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

Gene ID: 23, updated on 13-Mar-2020

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
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

Genomic context

See ABCF1 in Genome Data Viewer
Location:
6p21.33
Exon count:
25
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (30571442..30591522)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30539170..30559309)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene G protein nucleolar 1 (putative) Neighboring gene proline rich 3 Neighboring gene ABCF1 divergent transcript Neighboring gene microRNA 877 Neighboring gene protein phosphatase 1 regulatory subunit 10 Neighboring gene mitochondrial ribosomal protein S18B Neighboring gene Sharpr-MPRA regulatory region 13793 Neighboring gene alpha tubulin acetyltransferase 1

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of independent risk loci for Graves' disease within the MHC in the Japanese population.
NHGRI GWA Catalog

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ATPase activity IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
translation factor activity, RNA binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
inflammatory response TAS
Traceable Author Statement
more info
PubMed 
translation TAS
Traceable Author Statement
more info
PubMed 
transmembrane transport TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nuclear envelope IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
ribosome IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

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

  1. NG_047030.1 RefSeqGene

    Range
    5050..25130
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001025091.2NP_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
    Q8NE71
    UniProtKB/TrEMBL
    A0A1U9X609
    Related
    ENSP00000313603.8, ENST00000326195.13
    Conserved Domains (1) summary
    COG0488
    Location:302833
    Uup; ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
  2. NM_001090.3NP_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/Swiss-Prot
    Q8NE71
    UniProtKB/TrEMBL
    Q2L6I2
    Related
    ENSP00000365728.3, ENST00000376545.7
    Conserved Domains (3) summary
    cd03221
    Location:266487
    ABCF_EF-3; ATP-binding cassette domain of elongation factor 3, subfamily F
    COG0488
    Location:264795
    Uup; ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
    cl21455
    Location:659736
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    30571442..30591522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    2051164..2071240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    1827269..1847349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    1881671..1901751
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    1915488..1935568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    1826529..1846605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    1872199..1892278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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