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APOBEC3F apolipoprotein B mRNA editing enzyme catalytic subunit 3F [ Homo sapiens (human) ]

Gene ID: 200316, updated on 11-Jun-2021

Summary

Official Symbol
APOBEC3Fprovided by HGNC
Official Full Name
apolipoprotein B mRNA editing enzyme catalytic subunit 3Fprovided by HGNC
Primary source
HGNC:HGNC:17356
See related
Ensembl:ENSG00000128394 MIM:608993
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
A3F; KA6; ARP8; BK150C2.4.MRNA
Summary
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]
Expression
Broad expression in lymph node (RPKM 2.8), ovary (RPKM 2.8) and 24 other tissues See more
Orthologs
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Genomic context

See APOBEC3F in Genome Data Viewer
Location:
22q13.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (39019081..39055972)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39436869..39451977)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985562 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3B Neighboring gene APOBEC3B antisense RNA 1 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3C Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3D Neighboring gene uncharacterized LOC107985563 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 3G

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?

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV/tuberculosis coinfection upregulates APOBEC3F expression in pleural fluid mononuclear cells (PFMC) isolated from antiretroviral-naive coinfected patients (relative to patients infected with only tuberculosis) PubMed
Knockdown of APOBEC3F by siRNA enhances HIV-1 infection of immature dendritic cells (iDCs), indicating that APOBEC3F controls the sensitivity of iDCs to HIV-1 infection PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 Env gp120 variable loop 3 (V3) region mutation is increased by incomplete Vif neutralization (Vif K22E) of APOBEC3G/F activity and may contribute to genetic evolution from CCR5 to CXCR4 co-receptor usage PubMed
Pol gag-pol Analyses of longitudinal HIV-1 pol sequences from patients without hypermutated viruses during chronic infection indicate that A3F may increase HIV-1 diversification and facilitate viral adaption and propagation in vivo PubMed
Pr55(Gag) gag R7R10K11S, A30P, P31L, R32G, and RKK32-34SSS mutations in the NC domain of HIV-1 Gag result in a significant decrease in APOBEC3F incorporation into virus-like particles PubMed
gag Amino acids 104-156, located between the two cytidine deaminase domains of APOBEC3F, are required for its incorporation into Gag virus-like particles PubMed
gag The NC domain of HIV-1 Gag is required for 7SL RNA and APOBEC3F packaging PubMed
gag APOBEC3F may be incorporated into virions by HIV-1 Gag polyprotein PubMed
gag Single-virion fluorescence microscopy analysis demonstrates that the efficiency of A3G-YFP and A3F-YFP incorporation into HIV-1 Gag-CeFP virions is higher than that of A3C-YFP incorporation into HIV-1 Gag-CeFP virions PubMed
gag The efficiency of incorporation of Mov10, A3G, and A3F into viral particles, which contains both HIV-1 Gag and genomic RNA, is much higher than that of the other P-body proteins AGO2, DCP1a, DCP2, and DDX6 PubMed
gag In HIV-1 virions, APOBEC3F interacts with HIV-1 IN and NC, which are known to be important for reverse transcription and integration PubMed
Vif vif HIV-1 Vif binds APOBEC3F; the interaction is between amino acid residue R15 in Vif and E289 in APOBEC3F PubMed
vif HIV-1 Vif degrades APOBEC3F; degradation is dependent on interactions between amino acid residue R15 in Vif and E289 in APOBEC3F PubMed
vif HIV-1 Vif degrades APOBEC3F dependent upon L291, A292, R293, and E324 in APOBEC3F PubMed
vif HIV-1 Vif binds amino acids L291, A292 and R293 in APOBEC3F PubMed
vif HIV-1 Vif degrades APOBEC3C and APOBEC3F and is dependent on Vif F1, F2, and F3 box mutations involving residues D14, R15, M16, W79, D172, and W174 PubMed
vif HIV-1 Vif degrades APOBEC3F and APOBEC3C PubMed
vif HIV-1 Vif internal amino acid salt bridge (E171-K167-D101) mediates human APOBEC3C and APOBEC3F degradation PubMed
vif HIV-1 Vif specifically binds APOBEC3F, and Vif suppresses both the inhibition of virus infectivity caused by APOBEC3F and virion incorporation of APOBEC3F PubMed
vif APOBEC3F levels are increased by compound N.41 treatment only in cells co-expressing HIV-1 Vif, and APOBEC3F levels in virus particles are also increased PubMed
vif APOBEC3F, similar to APOBEC3G, induces G to A hypermutations in HIV-1 genomic DNA, and the HIV-1 Vif protein inhibits this activity PubMed
vif Certain residues L125, G126, R127, E134, Y135, G138 in HCCH motif (residues 125-141) of HIV-1 Vif are required for inhibition of APOBEC3F PubMed
vif Immunoblotting and crystal structure analyses reveal ten amino acids L225, F258, C259, I262, L263, S264, Y269, D289, F290, and H294 in APOBEC3F are involved in forming Vif-interaction interface PubMed
vif A potent small molecular compound VEC-5 protects APOBEC3G, APOBEC3F, and APOBEC3C from HIV-1 Vif-induced degradation and enhances A3G incorporation into HIV-1 virions by inhibiting the interaction between Vif and elongin C PubMed
vif HIV-1 Vif W21A, S32A, W38A, Y69A, E76A, W79A, H108A, C114S, C133S, and H139A mutants have no viral ability to neutralize APOBEC3F PubMed
vif An extensive mutational analysis of HIV-1 Vif reveals that two distinct regions of Vif, amino acids Y(40)RHHY(44) and D(14)RMR(17), which are essential for binding to A3G and A3F, respectively PubMed
vif CBF-beta-mediated increase of HIV-1 Vif steady-state levels results in decreased cellular levels of all Vif-sensitive APOBEC proteins (A3C, A3D, A3F, A3G, and A3H haplotype II) PubMed
vif Endogenous APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, can potently inhibit HIV-1 propagation in a mouse model by mutating 14DRMR17 and/or 40YRHHY44 motifs in Vif PubMed
vif Amino acids P281, E282, D313, E316, Q323, and E324 in APOBEC3F are required for the interface binding to HIV-1 Vif(IIIB) PubMed
vif HIV-1 Vif mutants 84DVAAAA89, 88EW/AA89, G84A, G84D, W89A, D104A, L106S, and I107S result in upregulated APOBEC3F expression and show a reduced ability to neutralize the antiviral activity of APOBEC3F PubMed
vif HIV-1 Vif mutant E88A/W89A fails to bind to CBF-beta, which impairs Vif-mediated degradation of both A3F and A3G proteins and HIV-1 replication in non-permissive CEM cells PubMed
vif A novel conserved 69YXXL72 motif in HIV-1 Vif mediates binding to human A3F and its subsequent degradation. Tyr69 and Leu72 residues in the YXXL motif are important for degradation of A3F PubMed
vif HIV-1 Vif, which suppresses both APOBEC3G and APOBEC3F antiviral function by inducing their degradation, may selectively remove these proteins from, and/or restrict their localization to, P-bodies PubMed
vif HIV-1 Vif mutants W11R and R15G are restricted in permissive SupT11 and nonpermissive CEM2n cell lines that express A3F, while H43N and H43N/E117K Vif mutants are capable of spreading efficiently in the presence of A3F PubMed
vif HIV-1 Vif mutants W5S, W21S, W38S, W89S, F112S, and F115S have a reduced ability to interact with CBF-beta and these Vif hydrophobic residues are important for Vif-mediated degradation of A3F PubMed
vif The crystal structure provides a structural basis that L255A, L255D, F258A, C259K, C259S, I262A, Y269A, E286A, E289Q, F290A, F290K, H294A, H294D, E316Q, S320A, and E324Q mutations fail to bind to HIV-1 Vif PubMed
vif The HIV-1 Vif N-terminal motif (residues 18-38) binds CUL5 in mammalian cells and is reguired for A3F and A3G degradation and HIV-1 infectivity PubMed
vif Replacement of all lysines with arginines in A3F results in inhibition of HIV-1 Vif-mediated A3F degradation by polyubiquitination. Lysines at positions 40, 52, 209, 334, 337, 355, and 358 in A3F are important for its degradation by Vif PubMed
vif A3F mutants C259K and IL262-263AA are resistant to HIV-1 Vif-mediated A3F degradation PubMed
vif The amino acids 223-232 of A3F-CTD beta1-2 loop is conserved to the amino acids 23-32 of HIV-1 Vif, while the amino acids 305-313 of A3F-CTD beta4-alpha4 loop is conserved to the amino acids 108-113 of HIV-1 Vif PubMed
vif Unusual substitutions V13I, V55T, and L81M in HIV-1 Vif from children infected perinatally without progression to AIDS are located in three distinct Vif motifs important for the interaction with A3G/A3F PubMed
vif The antiviral activity of A3G to HIV-1 vif mutants NL4-3 40YRHHY44>A5 and NL4-3 14DRMR17>A4 with G-to-A hypermutations confers a greater restriction than the combined antiviral activity of A3F and A3DE in activated CD4+ T cells and macrophages PubMed
vif HIV-1 Vif alleles from seven HIV-1 subtypes show their abilities to degrade and counteract A3F efficiently PubMed
vif Highly conserved Tryptophan residues in the N-terminal region of HIV-1 Vif are required for the suppression of both APOBEC3G and APOBEC3F PubMed
vif HIV-1 Vif motif TGERxW (amino acids 74-79) is important for A3F interaction and inhibition PubMed
vif Stress causes A3A, A3B, A3C, and A3F to co-localize efficiently with Vif(IIIB) and mRNA-PABP1 complexes in stress granules PubMed
vif Vif-deficient HIV-1 replicates as equally well as wild-type virus in CEM-T4 cells expressing high levels of A3G and A3F, indicating CEM-T4 cells lack a cellular co-factor for these endogenous antiretroviral proteins PubMed
vif Small molecule RN-18 specifically inhibits HIV-1 Vif-mediated downregulation of APOBEC3C/F/G proteins by decreasing Vif protein levels when Vif interacts with these proteins PubMed
vif Amino acids 283 to 300 of A3F are critical for binding to the DRMR region of HIV-1 Vif and for A3F degradation PubMed
vif The SLV portion of the Vif SLV/Ix4Yx9Y motif is required for optimal suppression of A3F PubMed
vif The carboxyl-terminal domain (residues 183-373) of A3F alone binds to HIV-1 Vif and behaves like the full-length A3F in terms of Vif sensitivity PubMed
vif Human T cell line CEM.NKR clones display inhibition of HIV-1 replication although these clones retain low levels of A3DE, A3F, A3G, and A3H expression, suggesting that a novel restriction factor distinct from APOBEC3s exists in CEM.NKR cells PubMed
vif Incorporation of Vif into virions is dependent on its interaction with A3G/A3F PubMed
vif Long-term restriction by A3F selects HIV-1 clones with Vif Q26-Q27 or Y26-Q27 mutations, which are fully capable of overcoming A3F but susceptible to restriction by A3G PubMed
vif Alternative splice removal of exon 2 of A3F produces a Vif-resistant protein that retains significant antiviral activity. Splice removal of exons 2-4 results in a Vif-sensitive A3F protein with weaker antiviral activity PubMed
vif The T(Q/D/E)x(5)ADx(2)(I/L) motif, located at residues 96 to 107 in HIV-1 Vif, plays a critical role in neutralizing activity toward A3F. This motif regulates Vif interaction with Cul5 PubMed
vif All residues except N175 in the (171)EDRWN(175) domain of Vif are equally important for regulation of A3F neutralization PubMed
vif Residues L81, G82, and G84, and, to a lesser extent, I87 and W89 within the (81)LGxGxxIxW(89) domain affect Vif binding to A3F and play very critical roles in A3F neutralizing activity PubMed
vif Amino-acid residues QE323-324EK in A3F affect the differential susceptibility of human A3F and monkey A3F to HIV-1 Vif. Mutation of A3F E324 alone alters functional susceptibility of its binding to Vif PubMed
vif Amino acid E289 in the EFLARH sequence of A3F is critical for HIV-1 Vif sensitivity PubMed
Vpu vpu The expression of APOBEC3F is enhanced in Vpu-deficient HIV-1-infected cells as compared to that in wild-type-infected cells PubMed
capsid gag HIV-1 CA mutations (K203A and E128A/R132A) that alter HIV-1 core stability decrease nuclear import of A3F-YFP-labeled preintegration complexes (PICs) in infected cells PubMed
integrase gag-pol In HIV-1 virions, APOBEC3F interacts with HIV-1 IN and NC, which are known to be important for reverse transcription and integration PubMed
nucleocapsid gag The NC domain of HIV-1 Gag is required for 7SL RNA and APOBEC3F packaging PubMed
gag In HIV-1 virions, APOBEC3F interacts with HIV-1 IN and NC, which are known to be important for reverse transcription and integration PubMed
reverse transcriptase gag-pol Vif-negative HIV-1 produced from 293T cells transiently expressing hA3F is impaired in early and late viral DNA production, and in viral infectivity, effects that are correlated with an inability of tRNA(3)(Lys) to prime reverse transcription PubMed
gag-pol APOBEC3-driven mutagenesis contributes to the generation of both M184I and E138K mutations in HIV-1 RT in the absence of drug exposure PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC74891

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables cytidine deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables cytidine deaminase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables deoxycytidine deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA cytosine deamination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in DNA cytosine deamination IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in DNA demethylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in base conversion or substitution editing IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cytidine deamination IEA
Inferred from Electronic Annotation
more info
 
involved_in cytidine to uridine editing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in defense response to virus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
involved_in innate immune response IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transposition IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of transposition IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of viral genome replication IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of viral process IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of defense response to virus by host IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
is_active_in P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in P-body IDA
Inferred from Direct Assay
more info
PubMed 
part_of apolipoprotein B mRNA editing enzyme complex TAS
Traceable Author Statement
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA dC->dU-editing enzyme APOBEC-3F
Names
apolipoprotein B editing enzyme catalytic polypeptide-like 3F
apolipoprotein B mRNA editing enzyme cytidine deaminase
apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F
induced upon T-cell activation
NP_001006667.1
NP_660341.2
XP_016884131.1
XP_016884132.1
XP_024307946.1
XP_024307947.1

NCBI Reference Sequences (RefSeq)

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.

mRNA and Protein(s)

  1. NM_001006666.2NP_001006667.1  DNA dC->dU-editing enzyme APOBEC-3F isoform b

    See identical proteins and their annotated locations for NP_001006667.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a distinct 3' UTR and 3' coding region, compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus when compared to isoform a.
    Source sequence(s)
    BM681311, CR456395
    Consensus CDS
    CCDS33649.1
    UniProtKB/Swiss-Prot
    Q8IUX4
    Related
    ENSP00000370977.2, ENST00000381565.2
    Conserved Domains (1) summary
    pfam08210
    Location:1788
    APOBEC_N; APOBEC-like N-terminal domain
  2. NM_145298.6NP_660341.2  DNA dC->dU-editing enzyme APOBEC-3F isoform a

    See identical proteins and their annotated locations for NP_660341.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript, and encodes the longer isoform (a).
    Source sequence(s)
    AL022318, BC038808, BQ182066, CX165430, DA221480
    Consensus CDS
    CCDS33648.1
    UniProtKB/Swiss-Prot
    Q8IUX4
    Related
    ENSP00000309749.5, ENST00000308521.10
    Conserved Domains (1) summary
    pfam08210
    Location:200370
    APOBEC_N; APOBEC-like N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    39019081..39055972
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452178.1XP_024307946.1  DNA dC->dU-editing enzyme APOBEC-3F isoform X1

    Conserved Domains (1) summary
    pfam08210
    Location:269439
    APOBEC_N; APOBEC-like N-terminal domain
  2. XM_024452179.1XP_024307947.1  DNA dC->dU-editing enzyme APOBEC-3F isoform X2

    Conserved Domains (1) summary
    pfam08210
    Location:200370
    APOBEC_N; APOBEC-like N-terminal domain
  3. XM_017028642.2XP_016884131.1  DNA dC->dU-editing enzyme APOBEC-3F isoform X3

  4. XM_017028643.2XP_016884132.1  DNA dC->dU-editing enzyme APOBEC-3F isoform X4

    UniProtKB/Swiss-Prot
    Q8IUX4
    Conserved Domains (1) summary
    pfam08210
    Location:1788
    APOBEC_N; APOBEC-like N-terminal domain

RNA

  1. XR_002958675.1 RNA Sequence

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