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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
  • EC 3.6.3.17 58
  • EC 2.7.7.6 58
  • 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 Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and CDK-mediated phosphorylation and removal of Cdc6. GO annotations related to this gene include poly(A) RNA binding and 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

Regulatory Elements for ABCF1 Gene

Enhancers for ABCF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H030611 1.7 Ensembl ENCODE dbSUPER 66.2 +44.2 44177 8 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 MDC1 DDX39B TRIM39 PPP1R10 ABCF1 NRM DHX16 ZNRD1 GTF2H4 TRIM26
GH06H030715 1.5 ENCODE dbSUPER 51.3 +148.2 148151 7 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 SP3 NFYC MDC1 LY6G5B TRIM39 DDX39B DHX16 ABCF1 PPP1R10 ZNRD1 NRM HCG18
GH06H030875 1.7 FANTOM5 ENCODE dbSUPER 38.2 +305.4 305444 3 HDGF PKNOX1 FOXA2 ARNT ARID4B ZNF2 YY1 ZNF766 ZNF143 DEK VARS2 ABCF1 LSM2 VARS TRIM39 PPP1R10 TRIM26 MDC1 DDX39B LY6G5B
GH06H030907 1.2 ENCODE 53.9 +337.1 337082 2 DMAP1 YBX1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A MEF2D MDC1 GTF2H4 TRIM39 LY6G5B LSM2 DDX39B HCG18 PPP1R10 ENSG00000233892 DHX16
GH06H030541 1.5 Ensembl ENCODE dbSUPER 31.8 -28.5 -28476 3 PKNOX1 ATF1 ARID4B SIN3A ZNF2 YY1 TCF12 ELK1 ZNF143 ATF7 ABCF1 PPP1R10 TRIM39 DHX16 MDC1 ZNRD1 DDX39B ENSG00000233892 TRIM26 LINC02569
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ABCF1 on UCSC Golden Path with GeneCards custom track

Promoters for ABCF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195413 24 1601 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1

Genomic Location for ABCF1 Gene

Chromosome:
6
Start:
30,571,376 bp from pter
End:
30,597,179 bp from pter
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

Selected DME Specific Peptides for ABCF1 Gene

Q8NE71:
  • KRLKLLE
  • LILDEPT
  • LMLDEPT

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 posLast=3939, posLast=451451, Lys573, Lys582, and posLast=689689
  • Modification sites at PhosphoSitePlus

Other Protein References for ABCF1 Gene

Domains & Families for ABCF1 Gene

Gene Families for ABCF1 Gene

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

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

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
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.

Enzyme Numbers (IUBMB) for ABCF1 Gene

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 IDA 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

GenomeRNAi human phenotypes for ABCF1:
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

Clone Products

  • Applied Biological Materials Clones for ABCF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for 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 IDA,TAS --
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 Nutra Agonist 0
genes like me logo Genes that share compounds with ABCF1: view

Transcripts for ABCF1 Gene

Unigene Clusters for ABCF1 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for ABCF1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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, PaxDb, 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

Primer Products

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 33 34
  • 99.38 (n)
cow
(Bos Taurus)
Mammalia ABCF1 33 34
  • 90.83 (n)
dog
(Canis familiaris)
Mammalia ABCF1 33 34
  • 90.24 (n)
oppossum
(Monodelphis domestica)
Mammalia ABCF1 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Abcf1 33 16 34
  • 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 33 34
  • 72.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG1703 35 33 34
  • 63.18 (n)
worm
(Caenorhabditis elegans)
Secernentea F18E2.2 35
  • 61 (a)
abcf-1 33 34
  • 58.84 (n)
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)

Paralogs for ABCF1 Gene

Paralogs for ABCF1 Gene

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

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 Sequence Context AA Info Type
rs754981516 Likely benign 30,590,190(+) CCTGT(C/T)GGGAA reference, missense
rs1000030264 -- 30,588,487(+) CTCCC(A/G)AGTAG intron-variant
rs1000177520 -- 30,570,431(+) GGGAG(A/G)GTGAG intron-variant, upstream-variant-2KB
rs1000225697 -- 30,575,025(+) AGTCT(A/G)AGAAT intron-variant
rs1000479465 -- 30,586,002(+) CACCT(G/T)AGGGA 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)

Relevant External Links for ABCF1 Gene

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

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

Disorders for ABCF1 Gene

Relevant External Links for ABCF1

Genetic Association Database (GAD)
ABCF1
Human Genome Epidemiology (HuGE) Navigator
ABCF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ABCF1

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 60
  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 60
  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 45 60
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 60
  5. 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 45 60

Products for ABCF1 Gene

Sources for ABCF1 Gene

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