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Term
Gene name

Class

Subclass

Chromosome

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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

 
 
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A1CF
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  • PATHOLOGY

PATHOLOGY ATLAS

GENE/PROTEIN

Antibody validation

Dictionary

Level of antibody staining/expression





High
Medium
Low
Not detected

GENERAL INFORMATION

Gene namei

Gene name according to HGNC.

A1CF

Gene descriptioni

Gene description according to HGNC.

APOBEC1 complementation factor

Protein classi

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

Predicted intracellular proteins

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.

8
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):Tissue enriched (liver cancer)
HPA (cell line):Group enriched (CACO-2, Hep G2)
HPA (normal tissue):Tissue enhanced (duodenum, liver, small intestine)

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 expression
normal tissuei

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

Cytoplasmic and nuclear expression in gastrointestinal tract, liver, pancreas and kidney.

ANTIBODY IHC 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 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 2 antibodies.
HPA037779 , HPA044079
SHOW MORE

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: Tissue enriched (liver cancer)

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.

Colorectal cancer
Breast cancer
Prostate cancer
Lung cancer
Liver cancer

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.

HPA037779
HPA044079

Cancer

Cancer staining

Protein
expression of
normal tissue

Breast cancer
 
Carcinoid
 
Cervical cancer
 
 
Colorectal cancer
 
 
Endometrial cancer
 
 
Glioma
 
Head and neck cancer
 
 
Liver cancer
 
 
Lung cancer
 
 
Lymphoma
 
 

Cancer

Cancer staining

Protein
expression of
normal tissue

Melanoma
 
Ovarian cancer
 
Pancreatic cancer
 
Prostate cancer
 
Renal cancer
 
Skin cancer
 
Stomach cancer
 
 
Testis cancer
 
Thyroid cancer
 
Urothelial cancer
 

Staining summaryi

A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.

Carcinoids, hepatocellular carcinomas and a few renal cancers exhibited moderate cytoplasmic and nuclear positivity. Remaining cancers were negative.

Cancer

Cancer staining

Protein
expression of
normal tissue

Breast cancer
 
Carcinoid
 
Cervical cancer
 
 
Colorectal cancer
 
 
Endometrial cancer
 
 
Glioma
 
Head and neck cancer
 
 
Liver cancer
 
 
Lung cancer
 
 
Lymphoma
 
 

Cancer

Cancer staining

Protein
expression of
normal tissue

Melanoma
 
Ovarian cancer
 
Pancreatic cancer
 
Prostate cancer
 
Renal cancer
 
Skin cancer
 
Stomach cancer
 
 
Testis cancer
 
Thyroid cancer
 
Urothelial cancer
 

Staining summaryi

A manually written summary of the overall protein expression pattern across the analyzed cancer tissues.

Moderate to strong nuclear and/or cytoplasmic immunoreactivity was observed in most carcinoids along with few colorectal, pancreatic, renal and liver cancers. Remaining cancer tissues were generally negative.

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

A1CF (HGNC Symbol)

Synonyms

ACF, ACF64, ACF65, APOBEC1CF, ASP

Description

APOBEC1 complementation factor (HGNC Symbol)

Entrez gene summary

Mammalian apolipoprotein B mRNA undergoes site-specific C to U deamination, which is mediated by a multi-component enzyme complex containing a minimal core composed of APOBEC-1 and a complementation factor encoded by this gene. The gene product has three non-identical RNA recognition motifs and belongs to the hnRNP R family of RNA-binding proteins. It has been proposed that this complementation factor functions as an RNA-binding subunit and docks APOBEC-1 to deaminate the upstream cytidine. Studies suggest that the protein may also be involved in other RNA editing or RNA processing events. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

Chromosome

10

Cytoband

q11.23

Chromosome location (bp)

50799409 - 50885675

Protein evidence

Evidence at protein level (all genes)

Ensembl

ENSG00000148584 (version 83.38)

Entrez gene

29974

UniProt

Q9NQ94 (UniProt - Evidence at protein level)

neXtProt

NX_Q9NQ94

Antibodypedia

A1CF 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.

A1CF-001
A1CF-002
A1CF-003
A1CF-004
A1CF-006
A1CF-201
A1CF-202
A1CF-203

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)

A1CF-001
ENSP00000363113
ENST00000374001
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZJ5 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_b
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
586 aa
64.3 kDa
No 0
A1CF-002
ENSP00000363105
ENST00000373993
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZM7 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_a
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
594 aa
65.2 kDa
No 0
A1CF-003
ENSP00000397953
ENST00000414883
Q5T0W7 [Direct mapping]
APOBEC1 complementation factor
Show all
Predicted intracellular proteins
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
Show all
201 aa
22.5 kDa
No 0
A1CF-004
ENSP00000363109
ENST00000373997
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZJ5 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_b
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
586 aa
64.3 kDa
No 0
A1CF-006
ENSP00000363107
ENST00000373995
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZI9 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_c
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
594 aa
65 kDa
No 0
A1CF-201
ENSP00000282641
ENST00000282641
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZJ5 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_b
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
586 aa
64.3 kDa
No 0
A1CF-202
ENSP00000378868
ENST00000395489
F8W9F8 [Direct mapping]
APOBEC1 complementation factor
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0005515 [protein binding]
GO:0005634 [nucleus]
GO:0005654 [nucleoplasm]
GO:0010609 [mRNA localization resulting in posttranscriptional regulation of gene expression]
GO:0016556 [mRNA modification]
Show all
602 aa
66 kDa
No 0
A1CF-203
ENSP00000378873
ENST00000395495
Q9NQ94 [Direct mapping]
APOBEC1 complementation factor
A0A024QZI9 [Target identity:100%; Query identity:100%]
Apobec-1 complementation factor, isoform CRA_c
Show all
Predicted intracellular proteins
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000166 [nucleotide binding]
GO:0003676 [nucleic acid binding]
GO:0003723 [RNA binding]
GO:0003727 [single-stranded RNA binding]
GO:0005515 [protein binding]
GO:0005654 [nucleoplasm]
GO:0005737 [cytoplasm]
GO:0005783 [endoplasmic reticulum]
GO:0006397 [mRNA processing]
GO:0010467 [gene expression]
GO:0016554 [cytidine to uridine editing]
GO:0016556 [mRNA modification]
GO:0030895 [apolipoprotein B mRNA editing enzyme complex]
GO:0050821 [protein stabilization]
Show all
594 aa
65 kDa
No 0

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