We use cookies to enhance the usability of our website. If you continue, we'll assume that you are happy to receive all cookies. More information. Don't show this again.
Fields »
 

Field

Term
Gene name

Class

Subclass

Chromosome

External id

In atlas

Reliability

Reliability

Reliability

Validation

Method

Validation

Method

Validation

Method

Validation

Location

Searches

Tissue

Cell type

Expression

Tissue

Specificity

Cell line

Specificity

Cancer

Specificity

Tissue

Detectable

Cell line

Detectable

Cancer

Detectable

Cancer

Prognosis

Category

Score

Score

Score

Antibodies

Column

 
 
ABOUT
HELP
BLOG
  • THE HUMAN PROTEOME
  • THE HUMAN TISSUES
  • THE HUMAN CELL
  • HUMAN PATHOLOGY
  • PROTEIN CLASSES
  • PROTEIN EVIDENCE
    • NEWS
    • BLOG
    • EVENTS
    • PRESS ROOM
    • LEARN
    • DICTIONARY
    • METHODS
    • CELL LINES
  • THE PROJECT
  • INTRODUCTION
  • ORGANIZATION
  • PUBLICATIONS
  • PUBLICATION DATA
  • ANTIBODY SUBMISSION
  • ANTIBODY AVAILABILITY
  • LINKS
  • CONTACT
  • TECHNICAL DATA
  • ANTIBODY VALIDATION
  • ASSAYS & ANNOTATION
  • DISCLAIMER
  • DOWNLOADABLE DATA
  • HELP & FAQ
  • LICENCE & CITATION
  • PRIVACY STATEMENT
  • RELEASE HISTORY
ABCA13
  • TISSUE

  • CELL

  • PATHOLOGY

PATHOLOGY ATLAS

GENE/PROTEIN

Dictionary

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

ABCA13

Gene descriptioni

Gene description according to HGNC.

ATP-binding cassette, sub-family A (ABC1), member 13

Protein classi

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

Predicted membrane proteins

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Membrane

Number of transcriptsi

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

4
SHOW MORE

HUMAN PROTEIN ATLAS INFORMATION

RNA 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.

TCGA (cancer tissue):Mixed
HPA (cell line):Cell line enhanced (HDLM-2, U-2 OS)
HPA (normal tissue):Tissue enriched (bone marrow)

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 transcript level

ANTIBODY IHC RELIABILITY

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

Pending cancer tissue analysis.

PROGNOSTIC SUMMARYi

Kaplan-Meier plots for all cancers where high expression of this gene has significant (p<0.001) association with patient survival are shown in this summary. Whether the prognosis is favourable or unfavourable is indicated in brackets. Each Kaplan-Meier plot is clickable and redirects to a detailed page that includes individual expression and survival data for patients with the selected cancer.

Gene product is not prognostic.
Show all

RNA EXPRESSION OVERVIEWi

RNA expression overview shows RNA-seq data from The Cancer Genome Atlas (TCGA).

TCGA dataseti
RNA-seq data in 17 cancer types are reported as median FPKM (number Fragments Per Kilobase of exon per Million reads), generated by the The Cancer Genome Atlas (TCGA). RNA cancer tissue category is calculated based on mRNA expression levels across all 17 cancer tissues and include: cancer tissue enriched, cancer group enriched, cancer tissue enhanced, expressed in all, mixed and not detected. To access cancer specific RNA and prognostic data, click on the cancer name.

Read more
RNA cancer category: Mixed

PROTEIN EXPRESSIONi

Antibody staining in 20 different cancers is summarized by a selection of four standard cancer tissue samples representative of the overall staining pattern. From left: colorectal cancer, breast cancer, prostate cancer and lung cancer. An additional fifth image can be added as a complement. The assay and annotation is described here. Note that samples used for immunohistochemistry by the Human Protein Atlas do not correspond to samples in the TCGA dataset.

For histological reference, visit the histological dictionary.

Pending cancer tissue analysis


STAINING SUMMARYi

For each cancer, the fraction of samples with protein expression level high, medium, low, or not detected are provided by the blue-scale color-coding (as described by the color-coding scale in the box to the left). The length of the bar represents the number of patient samples analyzed (max=12 patients). The images and annotations can be accessed by clicking on the cancer name or protein expression bar. If more than one antibody is analyzed, the tabs at the top of the staining summary section can be used to toggle between the different antibodies. The mouse-over function displays additional data for the features in the staining summary view.

Next to the cancer staining data, the protein expression data of normal tissues or specific cell types corresponding to each cancer are shown and protein expression levels are indicated by the blue-scale color coding.

 

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

ABCA13 (HGNC Symbol)

Synonyms

FLJ33876, FLJ33951

Description

ATP-binding cassette, sub-family A (ABC1), member 13 (HGNC Symbol)

Entrez gene summary

In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.[provided by RefSeq, Mar 2009]

Chromosome

7

Cytoband

p12.3

Chromosome location (bp)

48171458 - 48647496

Protein evidence

Evidence at transcript level (all genes)

Ensembl

ENSG00000179869 (version 83.38)

Entrez gene

154664

UniProt

neXtProt

Antibodypedia

ABCA13 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.

ABCA13-001
ABCA13-003
ABCA13-005
ABCA13-008

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)

ABCA13-001
ENSP00000411096
ENST00000435803
A0A0A0MT16 [Direct mapping]
ATP-binding cassette sub-family A member 13
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Show all
GO:0005524 [ATP binding]
GO:0005548 [phospholipid transporter activity]
GO:0005887 [integral component of plasma membrane]
GO:0008152 [metabolic process]
GO:0016887 [ATPase activity]
GO:0017127 [cholesterol transporter activity]
GO:0033344 [cholesterol efflux]
GO:0033700 [phospholipid efflux]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0055085 [transmembrane transport]
Show all
5058 aa
576.2 kDa
No >9
ABCA13-003
ENSP00000391042
ENST00000411975
H0Y4D2 [Direct mapping]
ATP-binding cassette sub-family A member 13
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   7TM proteins predicted by MDM
Show all
GO:0005524 [ATP binding]
GO:0005548 [phospholipid transporter activity]
GO:0005887 [integral component of plasma membrane]
GO:0008152 [metabolic process]
GO:0016887 [ATPase activity]
GO:0017127 [cholesterol transporter activity]
GO:0033344 [cholesterol efflux]
GO:0033700 [phospholipid efflux]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0055085 [transmembrane transport]
Show all
831 aa
93.4 kDa
No 7
ABCA13-005
ENSP00000389861
ENST00000435451
H7BZI9 [Direct mapping]
ATP-binding cassette sub-family A member 13
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   4TM proteins predicted by MDM
Show all
GO:0005548 [phospholipid transporter activity]
GO:0005887 [integral component of plasma membrane]
GO:0017127 [cholesterol transporter activity]
GO:0033344 [cholesterol efflux]
GO:0033700 [phospholipid efflux]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0055085 [transmembrane transport]
Show all
155 aa
17.2 kDa
No 4
ABCA13-008
ENSP00000442634
ENST00000544596
F5H7B7 [Direct mapping]
ATP-binding cassette sub-family A member 13
Show all
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   >9TM proteins predicted by MDM
Show all
GO:0005524 [ATP binding]
GO:0005548 [phospholipid transporter activity]
GO:0005887 [integral component of plasma membrane]
GO:0008152 [metabolic process]
GO:0016887 [ATPase activity]
GO:0017127 [cholesterol transporter activity]
GO:0033344 [cholesterol efflux]
GO:0033700 [phospholipid efflux]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0055085 [transmembrane transport]
Show all
2366 aa
266.9 kDa
No >9

Contact

  • BLOG
  • PRESS ROOM
  • contact@proteinatlas.org

The Project

  • INTRODUCTION
  • ORGANIZATION
  • PUBLICATIONS
  • DOWNLOADABLE DATA

The Human Protein Atlas

  • ANTIBODY AVAILABILITY
  • LICENCE & CITATION
  • HELP & FAQ
The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg foundation.