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Method

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Expression

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ABCA1
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TISSUE ATLAS PRIMARY DATA

GENE/PROTEIN

Antibody validation


Dictionary


Tissue proteome

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

ABCA1

Gene descriptioni

Gene description according to HGNC.

ATP-binding cassette, sub-family A (ABC1), member 1

Protein classi

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

Disease related genes
FDA approved drug targets
Plasma proteins
Predicted intracellular proteins
Predicted membrane proteins
Transporters

Predicted localizationi

Protein localization predicted from several bioinformatic algorithms.

Read more

Intracellular,Membrane

Number of transcriptsi

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

3
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:Mixed
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 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 membranous and cytoplasmic expression.

DATA RELIABILITY

Data reliability
descriptioni

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

Antibody staining mainly consistent with RNA expression data.

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.
CAB069889
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
N/A
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

Lung

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: Mixed
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

ABCA1 (HGNC Symbol)

Synonyms

ABC1, HDLDT1, TGD

Description

ATP-binding cassette, sub-family A (ABC1), member 1 (HGNC Symbol)

Entrez gene summary

The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in this gene have been associated with Tangier's disease and familial high-density lipoprotein deficiency. [provided by RefSeq, Jul 2008]

Chromosome

9

Cytoband

q31.1

Chromosome location (bp)

104781002 - 104928237

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000165029 (version 83.38)

Entrez gene

19

UniProt

O95477 (UniProt - Evidence at protein level)

neXtProt

NX_O95477

Antibodypedia

ABCA1 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.

ABCA1-001
ABCA1-002
ABCA1-004

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)

ABCA1-001
ENSP00000416623
ENST00000423487
B1AMI2 [Direct mapping]
ATP-binding cassette sub-family A member 1; ATP-binding cassette, sub-family A (ABC1), member 1, isoform CRA_b
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
   2TM proteins predicted by MDM
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005524 [ATP binding]
GO:0005887 [integral component of plasma membrane]
GO:0006911 [phagocytosis, engulfment]
GO:0033344 [cholesterol efflux]
GO:0034186 [apolipoprotein A-I binding]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0043691 [reverse cholesterol transport]
GO:0055085 [transmembrane transport]
Show all
363 aa
41.1 kDa
No 2
ABCA1-002
ENSP00000363868
ENST00000374736
O95477 [Direct mapping]
ATP-binding cassette sub-family A member 1
Show all
Transporters
   Primary Active Transporters
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
Plasma proteins
Disease related genes
FDA approved drug targets
   Small molecule drugs
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0002790 [peptide secretion]
GO:0005102 [receptor binding]
GO:0005515 [protein binding]
GO:0005524 [ATP binding]
GO:0005543 [phospholipid binding]
GO:0005548 [phospholipid transporter activity]
GO:0005794 [Golgi apparatus]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0006497 [protein lipidation]
GO:0006911 [phagocytosis, engulfment]
GO:0007040 [lysosome organization]
GO:0007186 [G-protein coupled receptor signaling pathway]
GO:0007584 [response to nutrient]
GO:0008203 [cholesterol metabolic process]
GO:0008509 [anion transmembrane transporter activity]
GO:0009897 [external side of plasma membrane]
GO:0009986 [cell surface]
GO:0010745 [negative regulation of macrophage derived foam cell differentiation]
GO:0010875 [positive regulation of cholesterol efflux]
GO:0010887 [negative regulation of cholesterol storage]
GO:0015485 [cholesterol binding]
GO:0016197 [endosomal transport]
GO:0016887 [ATPase activity]
GO:0017127 [cholesterol transporter activity]
GO:0019905 [syntaxin binding]
GO:0030139 [endocytic vesicle]
GO:0030301 [cholesterol transport]
GO:0030819 [positive regulation of cAMP biosynthetic process]
GO:0031267 [small GTPase binding]
GO:0032367 [intracellular cholesterol transport]
GO:0032489 [regulation of Cdc42 protein signal transduction]
GO:0033344 [cholesterol efflux]
GO:0033700 [phospholipid efflux]
GO:0034185 [apolipoprotein binding]
GO:0034186 [apolipoprotein A-I binding]
GO:0034188 [apolipoprotein A-I receptor activity]
GO:0034364 [high-density lipoprotein particle]
GO:0034380 [high-density lipoprotein particle assembly]
GO:0034616 [response to laminar fluid shear stress]
GO:0038027 [apolipoprotein A-I-mediated signaling pathway]
GO:0042157 [lipoprotein metabolic process]
GO:0042158 [lipoprotein biosynthetic process]
GO:0042493 [response to drug]
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0042632 [cholesterol homeostasis]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0043691 [reverse cholesterol transport]
GO:0044255 [cellular lipid metabolic process]
GO:0044281 [small molecule metabolic process]
GO:0045121 [membrane raft]
GO:0045332 [phospholipid translocation]
GO:0045335 [phagocytic vesicle]
GO:0048471 [perinuclear region of cytoplasm]
GO:0050702 [interleukin-1 beta secretion]
GO:0051117 [ATPase binding]
GO:0055085 [transmembrane transport]
GO:0055091 [phospholipid homeostasis]
GO:0055098 [response to low-density lipoprotein particle]
GO:0060155 [platelet dense granule organization]
GO:0071222 [cellular response to lipopolysaccharide]
GO:0071300 [cellular response to retinoic acid]
GO:0071397 [cellular response to cholesterol]
GO:0098656 [anion transmembrane transport]
Show all
2261 aa
254.3 kDa
No >9
ABCA1-004
ENSP00000363865
ENST00000374733
B1AMI1 [Direct mapping]
ATP-binding cassette sub-family A member 1
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0042626 [ATPase activity, coupled to transmembrane movement of substances]
GO:0055085 [transmembrane transport]
Show all
123 aa
13.8 kDa
No 0

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