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ATRX
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TISSUE ATLAS PRIMARY DATA

GENE/PROTEIN

Antibody validation


Dictionary


Tissue proteome

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

ATRX

Gene descriptioni

Gene description according to HGNC.

Alpha thalassemia/mental retardation syndrome X-linked

Protein classi

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

Cancer-related genes
Disease related genes
Enzymes
Potential drug targets
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.

10
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA tissue categoryi

RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue/cell line enriched, group enriched, tissue/cell line enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for The Cancer Genome Atlas (TCGA) data from cancer tissues and internally generated Human Protein Atlas (HPA) data from normal tissues and cell lines.

Read more

HPA:Expressed in all
GTEx:Expressed in all
FANTOM5: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 normal 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

General nuclear expression.

DATA RELIABILITY

Data reliability
descriptioni

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

Antibody staining consistent with RNA expression data.

Reliability scorei

Reliability score (score description), divided into Supported, Approved, or Uncertain, is evaluated in normal tissues and 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

Supported based on 3 antibodies.
HPA001906 , CAB009372 , CAB068176
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

Liver

Pancreas

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
FANTOM5 dataseti

FANTOM5 dataset
Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.

RNA tissue category FANTOM5
FANTOM5 RNA tissue category (category description) is calculated based on gene 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

ATRX (HGNC Symbol)

Synonyms

JMS, MRX52, RAD54, XH2, XNP

Description

Alpha thalassemia/mental retardation syndrome X-linked (HGNC Symbol)

Entrez gene summary

The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. This protein is found to undergo cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis. Mutations in this gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2013]

Chromosome

X

Cytoband

q21.1

Chromosome location (bp)

77504878 - 77786269

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000085224 (version 83.38)

Entrez gene

546

UniProt

P46100 (UniProt - Evidence at protein level)

neXtProt

NX_P46100

Antibodypedia

ATRX 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.

ATRX-001
ATRX-002
ATRX-004
ATRX-005
ATRX-007
ATRX-009
ATRX-010
ATRX-012
ATRX-013
ATRX-015

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)

ATRX-001
ENSP00000362441
ENST00000373344
P46100 [Direct mapping]
Transcriptional regulator ATRX
A4LAA3 [Target identity:100%; Query identity:100%]
Alpha thalassemia/mental retardation syndrome X-linked
Show all
Enzymes
   ENZYME proteins
   Hydrolases
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
Predicted intracellular proteins
Transcription factors
   Zinc-coordinating DNA-binding domains
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Disease related genes
Potential drug targets
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000228 [nuclear chromosome]
GO:0000792 [heterochromatin]
GO:0003677 [DNA binding]
GO:0003678 [DNA helicase activity]
GO:0003682 [chromatin binding]
GO:0004386 [helicase activity]
GO:0005515 [protein binding]
GO:0005524 [ATP binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005720 [nuclear heterochromatin]
GO:0006281 [DNA repair]
GO:0006306 [DNA methylation]
GO:0006310 [DNA recombination]
GO:0006334 [nucleosome assembly]
GO:0006336 [DNA replication-independent nucleosome assembly]
GO:0006338 [chromatin remodeling]
GO:0006351 [transcription, DNA-templated]
GO:0006355 [regulation of transcription, DNA-templated]
GO:0007283 [spermatogenesis]
GO:0008270 [zinc ion binding]
GO:0010571 [positive regulation of nuclear cell cycle DNA replication]
GO:0015616 [DNA translocase activity]
GO:0016605 [PML body]
GO:0030330 [DNA damage response, signal transduction by p53 class mediator]
GO:0030900 [forebrain development]
GO:0031297 [replication fork processing]
GO:0031933 [telomeric heterochromatin]
GO:0032206 [positive regulation of telomere maintenance]
GO:0032508 [DNA duplex unwinding]
GO:0035064 [methylated histone binding]
GO:0035128 [post-embryonic forelimb morphogenesis]
GO:0035264 [multicellular organism growth]
GO:0042393 [histone binding]
GO:0045944 [positive regulation of transcription from RNA polymerase II promoter]
GO:0060009 [Sertoli cell development]
GO:0070087 [chromo shadow domain binding]
GO:0070603 [SWI/SNF superfamily-type complex]
GO:0072520 [seminiferous tubule development]
GO:0072711 [cellular response to hydroxyurea]
GO:1901581 [negative regulation of telomeric RNA transcription from RNA pol II promoter]
Show all
2492 aa
282.6 kDa
No 0
ATRX-002
ENSP00000378967
ENST00000395603
P46100 [Direct mapping]
Transcriptional regulator ATRX
Show all
Enzymes
   ENZYME proteins
   Hydrolases
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
Predicted intracellular proteins
Transcription factors
   Zinc-coordinating DNA-binding domains
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Disease related genes
Potential drug targets
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0003677 [DNA binding]
GO:0003678 [DNA helicase activity]
GO:0004386 [helicase activity]
GO:0005515 [protein binding]
GO:0005524 [ATP binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0005720 [nuclear heterochromatin]
GO:0006281 [DNA repair]
GO:0006306 [DNA methylation]
GO:0006310 [DNA recombination]
GO:0006334 [nucleosome assembly]
GO:0006336 [DNA replication-independent nucleosome assembly]
GO:0006338 [chromatin remodeling]
GO:0006351 [transcription, DNA-templated]
GO:0006355 [regulation of transcription, DNA-templated]
GO:0008270 [zinc ion binding]
GO:0010571 [positive regulation of nuclear cell cycle DNA replication]
GO:0015616 [DNA translocase activity]
GO:0016605 [PML body]
GO:0030330 [DNA damage response, signal transduction by p53 class mediator]
GO:0031297 [replication fork processing]
GO:0031933 [telomeric heterochromatin]
GO:0032206 [positive regulation of telomere maintenance]
GO:0032508 [DNA duplex unwinding]
GO:0035064 [methylated histone binding]
GO:0042393 [histone binding]
GO:0045944 [positive regulation of transcription from RNA polymerase II promoter]
GO:0070087 [chromo shadow domain binding]
GO:0070603 [SWI/SNF superfamily-type complex]
GO:0072711 [cellular response to hydroxyurea]
GO:1901581 [negative regulation of telomeric RNA transcription from RNA pol II promoter]
Show all
2454 aa
278.2 kDa
No 0
ATRX-004
ENSP00000485253
ENST00000624032
A0A096LNW1 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
954 aa
107 kDa
No 0
ATRX-005
ENSP00000485408
ENST00000493470
A0A096LP59 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
293 aa
33.1 kDa
No 0
ATRX-007
ENSP00000383663
ENST00000400866
H0Y3T0 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005524 [ATP binding]
Show all
198 aa
22.9 kDa
No 0
ATRX-009
ENSP00000485127
ENST00000623321
A0A096LNN3 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
528 aa
59.4 kDa
No 0
ATRX-010
ENSP00000485103
ENST00000624166
A0A096LNL9 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
1351 aa
151.7 kDa
No 0
ATRX-012
ENSP00000485587
ENST00000622960
A0A096LPG6 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
47 aa
5 kDa
No 0
ATRX-013
ENSP00000485100
ENST00000624668
A0A096LNL7 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
108 aa
12 kDa
No 0
ATRX-015
ENSP00000485099
ENST00000625063
A0A096LNL6 [Direct mapping]
Transcriptional regulator ATRX
Show all
Predicted intracellular proteins
Cancer-related genes
   Mutational cancer driver genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Nonsense Mutations
   COSMIC Missense Mutations
   COSMIC Frameshift Mutations
Protein evidence (Ezkurdia et al 2014)
Show all
198 aa
22.2 kDa
No 0

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The Human Protein Atlas project is funded
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