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SOX9
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  • SOX9
PROTEIN STRUCTURE
ANTIBODIES
AND
VALIDATION
Protein structures
GENERAL INFORMATIONi

General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.

Gene namei

Official gene symbol, which is typically a short form of the gene name, according to HGNC.

SOX9
Synonyms CMD1, CMPD1, SRA1
Gene descriptioni

Full gene name according to HGNC.

SRY-box transcription factor 9
Protein classi

Assigned HPA protein class(es) for the encoded protein(s).

Read more
Cancer-related genes
Disease related genes
Human disease related genes
Transcription factors
Predicted locationi

All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.

  • Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.

  • Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).

The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.

Read more
Intracellular
Protein evidence Evidence at protein level (all genes)
GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Chromosome 17
Cytoband q24.3
Chromosome location (bp) 72121020 - 72126416
Number of transcriptsi

Number of protein-coding transcripts from the gene as defined by Ensembl.

1
Ensembl ENSG00000125398 (version 103.38)
Entrez gene 6662
HGNC HGNC:11204
UniProt P48436 (UniProt - Evidence at protein level)
neXtProt NX_P48436
Antibodypedia SOX9 antibodies


PROTEIN STRUCTUREi

The Structure section provides predicted structures from the Alphafold protein structure database and available experimental structures from Protein Data Bank (PDB).

In the Structure drop-down menu all experimental structures from PDB are available for selection and display. The structures are displayed using the NGL Viewer and can be zoomed-in and rotated either manually or by checking the Autorotate box. The Color scheme can be selected to show the residue index, chain name or confidence score (as B-factors and pLDDT score for experimental and predicted structures, respectively). The positions for available antigen sequences in the structure are shown if Antigens is turned to ON, and the Variants slider can be used to show the positions of clinical and population variants.https://github.com/nglviewer/ngl

Read more

Predicted


Description: Structure prediction from Alphafold project. Structure version 2

# Chains: 1      # Clinical variants: 17      # Population variants: 310

Antigens:

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On

Variants:

Off
Clinical
Population

Color scheme:

Confidence
Residue index
Chain name

Autorotate:

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On



PROTEIN BROWSERi

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Below the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).

The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
SOX9-201


PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant UniProt Protein class Gene ontology Length & mass Signal peptide
(predicted)
Transmembrane regions
(predicted)
SOX9-201
ENSP00000245479
ENST00000245479
P48436 [Direct mapping]
Transcription factor SOX-9
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
Transcription factors
   Other all-alpha-helical DNA-binding domains
Cancer-related genes
   Candidate cancer biomarkers
Disease related genes
Human disease related genes
   Congenital malformations
   Other congenital malformations
   Reproductive system diseases
   Reproductive system diseases
Mapped to neXtProt
   neXtProt - Evidence at protein level
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000122 [negative regulation of transcription by RNA polymerase II]
GO:0000785 [chromatin]
GO:0000976 [transcription regulatory region sequence-specific DNA binding]
GO:0000978 [RNA polymerase II cis-regulatory region sequence-specific DNA binding]
GO:0000981 [DNA-binding transcription factor activity, RNA polymerase II-specific]
GO:0000987 [cis-regulatory region sequence-specific DNA binding]
GO:0001228 [DNA-binding transcription activator activity, RNA polymerase II-specific]
GO:0001501 [skeletal system development]
GO:0001502 [cartilage condensation]
GO:0001503 [ossification]
GO:0001658 [branching involved in ureteric bud morphogenesis]
GO:0001708 [cell fate specification]
GO:0001837 [epithelial to mesenchymal transition]
GO:0001894 [tissue homeostasis]
GO:0001934 [positive regulation of protein phosphorylation]
GO:0001942 [hair follicle development]
GO:0002009 [morphogenesis of an epithelium]
GO:0002053 [positive regulation of mesenchymal cell proliferation]
GO:0002062 [chondrocyte differentiation]
GO:0002063 [chondrocyte development]
GO:0002683 [negative regulation of immune system process]
GO:0003170 [heart valve development]
GO:0003179 [heart valve morphogenesis]
GO:0003180 [aortic valve morphogenesis]
GO:0003188 [heart valve formation]
GO:0003203 [endocardial cushion morphogenesis]
GO:0003413 [chondrocyte differentiation involved in endochondral bone morphogenesis]
GO:0003415 [chondrocyte hypertrophy]
GO:0003430 [growth plate cartilage chondrocyte growth]
GO:0003677 [DNA binding]
GO:0003682 [chromatin binding]
GO:0003700 [DNA-binding transcription factor activity]
GO:0005515 [protein binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005667 [transcription regulator complex]
GO:0006334 [nucleosome assembly]
GO:0006338 [chromatin remodeling]
GO:0006355 [regulation of transcription, DNA-templated]
GO:0006357 [regulation of transcription by RNA polymerase II]
GO:0006367 [transcription initiation from RNA polymerase II promoter]
GO:0007010 [cytoskeleton organization]
GO:0007165 [signal transduction]
GO:0007173 [epidermal growth factor receptor signaling pathway]
GO:0007219 [Notch signaling pathway]
GO:0007283 [spermatogenesis]
GO:0007417 [central nervous system development]
GO:0007507 [heart development]
GO:0008013 [beta-catenin binding]
GO:0008284 [positive regulation of cell population proliferation]
GO:0008285 [negative regulation of cell population proliferation]
GO:0008584 [male gonad development]
GO:0010468 [regulation of gene expression]
GO:0010564 [regulation of cell cycle process]
GO:0010628 [positive regulation of gene expression]
GO:0010629 [negative regulation of gene expression]
GO:0010634 [positive regulation of epithelial cell migration]
GO:0014032 [neural crest cell development]
GO:0014036 [neural crest cell fate specification]
GO:0014068 [positive regulation of phosphatidylinositol 3-kinase signaling]
GO:0019100 [male germ-line sex determination]
GO:0019933 [cAMP-mediated signaling]
GO:0030154 [cell differentiation]
GO:0030155 [regulation of cell adhesion]
GO:0030198 [extracellular matrix organization]
GO:0030238 [male sex determination]
GO:0030279 [negative regulation of ossification]
GO:0030502 [negative regulation of bone mineralization]
GO:0030850 [prostate gland development]
GO:0030857 [negative regulation of epithelial cell differentiation]
GO:0030858 [positive regulation of epithelial cell differentiation]
GO:0030879 [mammary gland development]
GO:0030903 [notochord development]
GO:0030916 [otic vesicle formation]
GO:0031018 [endocrine pancreas development]
GO:0032331 [negative regulation of chondrocyte differentiation]
GO:0032332 [positive regulation of chondrocyte differentiation]
GO:0032808 [lacrimal gland development]
GO:0032991 [protein-containing complex]
GO:0034236 [protein kinase A catalytic subunit binding]
GO:0034504 [protein localization to nucleus]
GO:0035019 [somatic stem cell population maintenance]
GO:0035622 [intrahepatic bile duct development]
GO:0042127 [regulation of cell population proliferation]
GO:0042981 [regulation of apoptotic process]
GO:0043066 [negative regulation of apoptotic process]
GO:0043425 [bHLH transcription factor binding]
GO:0043491 [protein kinase B signaling]
GO:0043565 [sequence-specific DNA binding]
GO:0045165 [cell fate commitment]
GO:0045595 [regulation of cell differentiation]
GO:0045662 [negative regulation of myoblast differentiation]
GO:0045668 [negative regulation of osteoblast differentiation]
GO:0045732 [positive regulation of protein catabolic process]
GO:0045892 [negative regulation of transcription, DNA-templated]
GO:0045893 [positive regulation of transcription, DNA-templated]
GO:0045944 [positive regulation of transcription by RNA polymerase II]
GO:0046322 [negative regulation of fatty acid oxidation]
GO:0046533 [negative regulation of photoreceptor cell differentiation]
GO:0048709 [oligodendrocyte differentiation]
GO:0048873 [homeostasis of number of cells within a tissue]
GO:0050679 [positive regulation of epithelial cell proliferation]
GO:0050680 [negative regulation of epithelial cell proliferation]
GO:0051216 [cartilage development]
GO:0060008 [Sertoli cell differentiation]
GO:0060009 [Sertoli cell development]
GO:0060018 [astrocyte fate commitment]
GO:0060041 [retina development in camera-type eye]
GO:0060174 [limb bud formation]
GO:0060221 [retinal rod cell differentiation]
GO:0060350 [endochondral bone morphogenesis]
GO:0060441 [epithelial tube branching involved in lung morphogenesis]
GO:0060487 [lung epithelial cell differentiation]
GO:0060512 [prostate gland morphogenesis]
GO:0060517 [epithelial cell proliferation involved in prostatic bud elongation]
GO:0060532 [bronchus cartilage development]
GO:0060534 [trachea cartilage development]
GO:0060729 [intestinal epithelial structure maintenance]
GO:0060784 [regulation of cell proliferation involved in tissue homeostasis]
GO:0061036 [positive regulation of cartilage development]
GO:0061046 [regulation of branching involved in lung morphogenesis]
GO:0061138 [morphogenesis of a branching epithelium]
GO:0061145 [lung smooth muscle development]
GO:0065003 [protein-containing complex assembly]
GO:0070168 [negative regulation of biomineral tissue development]
GO:0070371 [ERK1 and ERK2 cascade]
GO:0070384 [Harderian gland development]
GO:0070542 [response to fatty acid]
GO:0071260 [cellular response to mechanical stimulus]
GO:0071300 [cellular response to retinoic acid]
GO:0071347 [cellular response to interleukin-1]
GO:0071364 [cellular response to epidermal growth factor stimulus]
GO:0071504 [cellular response to heparin]
GO:0071560 [cellular response to transforming growth factor beta stimulus]
GO:0071599 [otic vesicle development]
GO:0071773 [cellular response to BMP stimulus]
GO:0072034 [renal vesicle induction]
GO:0072170 [metanephric tubule development]
GO:0072189 [ureter development]
GO:0072190 [ureter urothelium development]
GO:0072193 [ureter smooth muscle cell differentiation]
GO:0072197 [ureter morphogenesis]
GO:0072289 [metanephric nephron tubule formation]
GO:0090090 [negative regulation of canonical Wnt signaling pathway]
GO:0090103 [cochlea morphogenesis]
GO:0090184 [positive regulation of kidney development]
GO:0090190 [positive regulation of branching involved in ureteric bud morphogenesis]
GO:0097065 [anterior head development]
GO:0097157 [pre-mRNA intronic binding]
GO:0098609 [cell-cell adhesion]
GO:1901203 [positive regulation of extracellular matrix assembly]
GO:1902732 [positive regulation of chondrocyte proliferation]
GO:1902894 [negative regulation of pri-miRNA transcription by RNA polymerase II]
GO:1904864 [negative regulation of beta-catenin-TCF complex assembly]
GO:1990837 [sequence-specific double-stranded DNA binding]
GO:2000020 [positive regulation of male gonad development]
GO:2000138 [positive regulation of cell proliferation involved in heart morphogenesis]
GO:2000741 [positive regulation of mesenchymal stem cell differentiation]
GO:2000794 [regulation of epithelial cell proliferation involved in lung morphogenesis]
GO:2001054 [negative regulation of mesenchymal cell apoptotic process]
Show all
509 aa
56.1 kDa
No 0

Contact

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The Project

  • INTRODUCTION
  • ORGANIZATION
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The Human Protein Atlas

  • DOWNLOADABLE DATA
  • LICENCE & CITATION
  • HELP & FAQ
The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.