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Aliases for ABCF1 Gene

Aliases for ABCF1 Gene

  • ATP Binding Cassette Subfamily F Member 1 2 3 5
  • ATP-Binding Cassette, Sub-Family F (GCN20), Member 1 2 3
  • TNF-Alpha-Stimulated ABC Protein 3 4
  • ABC50 3 4
  • ATP-Binding Cassette 50 (TNF-Alpha Stimulated) 3
  • ATP-Binding Cassette Sub-Family F Member 1 3
  • TNFalpha-Inducible ATP-Binding Protein 3
  • ATP-Binding Cassette 50 4
  • ABC27 3

External Ids for ABCF1 Gene

Previous HGNC Symbols for ABCF1 Gene

  • ABC50

Previous GeneCards Identifiers for ABCF1 Gene

  • GC06P030594
  • GC06P030309
  • GC06P030645
  • GC06P030647
  • GC06P030539
  • GC06P030339

Summaries for ABCF1 Gene

Entrez Gene Summary for ABCF1 Gene

  • 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]

GeneCards Summary for ABCF1 Gene

ABCF1 (ATP Binding Cassette Subfamily F Member 1) is a Protein Coding gene. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include ribosome binding. An important paralog of this gene is ABCF3.

UniProtKB/Swiss-Prot for ABCF1 Gene

  • Isoform 2 is required for efficient Cap- and IRES-mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis.

Gene Wiki entry for ABCF1 Gene

Additional gene information for ABCF1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ABCF1 Gene

Genomics for ABCF1 Gene

GeneHancer (GH) Regulatory Elements for ABCF1 Gene

Promoters and enhancers for ABCF1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J030570 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 663.5 +1.3 1267 4.6 CLOCK MLX ZFP64 DMAP1 YBX1 YY1 SLC30A9 E2F8 ZNF143 SP3 ABCF1 GNL1 DDX39B TRIM26 ENSG00000272540 HLA-H HCG4P7 PPP1R10 PAIP1P1 HLA-F-AS1
GH06J030611 Promoter/Enhancer 2.6 EPDnew Ensembl ENCODE dbSUPER 66.2 +44.2 44176 8.7 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 PPP1R10 MRPS18B MDC1 DDX39B TRIM39 NRM DHX16 ZNRD1 ABCF1 TRIM26
GH06J030715 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 61.5 +148.2 148150 7.7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 MDC1 TUBB DDX39B LY6G5B TRIM39 DHX16 PPP1R10 ZNRD1 PAIP1P1 NRM
GH06J030907 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 62.9 +337.1 337081 2.2 CLOCK DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 GTF2H4 VARS2 GC06P032276 MDC1 DDX39B LY6G5B LSM2 TRIM39 DHX16 PPP1R10
GH06J031538 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 51.7 +969.8 969763 4.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF263 DDX39B DDX39B-AS1 GC06M031542 GC06M031543 GC06M031550 GC06M031555 GC06M031573 GC06M032007 GC06M032013 GC06M032015
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ABCF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ABCF1 gene promoter:
  • AREB6
  • C/EBPalpha
  • Pax-5
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • p53
  • IRF-2

Genomic Locations for ABCF1 Gene

Genomic Locations for ABCF1 Gene
chr6:30,571,376-30,597,179
(GRCh38/hg38)
Size:
25,804 bases
Orientation:
Plus strand
chr6:30,539,153-30,564,956
(GRCh37/hg19)
Size:
25,804 bases
Orientation:
Plus strand

Genomic View for ABCF1 Gene

Genes around ABCF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ABCF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ABCF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for ABCF1 Gene

  • Protein details for ABCF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NE71-ABCF1_HUMAN
    Recommended name:
    ATP-binding cassette sub-family F member 1
    Protein Accession:
    Q8NE71
    Secondary Accessions:
    • A2BF75
    • O14897
    • Q69YP6

    Protein attributes for ABCF1 Gene

    Size:
    845 amino acids
    Molecular mass:
    95926 Da
    Quaternary structure:
    • Isoform 2 interacts (via N-terminus) with EIF2S1; the interaction is independent of its phosphorylated status. Isoform 2 associates (via both ABC transporter domains) with the ribosomes.

    Alternative splice isoforms for ABCF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ABCF1 Gene

Post-translational modifications for ABCF1 Gene

  • Isoform 2 is phosphorylated at phosphoserine and phosphothreonine. Isoform 2 phosphorylation on Ser-109 and Ser-140 by CK2 inhibits association of EIF2 with ribosomes.
  • Ubiquitination at Lys689, posLast=582582, Lys573, posLast=451451, and Lys39
  • Modification sites at PhosphoSitePlus

Other Protein References for ABCF1 Gene

No data available for DME Specific Peptides for ABCF1 Gene

Domains & Families for ABCF1 Gene

Gene Families for ABCF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for ABCF1 Gene

Graphical View of Domain Structure for InterPro Entry

Q8NE71

UniProtKB/Swiss-Prot:

ABCF1_HUMAN :
  • Belongs to the ABC transporter superfamily. ABCF family. EF3 subfamily.
Family:
  • Belongs to the ABC transporter superfamily. ABCF family. EF3 subfamily.
genes like me logo Genes that share domains with ABCF1: view

Function for ABCF1 Gene

Molecular function for ABCF1 Gene

UniProtKB/Swiss-Prot Function:
Isoform 2 is required for efficient Cap- and IRES-mediated mRNA translation initiation. Isoform 2 is not involved in the ribosome biogenesis.
UniProtKB/Swiss-Prot Induction:
By TNF in cultured synoviocytes.
GENATLAS Biochemistry:
ATP binding cassette superfamily,subfamily F (GCN20) member 1,widely expressed,putative ribosomal protein,involved in translation of mRNA,present in synoviocytes after TNFA induction,potentially involved in inflammatory process

Phenotypes From GWAS Catalog for ABCF1 Gene

Gene Ontology (GO) - Molecular Function for ABCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 17894550
GO:0005524 ATP binding IEA --
GO:0008135 translation factor activity, RNA binding TAS 9790762
GO:0016887 ATPase activity IEA --
genes like me logo Genes that share ontologies with ABCF1: view

Phenotypes for ABCF1 Gene

genes like me logo Genes that share phenotypes with ABCF1: view

Animal Model Products

CRISPR Products

miRNA for ABCF1 Gene

miRTarBase miRNAs that target ABCF1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ABCF1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ABCF1 Gene

Localization for ABCF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ABCF1 Gene

Isoform 2: Cytoplasm. Nucleus, nucleoplasm. Nucleus envelope.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ABCF1 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ABCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IEA --
GO:0005654 nucleoplasm IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS,IDA --
genes like me logo Genes that share ontologies with ABCF1: view

Pathways & Interactions for ABCF1 Gene

genes like me logo Genes that share pathways with ABCF1: view

Pathways by source for ABCF1 Gene

SIGNOR curated interactions for ABCF1 Gene

Other effect:

Gene Ontology (GO) - Biological Process for ABCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation TAS 9790762
GO:0006954 inflammatory response TAS 9790762
GO:0055085 transmembrane transport TAS --
genes like me logo Genes that share ontologies with ABCF1: view

Drugs & Compounds for ABCF1 Gene

(1) Drugs for ABCF1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0
genes like me logo Genes that share compounds with ABCF1: view

Transcripts for ABCF1 Gene

mRNA/cDNA for ABCF1 Gene

Unigene Clusters for ABCF1 Gene

ATP-binding cassette, sub-family F (GCN20), member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ABCF1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ABCF1 Gene

No ASD Table

Relevant External Links for ABCF1 Gene

GeneLoc Exon Structure for
ABCF1
ECgene alternative splicing isoforms for
ABCF1

Expression for ABCF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ABCF1 Gene

Protein differential expression in normal tissues from HIPED for ABCF1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.4) and Lymph node (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ABCF1 Gene



Protein tissue co-expression partners for ABCF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ABCF1 Gene:

ABCF1

SOURCE GeneReport for Unigene cluster for ABCF1 Gene:

Hs.655285

mRNA Expression by UniProt/SwissProt for ABCF1 Gene:

Q8NE71-ABCF1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for ABCF1 Gene

  • Liver(4.4)
  • Blood(4.2)
  • Nervous system(3)
  • Lung(2.7)
  • Stomach(2.7)
  • Muscle(2)
genes like me logo Genes that share expression patterns with ABCF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ABCF1 Gene

Orthologs for ABCF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ABCF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ABCF1 34 33
  • 99.38 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ABCF1 34 33
  • 90.83 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ABCF1 34 33
  • 90.24 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ABCF1 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Abcf1 16 34 33
  • 86.45 (n)
rat
(Rattus norvegicus)
Mammalia Abcf1 33
  • 85.83 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ABCF1 34
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ABCF1 34
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia abcf1 33
  • 73.09 (n)
Str.1025 33
zebrafish
(Danio rerio)
Actinopterygii abcf1 34 33
  • 72.77 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG1703 34 35 33
  • 63.18 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F18E2.2 35
  • 61 (a)
abcf-1 34 33
  • 58.84 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GCN20 34
  • 29 (a)
OneToMany
-- 36
thale cress
(Arabidopsis thaliana)
eudicotyledons GCN4 33
  • 52.79 (n)
rice
(Oryza sativa)
Liliopsida Os03g0441500 33
  • 55.93 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 57 (a)
OneToOne
Species where no ortholog for ABCF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ABCF1 Gene

ENSEMBL:
Gene Tree for ABCF1 (if available)
TreeFam:
Gene Tree for ABCF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ABCF1: view image

Paralogs for ABCF1 Gene

Paralogs for ABCF1 Gene

(2) SIMAP similar genes for ABCF1 Gene using alignment to 8 proteins:

  • ABCF1_HUMAN
  • A0PJ72_HUMAN
  • F5GYK6_HUMAN
  • H0YGW7_HUMAN
  • L0R6B8_HUMAN
  • Q2L6I2_HUMAN
  • Q5STZ7_HUMAN
  • Q5STZ8_HUMAN
genes like me logo Genes that share paralogs with ABCF1: view

Variants for ABCF1 Gene

Sequence variations from dbSNP and Humsavar for ABCF1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs754981516 likely-benign, Long QT syndrome 30,590,190(+) C/T coding_sequence_variant, missense_variant
rs1000030264 -- 30,588,487(+) G/A intron_variant
rs1000177520 -- 30,570,431(+) A/G upstream_transcript_variant
rs1000225697 -- 30,575,025(+) G/A intron_variant
rs1000479465 -- 30,586,002(+) G/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ABCF1 Gene

Variant ID Type Subtype PubMed ID
esv2670269 CNV deletion 23128226
esv2731791 CNV deletion 23290073
esv3411275 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv5244 CNV deletion 18451855
nsv601264 CNV loss 21841781
nsv601481 CNV loss 21841781
nsv830626 CNV loss 17160897

Variation tolerance for ABCF1 Gene

Residual Variation Intolerance Score: 65.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.39; 54.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ABCF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ABCF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ABCF1 Gene

Disorders for ABCF1 Gene

Additional Disease Information for ABCF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for ABCF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ABCF1 Gene

Publications for ABCF1 Gene

  1. The N-terminal region of ABC50 interacts with eukaryotic initiation factor eIF2 and is a target for regulatory phosphorylation by CK2. (PMID: 17894550) Paytubi S … Proud CG (The Biochemical journal 2008) 3 4 22 58
  2. ABC50, a novel human ATP-binding cassette protein found in tumor necrosis factor-alpha-stimulated synoviocytes. (PMID: 9790762) Richard M … Beaulieu AD (Genomics 1998) 2 3 4 58
  3. Identification of independent risk loci for Graves' disease within the MHC in the Japanese population. (PMID: 21900946) Nakabayashi K … Shirasawa S (Journal of human genetics 2011) 3 44 58
  4. Association study between single-nucleotide polymorphisms in 199 drug-related genes and commonly measured quantitative traits of 752 healthy Japanese subjects. (PMID: 19343046) Saito A … Kamatani N (Journal of human genetics 2009) 3 44 58
  5. ABC50 promotes translation initiation in mammalian cells. (PMID: 19570978) Paytubi S … Proud CG (The Journal of biological chemistry 2009) 3 4 58

Products for ABCF1 Gene

Sources for ABCF1 Gene