072).Curated1

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
AF421878 mRNA Translation: AAL16093.1
AK030187 mRNA Translation: BAC26830.1
AK049986 mRNA Translation: BAC34018.1
BC004064 mRNA Translation: AAH04064.1
BC023796 mRNA Translation: AAH23796.1
BC023808 mRNA Translation: AAH23808.1
BC023953 mRNA Translation: AAH23953.1
BC024958 mRNA Translation: AAH24958.1
BC034264 mRNA Translation: AAH34264.1
Z18958 mRNA Translation: CAA79483.1

The Consensus CDS (CCDS) project

More...CCDSi		CCDS25595.1

Protein sequence database of the Protein Information Resource

More...PIRi		S30243
S52469

NCBI Reference Sequences

More...RefSeqi		NP_035578.3, NM_011448.4

UniGene gene-oriented nucleotide sequence clusters

More...UniGenei		Mm.286407

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSMUST00000000579; ENSMUSP00000000579; ENSMUSG00000000567

Database of genes from NCBI RefSeq genomes

More...GeneIDi		20682

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		mmu:20682

UCSC genome browser

More...UCSCi		uc007med.2 mouse

<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
AF421878 mRNA Translation: AAL16093.1
AK030187 mRNA Translation: BAC26830.1
AK049986 mRNA Translation: BAC34018.1
BC004064 mRNA Translation: AAH04064.1
BC023796 mRNA Translation: AAH23796.1
BC023808 mRNA Translation: AAH23808.1
BC023953 mRNA Translation: AAH23953.1
BC024958 mRNA Translation: AAH24958.1
BC034264 mRNA Translation: AAH34264.1
Z18958 mRNA Translation: CAA79483.1
CCDSiCCDS25595.1
PIRiS30243
S52469
RefSeqiNP_035578.3, NM_011448.4
UniGeneiMm.286407

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
4S2QX-ray2.70D103-178[»]
ProteinModelPortaliQ04887
SMRiQ04887
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi203413, 6 interactors
IntActiQ04887, 1 interactor
STRINGi10090.ENSMUSP00000000579

PTM databases

iPTMnetiQ04887
PhosphoSitePlusiQ04887

Proteomic databases

MaxQBiQ04887
PaxDbiQ04887
PeptideAtlasiQ04887
PRIDEiQ04887

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000000579; ENSMUSP00000000579; ENSMUSG00000000567
GeneIDi20682
KEGGimmu:20682
UCSCiuc007med.2 mouse

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		6662
MGIiMGI:98371 Sox9

Phylogenomic databases

eggNOGiKOG0527 Eukaryota
ENOG410XT0K LUCA
GeneTreeiENSGT00940000158269
HOVERGENiHBG002061
InParanoidiQ04887
KOiK18435
OMAiIAYSPFS
OrthoDBiEOG091G0EKD
TreeFamiTF351735

Enzyme and pathway databases

ReactomeiR-MMU-3769402 Deactivation of the beta-catenin transactivating complex
R-MMU-8878166 Transcriptional regulation by RUNX2

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q04887

The Stanford Online Universal Resource for Clones and ESTs

More...SOURCEi		Search...

Gene expression databases

BgeeiENSMUSG00000000567 Expressed in 465 organ(s), highest expression level in humerus cartilage element
CleanExiMM_SOX9
GenevisibleiQ04887 MM

Family and domain databases

Gene3Di1.10.30.10, 1 hit
InterProiView protein in InterPro
IPR009071 HMG_box_dom
IPR036910 HMG_box_dom_sf
IPR029548 SOX-9
IPR022151 Sox_N
PANTHERiPTHR10270:SF212 PTHR10270:SF212, 1 hit
PfamiView protein in Pfam
PF00505 HMG_box, 1 hit
PF12444 Sox_N, 1 hit
SMARTiView protein in SMART
SM00398 HMG, 1 hit
SUPFAMiSSF47095 SSF47095, 1 hit
PROSITEiView protein in PROSITE
PS50118 HMG_BOX_2, 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 nameiSOX9_MOUSE
<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: Q04887
Secondary accession number(s): Q8C7L2, Q91ZK2, Q99KQ0
<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: June 1, 1994
Last sequence update: May 10, 2004
Last modified: December 5, 2018
This is version 154 of the entry and version 2 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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