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Gene name

Class

Subclass

Chromosome

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In atlas

Reliability

Reliability

Reliability

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Method

Validation

Method

Validation

Method

Validation

Location

Searches

Tissue

Cell type

Expression

Tissue

Specificity

Cell line

Specificity

Tissue

Detectable

Cell line

Detectable

Category

Score

Score

Score

Antibodies

Column

 
 
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SOX4
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TISSUE ATLAS PRIMARY DATA

GENE/PROTEIN

Antibody validation


Dictionary


Tissue proteome

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

SOX4

Gene descriptioni

Gene description according to HGNC.

SRY (sex determining region Y)-box 4

Protein classi

Protein class the gene product belongs to according to selected gene lists. List of protein classes.

Predicted intracellular proteins
Transcription factors

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Intracellular

Number of transcriptsi

Number of protein-coding transcribed from this gene as defined by Ensembl.

1
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA tissue categoryi

The RNA tissue category is based on mRNA expression levels in the analyzed tissues (RNA assay description). The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected. RNA tissue category is calculated separately both for internally generated Human Protein Atlas (HPA) RNA-seq data, as well as RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project.

Read more

HPA:Expressed in all
GTEx:Expressed in all

Protein evidencei

Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.

Evidence at protein level

Protein expressioni

A summary of the overall protein expression pattern across the analyzed tissues. The summary is based on knowledge-based annotation.

"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.

Read more

Mainly nuclear expression in most tissues.

DATA RELIABILITY

Data reliability
descriptioni

Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.

Antibody staining mainly not consistent with RNA expression data. Presumed off target binding observed and disregarded.

Reliability scorei

Reliability score (score description), divided into Supported, Approved, or Uncertain, is based on consistency between the staining pattern of one antibody or several antibodies with RNA-seq data and available gene/protein characterization data.

Read more

Approved based on 1 antibody.
HPA029901
SHOW MORE

RNA AND PROTEIN EXPRESSION SUMMARYi

Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page. Images of selected tissues give a visual summary of the protein expression profile furthest to the right. The gray human body provides links to a histology dictionary when clicking on any part of the figure.

RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.

Read more
Brain
Cerebral cortex
Hippocampus
N/A
Caudate
N/A
Cerebellum
N/A
Endocrine tissues
Thyroid gland
Parathyroid gland
Adrenal gland
Bone marrow & immune system
Appendix
Bone marrow
Lymph node
Tonsil
Spleen
Muscle tissues
Heart muscle
Skeletal muscle
Smooth muscle
Lung
Nasopharynx
N/A
Bronchus
N/A
Lung
Liver & gallbladder
Liver
Gallbladder
Pancreas
Pancreas
Gastrointestinal tract
Oral mucosa
N/A
Salivary gland
Esophagus
Stomach
Duodenum
Small intestine
Colon
Rectum
Kidney & urinary bladder
Kidney
Urinary bladder
Male tissues
Testis
Epididymis
Prostate
Seminal vesicle
Female tissues
Breast
Vagina
N/A
Cervix, uterine
Endometrium
Fallopian tube
Ovary
Placenta
Adipose & soft tissue
Adipose tissue
Soft tissue
N/A
Skin
Skin
Cerebral cortex

Lymph node

Heart muscle

Liver

Colon

Kidney

Testis

PROTEIN EXPRESSION OVERVIEWi

Protein expression data is shown for each of the 44 tissues. The color-coding is based on tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types found in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.

For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview, however, all immunohistochemical images are still available and the annotation data can be found under Primary data.

Organ
Expression
Alphabetical

RNA EXPRESSION OVERVIEWi

RNA expression overview shows RNA-data from three different sources: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.

HPA dataseti

HPA dataset
RNA-seq tissue data is reported as mean TPM (transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.

RNA tissue category HPA
HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GTEx dataseti

GTEx dataset
RNA-seq data are reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.

RNA tissue category GTEx
GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all

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.

Gene name

SOX4

Synonyms

Description

SRY (sex determining region Y)-box 4 (HGNC Symbol)

Entrez gene summary

This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein. [provided by RefSeq, Jul 2008]

Chromosome

6

Cytoband

p22.3

Chromosome location (bp)

21592769 - 21598619

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000124766 (version 83.38)

Entrez gene

6659

UniProt

Q06945 (UniProt - Evidence at protein level)

neXtProt

NX_Q06945

Antibodypedia

SOX4 antibodies

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.

Under 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) (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.

SOX4-001

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)

SOX4-001
ENSP00000244745
ENST00000244745
Q06945 [Direct mapping]
Transcription factor SOX-4
Show all
Predicted intracellular proteins
Transcription factors
   Other all-alpha-helical DNA-binding domains
Show all
GO:0000976 [transcription regulatory region sequence-specific DNA binding]
GO:0000981 [RNA polymerase II transcription factor activity, sequence-specific DNA binding]
GO:0001046 [core promoter sequence-specific DNA binding]
GO:0001071 [nucleic acid binding transcription factor activity]
GO:0001077 [transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding]
GO:0001105 [RNA polymerase II transcription coactivator activity]
GO:0001501 [skeletal system development]
GO:0001841 [neural tube formation]
GO:0002328 [pro-B cell differentiation]
GO:0003183 [mitral valve morphogenesis]
GO:0003211 [cardiac ventricle formation]
GO:0003215 [cardiac right ventricle morphogenesis]
GO:0003289 [atrial septum primum morphogenesis]
GO:0003357 [noradrenergic neuron differentiation]
GO:0003700 [transcription factor activity, sequence-specific DNA binding]
GO:0005515 [protein binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005739 [mitochondrion]
GO:0006355 [regulation of transcription, DNA-templated]
GO:0006366 [transcription from RNA polymerase II promoter]
GO:0006977 [DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest]
GO:0007507 [heart development]
GO:0008284 [positive regulation of cell proliferation]
GO:0008285 [negative regulation of cell proliferation]
GO:0014009 [glial cell proliferation]
GO:0021510 [spinal cord development]
GO:0021522 [spinal cord motor neuron differentiation]
GO:0021782 [glial cell development]
GO:0030177 [positive regulation of Wnt signaling pathway]
GO:0030217 [T cell differentiation]
GO:0031018 [endocrine pancreas development]
GO:0031397 [negative regulation of protein ubiquitination]
GO:0031647 [regulation of protein stability]
GO:0032024 [positive regulation of insulin secretion]
GO:0035019 [somatic stem cell population maintenance]
GO:0035910 [ascending aorta morphogenesis]
GO:0042593 [glucose homeostasis]
GO:0042769 [DNA damage response, detection of DNA damage]
GO:0043065 [positive regulation of apoptotic process]
GO:0044798 [nuclear transcription factor complex]
GO:0045727 [positive regulation of translation]
GO:0045893 [positive regulation of transcription, DNA-templated]
GO:0045944 [positive regulation of transcription from RNA polymerase II promoter]
GO:0046826 [negative regulation of protein export from nucleus]
GO:0046982 [protein heterodimerization activity]
GO:0048485 [sympathetic nervous system development]
GO:0050821 [protein stabilization]
GO:0060070 [canonical Wnt signaling pathway]
GO:0060174 [limb bud formation]
GO:0060412 [ventricular septum morphogenesis]
GO:0060548 [negative regulation of cell death]
GO:0060563 [neuroepithelial cell differentiation]
GO:0060993 [kidney morphogenesis]
GO:0071333 [cellular response to glucose stimulus]
GO:0090263 [positive regulation of canonical Wnt signaling pathway]
GO:2000761 [positive regulation of N-terminal peptidyl-lysine acetylation]
Show all
474 aa
47.3 kDa
No 0

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The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg foundation.