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Protein

Transcription factor Sox-9-A

Gene

sox9-a

Organism
Xenopus laevis (African clawed frog)
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

May be involved in chondrogenesis (cartilage development) during bone formation. Unlikely to play a role in sex determination but may function during testicular and ovarian differentiation (By similarity). Transcriptional activator. Acts early in neural crest formation, functioning redundantly with the other group E Sox factors sox8 and sox10 to induce neural crest progenitors. Induces sox10 expression downstream of wnt-signaling. Principally involved in development of the cranial neural crest, which is fated to form skeletal elements. Also required for otic placode specification during inner ear development.By similarity6 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

GO - Biological processi

<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 functionActivator, Developmental protein, DNA-binding
Biological processChondrogenesis, Differentiation, Gonadal differentiation, Transcription, Transcription regulation

<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-A
<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-a
Synonyms:sox9Imported
<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>OrganismiXenopus laevis (African clawed frog)
<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 identifieri8355 [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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

Xenopus laevis and tropicalis biology and genomics resource

More...
Xenbasei
XB-GENE-6253910 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

Cytoplasm, Nucleus

<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

Loss of neural crest progenitors and an expansion of the neural plate, leading to loss or reduction of neural crest-derived skeletal elements later during development.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'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>Mutagenesisi61K → R: Abolishes interaction with sumoylation factors. Alters neural crest formation and inner ear development; when associated with R-365. 1 Publication1
Mutagenesisi365K → R: Eliminates the major sumoylated product. Alters neural crest formation and inner ear development; when associated with R-61. 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 describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003774151 – 477Transcription factor Sox-9-AAdd BLAST477

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 describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki61Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication
Cross-linki365Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)1 Publication

<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

Sumoylated. Lys-365 is the major site of sumoylation, although sumoylation at Lys-61 also occurs. Sumoylation plays a key role in regulating formation of the neural crest and otic placode.1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

<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 a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

From mid-gastrula (stage 10.5-11), expressed in a ring around the blastopore, with expression decreasing toward the dorsal side. At stage 12, expression around the blastopore decreases and begins to increase lateral to the neural plate in the presumptive neural crest, where expression dramatically increases around stage 14. Also expressed in the otic placode as early as stage 13/14. By the tailbud stage expression is restricted to the otic cup and then throughout the otic vesicle, with more intense staining at the dorsal-most region, the prospective region of the semicircular canals and endolymphatic duct. At the early tailbud stage (stage 23), expressed in migrating cranial neural crest cells and in the trunk neural crest. Also expressed in the genital ridges, developing eye, nasal placode and prospective pineal gland. Around stage 25, expression is down-regulated in the trunk neural crest but persists in the migrating cranial crest cells as they populate the pharyngeal arches, otic placode, developing eye, genital ridges and notochord. By stage 31, expression remains strong in the pharyngeal arches. Also expressed in the pancreas; first expressed at stage 25 in the pancreatic anlagen, dorsally in diverticulum. As development proceeds, expression continues in pancreatic tissue, being restricted to ventral and dorsal pancreatic buds.6 Publications

<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 both maternally and zygotically. Expressed from mid-gastrula (around stage 10.5) and persists at least through to tadpoles (stage 41).1 Publication

<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 with the sumoylation factors ube2i/ubc9 and sumo1.1 Publication

GO - Molecular functioni

<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

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SMRi
B7ZR65

Database of comparative protein structure models

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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 biasi338 – 385Gln-richSequence analysisAdd BLAST48

Phylogenomic databases

KEGG Orthology (KO)

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KOi
K18435

Database of Orthologous Groups

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OrthoDBi
782373at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
1.10.30.10, 1 hit

Integrated resource of protein families, domains and functional sites

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

The PANTHER Classification System

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PANTHERi
PTHR10270:SF212 PTHR10270:SF212, 1 hit

Pfam protein domain database

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

Simple Modular Architecture Research Tool; a protein domain database

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SMARTi
View protein in SMART
SM00398 HMG, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF47095 SSF47095, 1 hit

PROSITE; a protein domain and family database

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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.

B7ZR65-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNLLDPFMKM TEEQDKCMSG APSPTMSDDS AGSPCPSGSG SDTENTRPQE
60 70 80 90 100
NTFPKGDQEL KKETEDEKFP VCIREAVSQV LKGYDWTLVP MPVRVNGSSK
110 120 130 140 150
NKPHVKRPMN AFMVWAQAAR RKLADQYPHL HNAELSKTLG KLWRLLNEGE
160 170 180 190 200
KRPFVEEAER LRVQHKKDHP DYKYQPRRRK SVKNGQTEQE DGAEQTHISP
210 220 230 240 250
NAIFKALQAD SPHSSSSMSE VHSPGEHSGQ SQGPPTPPTT PKTDIQPGKP
260 270 280 290 300
DLKREGRPLQ ENGRQPPHID FRDVDIGELS SEVISTIETF DVNEFDQYLP
310 320 330 340 350
PNGHPGVGST QASYTGSYGI SSTPSATTGA GPAWMSKQQQ QQPQQHSLST
360 370 380 390 400
LNSEQSQSQQ RTHIKTEQLS PSHYSDQQQQ HSPQQLNYSS FNLQHYSSSY
410 420 430 440 450
PTITRAQYDY TEHQGSSTYY SHASGQNSGL YSTFSYMNPS QRPLYTPIAD
460 470
TTGVPSIPQT HSPQHWEQPV YTQLTRP
Length:477
Mass (Da):53,431
Last modified:March 3, 2009 - 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:iE544E09D9CF8FEDD
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 conflicti184N → Y in AAI70060 (Ref. 2) Curated1
Sequence conflicti268H → R in AAK61366 (PubMed:11807034).Curated1
Sequence conflicti289T → I in AAK61366 (PubMed:11807034).Curated1
Sequence conflicti334W → C in AAK61366 (PubMed:11807034).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AY035397 mRNA Translation: AAK61366.1
BC170058 mRNA Translation: AAI70058.1
BC170060 mRNA Translation: AAI70060.1

NCBI Reference Sequences

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RefSeqi
NP_001084276.1, NM_001090807.1

UniGene gene-oriented nucleotide sequence clusters

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UniGenei
Xl.1690

Genome annotation databases

Database of genes from NCBI RefSeq genomes

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GeneIDi
399405

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
xla:399405

<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
AY035397 mRNA Translation: AAK61366.1
BC170058 mRNA Translation: AAI70058.1
BC170060 mRNA Translation: AAI70060.1
RefSeqiNP_001084276.1, NM_001090807.1
UniGeneiXl.1690

3D structure databases

SMRiB7ZR65
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi399405
KEGGixla:399405

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
399405
XenbaseiXB-GENE-6253910 sox9

Phylogenomic databases

KOiK18435
OrthoDBi782373at2759

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 nameiSOX9A_XENLA
<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: B7ZR65
Secondary accession number(s): B7ZR67, Q90YL1
<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 16, 2009
Last sequence update: March 3, 2009
Last modified: January 16, 2019
This is version 39 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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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