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Aliases for APOBEC3F Gene

Aliases for APOBEC3F Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3F 2 3 5
  • Apolipoprotein B MRNA-Editing Enzyme Catalytic Polypeptide-Like 3F 3 4
  • A3F 3 4
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3F 2
  • Apolipoprotein B Editing Enzyme Catalytic Polypeptide-Like 3F 3
  • Apolipoprotein B MRNA Editing Enzyme Cytidine Deaminase 3
  • DNA DC->DU-Editing Enzyme APOBEC-3F 3
  • Induced Upon T-Cell Activation 3
  • BK150C2.4.MRNA 3
  • EC 3.5.4.- 4
  • EC 3.5.4 56
  • ARP8 3
  • KA6 3

External Ids for APOBEC3F Gene

Previous GeneCards Identifiers for APOBEC3F Gene

  • GC22P036031
  • GC22P036051
  • GC22P037679
  • GC22P037761
  • GC22P039436
  • GC22P022404

Summaries for APOBEC3F Gene

Entrez Gene Summary for APOBEC3F Gene

  • This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for APOBEC3F Gene

APOBEC3F (Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3F) is a Protein Coding gene. Diseases associated with APOBEC3F include Theileriasis and Human Immunodeficiency Virus Type 1. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines. An important paralog of this gene is ENSG00000284554.

UniProtKB/Swiss-Prot for APOBEC3F Gene

  • DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.

Gene Wiki entry for APOBEC3F Gene

Additional gene information for APOBEC3F Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC3F Gene

Genomics for APOBEC3F Gene

GeneHancer (GH) Regulatory Elements for APOBEC3F Gene

Promoters and enhancers for APOBEC3F 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
GH22I039039 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 556.5 +0.7 721 2.9 HDAC1 KLF17 NFXL1 ZNF335 GLIS2 ZNF143 IKZF2 EGR2 ZNF263 SP3 APOBEC3F APOBEC3G ENSG00000259421
GH22I038174 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.8 -861.8 -861795 8.7 MLX DMAP1 YBX1 IRF4 YY1 SLC30A9 E2F8 ZNF143 MCM3 SP3 PLA2G6 DDX17 MAFF ENSG00000228274 CSNK1E ANKRD54 CBY1 ENSG00000230912 GGA1 TMEM184B
GH22I038567 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.6 -471.2 -471216 4.7 PKNOX1 GLI4 ZNF2 ZNF213 E2F8 KLF7 ATF7 RUNX3 ZNF263 SP3 DMC1 LOC105373031 FAM227A DDX17 ENSG00000230149 ENSG00000230912 ENSG00000273076 SNORD83B ENSG00000272669 ENSG00000225450
GH22I039308 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +269.7 269729 4.3 HDGF PKNOX1 MLX ARNT ZFP64 SIN3A FEZF1 ZNF2 IRF4 POLR2B DDX17 RPL3 SYNGR1 APOBEC3A ENSG00000230149 SNORD83B ENSG00000273076 ENSG00000272669 ENSG00000225450 TAB1
GH22I039493 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.6 +454.5 454507 3.6 HDGF PKNOX1 ATF1 RB1 SIN3A RAD21 EGR1 ZNF143 FOS THAP11 DDX17 ENSG00000272834 ATF4 ENSG00000227413 ENSG00000230149 ENSG00000273076 SNORD83B ENSG00000272669 ENSG00000225450 APOBEC3D
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around APOBEC3F on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the APOBEC3F gene promoter:

Genomic Locations for APOBEC3F Gene

Genomic Locations for APOBEC3F Gene
chr22:39,040,604-39,055,972
(GRCh38/hg38)
Size:
15,369 bases
Orientation:
Plus strand
chr22:39,436,609-39,451,977
(GRCh37/hg19)

Genomic View for APOBEC3F Gene

Genes around APOBEC3F on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOBEC3F Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOBEC3F Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APOBEC3F Gene

Proteins for APOBEC3F Gene

  • Protein details for APOBEC3F Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IUX4-ABC3F_HUMAN
    Recommended name:
    DNA dC->dU-editing enzyme APOBEC-3F
    Protein Accession:
    Q8IUX4
    Secondary Accessions:
    • B0QYD4
    • Q45F03
    • Q6ICH3
    • Q7Z2N2
    • Q7Z2N5

    Protein attributes for APOBEC3F Gene

    Size:
    373 amino acids
    Molecular mass:
    45020 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Binds HIV-1 Vif. In the absence of Vif protein, specifically packaged into HIV-1 virions. Interacts with APOBEC3G in an RNA-dependent manner. Interacts with AGO1, AGO2 and AGO3.
    Miscellaneous:
    • It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.

    Three dimensional structures from OCA and Proteopedia for APOBEC3F Gene

    Alternative splice isoforms for APOBEC3F Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APOBEC3F Gene

Selected DME Specific Peptides for APOBEC3F Gene

Q8IUX4:
  • CFLSWFC
  • DSKLQEIL
  • WLCYEVK

Post-translational modifications for APOBEC3F Gene

No Post-translational modifications

Other Protein References for APOBEC3F Gene

Domains & Families for APOBEC3F Gene

Gene Families for APOBEC3F Gene

Suggested Antigen Peptide Sequences for APOBEC3F Gene

Graphical View of Domain Structure for InterPro Entry

Q8IUX4

UniProtKB/Swiss-Prot:

ABC3F_HUMAN :
  • The CMP/dCMP deaminase domain 1 mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase domain 2 confers deoxycytidine deaminase activity and substrate sequence specificity.
  • Belongs to the cytidine and deoxycytidylate deaminase family.
Domain:
  • The CMP/dCMP deaminase domain 1 mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase domain 2 confers deoxycytidine deaminase activity and substrate sequence specificity.
Family:
  • Belongs to the cytidine and deoxycytidylate deaminase family.
genes like me logo Genes that share domains with APOBEC3F: view

Function for APOBEC3F Gene

Molecular function for APOBEC3F Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Cytidine + H(2)O = uridine + NH(3).
UniProtKB/Swiss-Prot EnzymeRegulation:
Antiviral activity is neutralized by the HIV-1 virion infectivity factor (VIF), that prevents its incorporation into progeny virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome.
UniProtKB/Swiss-Prot Function:
DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits antiviral activity against vif-deficient HIV-1. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single- or double-stranded RNA. Exhibits antiviral activity also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation.
UniProtKB/Swiss-Prot Induction:
Up-regulated by IFN-alpha.

Enzyme Numbers (IUBMB) for APOBEC3F Gene

Phenotypes From GWAS Catalog for APOBEC3F Gene

Gene Ontology (GO) - Molecular Function for APOBEC3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 11863358
GO:0003824 catalytic activity IEA --
GO:0004126 cytidine deaminase activity IDA 17121840
GO:0005515 protein binding IPI 16699599
GO:0008270 zinc ion binding IDA 11863358
genes like me logo Genes that share ontologies with APOBEC3F: view
genes like me logo Genes that share phenotypes with APOBEC3F: view

Animal Model Products

miRNA for APOBEC3F Gene

miRTarBase miRNAs that target APOBEC3F

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for APOBEC3F Gene

Localization for APOBEC3F Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC3F Gene

Cytoplasm. Cytoplasm, P-body.

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 APOBEC3F gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APOBEC3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IDA 16699599
GO:0005737 cytoplasm IEA,IDA 16527742
GO:0030529 intracellular ribonucleoprotein complex IDA 16699599
GO:0030895 apolipoprotein B mRNA editing enzyme complex TAS 17121840
genes like me logo Genes that share ontologies with APOBEC3F: view

Pathways & Interactions for APOBEC3F Gene

SuperPathways for APOBEC3F Gene

No Data Available

Interacting Proteins for APOBEC3F Gene

Gene Ontology (GO) - Biological Process for APOBEC3F Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002230 positive regulation of defense response to virus by host IDA 17121840
GO:0002376 immune system process IEA --
GO:0009972 cytidine deamination IEA --
GO:0010529 negative regulation of transposition IDA 16527742
GO:0016553 base conversion or substitution editing IDA 17121840
genes like me logo Genes that share ontologies with APOBEC3F: view

No data available for Pathways by source and SIGNOR curated interactions for APOBEC3F Gene

Drugs & Compounds for APOBEC3F Gene

(4) Drugs for APOBEC3F Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ammonia Approved Pharma 0
Water Approved Pharma 0
Cytidine Experimental Pharma 0
Uridine Experimental, Investigational Pharma 0

(1) Additional Compounds for APOBEC3F Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with APOBEC3F: view

Transcripts for APOBEC3F Gene

mRNA/cDNA for APOBEC3F Gene

(5) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(1) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for APOBEC3F Gene

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for APOBEC3F Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b · 12c ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17
SP1: - - -
SP2: - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - -
SP4: -
SP5:
SP6:
SP7: - - - - - - - - - - - -
SP8: -
SP9: -
SP10: - - -

Relevant External Links for APOBEC3F Gene

GeneLoc Exon Structure for
APOBEC3F
ECgene alternative splicing isoforms for
APOBEC3F

Expression for APOBEC3F Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APOBEC3F Gene

Protein differential expression in normal tissues from HIPED for APOBEC3F Gene

This gene is overexpressed in Ovary (16.0), Lung (13.2), Blymphocyte (11.2), and NK cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for APOBEC3F Gene



Protein tissue co-expression partners for APOBEC3F Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of APOBEC3F Gene:

APOBEC3F

SOURCE GeneReport for Unigene cluster for APOBEC3F Gene:

Hs.659809

mRNA Expression by UniProt/SwissProt for APOBEC3F Gene:

Q8IUX4-ABC3F_HUMAN
Tissue specificity: Widely expressed. Highly expressed in ovary.

Evidence on tissue expression from TISSUES for APOBEC3F Gene

  • Spleen(4.2)
  • Pancreas(4)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with APOBEC3F: 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 APOBEC3F Gene

Orthologs for APOBEC3F Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for APOBEC3F Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia APOBEC3F 33
  • 98.48 (n)
Species where no ortholog for APOBEC3F 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for APOBEC3F Gene

ENSEMBL:
Gene Tree for APOBEC3F (if available)
TreeFam:
Gene Tree for APOBEC3F (if available)

Paralogs for APOBEC3F Gene

(11) SIMAP similar genes for APOBEC3F Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for APOBEC3F Gene

genes like me logo Genes that share paralogs with APOBEC3F: view

Variants for APOBEC3F Gene

Sequence variations from dbSNP and Humsavar for APOBEC3F Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000257527 -- 39,035,521(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000336007 -- 39,026,238(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000485119 -- 39,031,060(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000611010 -- 39,036,483(+) G/C genic_upstream_transcript_variant, intron_variant
rs1000861291 -- 39,053,489(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for APOBEC3F Gene

Variant ID Type Subtype PubMed ID
esv3647757 CNV loss 21293372
esv3647758 CNV loss 21293372
nsv1139065 CNV deletion 24896259
nsv522083 CNV loss 19592680
nsv834196 CNV loss 17160897
nsv964631 CNV duplication 23825009
esv3647756 CNV gain 21293372
esv3647755 CNV loss 21293372
esv3647751 CNV gain 21293372
esv2724243 CNV deletion 23290073
esv2724242 CNV deletion 23290073
esv2676044 CNV deletion 23128226
esv2673637 CNV deletion 23128226
esv22523 CNV gain 19812545

Variation tolerance for APOBEC3F Gene

Residual Variation Intolerance Score: 85.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.35; 70.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APOBEC3F Gene

Human Gene Mutation Database (HGMD)
APOBEC3F
SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOBEC3F

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC3F Gene

Disorders for APOBEC3F Gene

MalaCards: The human disease database

(2) MalaCards diseases for APOBEC3F Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
theileriasis
  • infection by theileria
human immunodeficiency virus type 1
  • human immunodeficiency virus type 1, susceptibility to
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for APOBEC3F

genes like me logo Genes that share disorders with APOBEC3F: view

No data available for UniProtKB/Swiss-Prot and Genatlas for APOBEC3F Gene

Publications for APOBEC3F Gene

  1. APOBEC3F can inhibit the accumulation of HIV-1 reverse transcription products in the absence of hypermutation. Comparisons with APOBEC3G. (PMID: 17121840) Holmes RK … Malim MH (The Journal of biological chemistry 2007) 2 3 22 58
  2. Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies. (PMID: 16699599) Wichroski MJ … Rana TM (PLoS pathogens 2006) 3 4 22 58
  3. A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins. (PMID: 15152192) Wiegand HL … Cullen BR (The EMBO journal 2004) 3 4 22 58
  4. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. (PMID: 11863358) Jarmuz A … Navaratnam N (Genomics 2002) 2 3 4 58
  5. APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages. (PMID: 23097438) Chaipan C … Pathak VK (Journal of virology 2013) 3 4 58

Products for APOBEC3F Gene

Sources for APOBEC3F Gene

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