ABCF1 ATP binding cassette subfamily F member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCF1provided by HGNC
Official Full Name: ATP binding cassette subfamily F member 1provided by HGNC
Primary source: HGNC:HGNC:70
See related: Ensembl:ENSG00000204574 MIM:603429; AllianceGenome:HGNC:70
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ABC27; ABC50
Summary: The 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 intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the GCN20 subfamily. Unlike other members of the superfamily, this protein lacks the transmembrane domains which are characteristic of most ABC transporters. This protein may be regulated by tumor necrosis factor-alpha and play a role in enhancement of protein synthesis and the inflammation process. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 25.4), bone marrow (RPKM 18.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (30571442..30591522)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (30435621..30455699)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (30539219..30559299)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ABCF1 functions as a transcriptional coactivator for OCT4 and SOX2 to stimulate transciption of pluripotency-associated genes in embryonic stem cells.
Title: ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low-complexity domain.
ABCF1/CXCL12/CXCR4 Enhances Glioblastoma Cell Proliferation, Migration, and Invasion by Activating the PI3K/AKT Signal Pathway.
Title: ABCF1/CXCL12/CXCR4 Enhances Glioblastoma Cell Proliferation, Migration, and Invasion by Activating the PI3K/AKT Signal Pathway.
ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells.
Title: ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells.
The ATP-binding cassette transporter ABCF1 is a hepatic oncofetal protein that promotes chemoresistance, epithelial mesenchymal transformation and cancer stemness in hepatocellular carcinoma cells.
Title: The ATP-binding cassette transporter ABCF1 is a hepatic oncofetal protein that promotes chemoresistance, EMT and cancer stemness in hepatocellular carcinoma.
The combined assessment of IGF2BP3 and ABCF1 predicts recurrence in Ewing sarcoma patients.
Title: Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 is a Novel Post-Transcriptional Regulator of Ewing Sarcoma Malignancy.
Study solves the crystal structure of an ATP-bound wild-type human ABCF1 at 2.3-A resolution. The comparative studies indicate that the structure is in a pre-activation intermediate conformation. This conformation is stabilized by the interaction between ATP and protein suggesting that this conformation is an important step in the activation of ABCF1.
Title: Crystal Structure of ATP-Bound Human ABCF1 Demonstrates a Unique Conformation of ABC Proteins.
The high copy number variant in the ABCF1 gene was the strongest risk factor for gout.
Title: Copy number variants of ABCF1, IL17REL, and FCGR3A are associated with the risk of gout.
ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis of shed photoreceptor outer segments.
Title: ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis.
Elevated microRNA-23a Expression Enhances the Chemoresistance of Colorectal Cancer Cells with Microsatellite Instability to 5-Fluorouracil by Directly Targeting ABCF1
Title: Elevated microRNA-23a Expression Enhances the Chemoresistance of Colorectal Cancer Cells with Microsatellite Instability to 5-Fluorouracil by Directly Targeting ABCF1.
expression of ABC50 mutants, which cannot hydrolyse ATP, decreases general translation and relaxes the discrimination against the use of non-AUG codons at translation start sites.
Title: ABC50 mutants modify translation start codon selection.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Identification of independent risk loci for Graves' disease within the MHC in the Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, ATP-binding cassette, sub-family F (ABCF1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with ABCF1 is increased by RRE	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

G62097 (e-PCR)
- UniSTS:139116

D1S1423 (e-PCR)
- UniSTS:149619

ABCF1_2136 (e-PCR)
- UniSTS:463229

D16S325 (e-PCR)
- UniSTS:147089

ABCF1_1054 (e-PCR)
- UniSTS:276954

D6S2266 (e-PCR)
- UniSTS:67326

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribosome binding	IDA Inferred from Direct Assay more info	PubMed
enables translation activator activity	IDA Inferred from Direct Assay more info	PubMed
enables translation factor activity, RNA binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in inflammatory response	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in ribosome biogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in translation	TAS Traceable Author Statement more info	PubMed
involved_in translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ATP-binding cassette sub-family F member 1

Names: ATP-binding cassette 50 (TNF-alpha stimulated); ATP-binding cassette, sub-family F (GCN20), member 1; TNF-alpha-stimulated ABC protein; TNFalpha-inducible ATP-binding protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_047030.1 RefSeqGene

Range

5050..25130

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001025091.2 → NP_001020262.1 ATP-binding cassette sub-family F member 1 isoform a

See identical proteins and their annotated locations for NP_001020262.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AF027302, BC034488, BI547952, BM556481, BU620927

Consensus CDS

CCDS34380.1

UniProtKB/Swiss-Prot

A2BF75, O14897, Q69YP6, Q8NE71

UniProtKB/TrEMBL

A0A1U9X609, Q5STZ8

Related

ENSP00000313603.8, ENST00000326195.13

Conserved Domains (1) summary

COG0488
Location:302 → 833

Uup; ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
NM_001090.3 → NP_001081.1 ATP-binding cassette sub-family F member 1 isoform b

See identical proteins and their annotated locations for NP_001081.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting protein (isoform b) is shorter than isoform a.

Source sequence(s)

AF027302, BM556481, BU620927

Consensus CDS

CCDS34381.1

UniProtKB/TrEMBL

Q2L6I2, Q5STZ8

Related

ENSP00000365728.3, ENST00000376545.7

Conserved Domains (3) summary

cd03221
Location:266 → 487

ABCF_EF-3; ATP-binding cassette domain of elongation factor 3, subfamily F

COG0488
Location:264 → 795

Uup; ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

cl21455
Location:659 → 736

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases