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

    Gene ID: 23, updated on 27-Nov-2024

    Summary

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    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

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    See ABCF1 in Genome Data Viewer
    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_000006.12Genomic Context describing neighboring genes Neighboring gene G protein nucleolar 1 (putative) Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30523544-30524109 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30524110-30524674 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30524675-30525239 Neighboring gene proline rich 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30538839-30539400 Neighboring gene microRNA 877 Neighboring gene protein phosphatase 1 regulatory subunit 10 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:30577096-30578295 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30585278-30585846 Neighboring gene mitochondrial ribosomal protein S18B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells. Cao QT, et al. Front Cell Infect Microbiol, 2020. PMID 33042865, Free PMC Article
    2. A novel rare copy number variant of the ABCF1 gene identified among dengue fever patients from Peninsular Malaysia. Hoh BP, et al. Genet Mol Res, 2014 Feb 19. PMID 24634119
    3. ABC50 mutants modify translation start codon selection. Stewart JD, et al. Biochem J, 2015 Apr 15. PMID 25597744
    4. ATP-binding cassette protein ABCF1 couples transcription and genome surveillance in embryonic stem cells through low-complexity domain. Choi EB, et al. Sci Adv, 2021 Oct 29. PMID 34714667, Free PMC Article
    5. Protein Aggregation and Disaggregation in Cells and Development. Fassler JS, et al. J Mol Biol, 2021 Oct 15. PMID 34450138, Free PMC Article

    See all (169) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells.
      Title: ABCF1 Regulates dsDNA-induced Immune Responses in Human Airway Epithelial Cells.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis of shed photoreceptor outer segments.
      Title: ABCF1 extrinsically regulates retinal pigment epithelial cell phagocytosis.
    9. 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.
    10. 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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 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 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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    NEW Try the new Transcript table

    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_001025091.2 → 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]

    2. 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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

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

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

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

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

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

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

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

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

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

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

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

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      30435621..30455699
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NE71.2 GenPept UniProtKB/Swiss-Prot:Q8NE71

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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