APOBEC3B Gene (Protein Coding)

Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3B

GC22P038982
GIFtS:
41
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 e... See more...

Aliases for APOBEC3B Gene

Aliases for APOBEC3B Gene

  • Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3B 2 3 5
  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3B 2 3
  • DNA DC->DU-Editing Enzyme APOBEC-3B 3 4
  • Phorbolin-1-Related Protein 3 4
  • Phorbolin-2/3 3 4
  • Phorbolin 3 2 3
  • A3B 3 4
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3B 3
  • Cytidine Deaminase 3
  • Phorbolin 2 3
  • EC 3.5.4.38 4
  • DJ742C19.2 3
  • BK150C2.2 3
  • APOBEC1L 3
  • EC 3.5.4 54
  • PHRBNL 3
  • ARCD3 3
  • ARP4 3

External Ids for APOBEC3B Gene

Previous GeneCards Identifiers for APOBEC3B Gene

  • GC22P035992
  • GC22P037621
  • GC22P037702
  • GC22P039378
  • GC22P022346

Summaries for APOBEC3B Gene

Entrez Gene Summary for APOBEC3B 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. A hybrid gene results from the deletion of approximately 29.5 kb of sequence between this gene, APOBEC3B, and the adjacent gene APOBEC3A. The breakpoints of the deletion are within the two genes, so the deletion allele is predicted to have the promoter and coding region of APOBEC3A, but the 3' UTR of APOBEC3B. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for APOBEC3B Gene

APOBEC3B (Apolipoprotein B MRNA Editing Enzyme Catalytic Subunit 3B) is a Protein Coding gene. Among its related pathways are Formation of the Editosome and Gene Expression. Gene Ontology (GO) annotations related to this gene include deoxycytidine deaminase activity. An important paralog of this gene is APOBEC3D.

UniProtKB/Swiss-Prot Summary for APOBEC3B Gene

  • DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. 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 against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.

Gene Wiki entry for APOBEC3B Gene

Additional gene information for APOBEC3B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for APOBEC3B Gene

Genomics for APOBEC3B Gene

GeneHancer (GH) Regulatory Elements for APOBEC3B Gene

Promoters and enhancers for APOBEC3B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around APOBEC3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the APOBEC3B gene promoter:
  • Arnt
  • Evi-1
  • LCR-F1
  • Max1
  • MAZR
  • Msx-1
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c
  • USF1

Genomic Locations for APOBEC3B Gene

Genomic Locations for APOBEC3B Gene
chr22:38,982,347-38,992,804
(GRCh38/hg38)
Size:
10,458 bases
Orientation:
Plus strand
chr22:39,378,352-39,388,809
(GRCh37/hg19)
Size:
10,458 bases
Orientation:
Plus strand

Genomic View for APOBEC3B Gene

Genes around APOBEC3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
APOBEC3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for APOBEC3B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for APOBEC3B Gene

Proteins for APOBEC3B Gene

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  • Protein details for APOBEC3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UH17-ABC3B_HUMAN
    Recommended name:
    DNA dC->dU-editing enzyme APOBEC-3B
    Protein Accession:
    Q9UH17
    Secondary Accessions:
    • B0QYD2
    • O95618
    • Q20WL1
    • Q5IFJ4
    • Q7Z2N3
    • Q7Z6D6
    • Q9UE74

    Protein attributes for APOBEC3B Gene

    Size:
    382 amino acids
    Molecular mass:
    45924 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Homodimer. Interacts with APOBEC3G. Does not interact with APOBEC1.
    Miscellaneous:
    • It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.
    SequenceCaution:
    • Sequence=AAD00089.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAD00090.1; Type=Frameshift; Positions=59, 134; Note=Frameshifts result in two separate ORFs termed phorbolins 2 and 3.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for APOBEC3B Gene

    Alternative splice isoforms for APOBEC3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APOBEC3B Gene

Protein Expression for APOBEC3B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for APOBEC3B Gene

Q9UH17:
  • EHSQALSGRL
  • CFLSWFC
  • PFQPWDGL
  • WLCYEVK

Post-translational modifications for APOBEC3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC3B Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for APOBEC3B Gene

Gene Families for APOBEC3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for APOBEC3B Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for APOBEC3B Gene

GenScript: Design optimal peptide antigens:
  • Phorbolin-2/3 (ABC3B_HUMAN)
  • BK150C2.2 protein (Q20WL1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UH17

UniProtKB/Swiss-Prot:

ABC3B_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 APOBEC3B: view

Function for APOBEC3B Gene

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Molecular function for APOBEC3B Gene

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. 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 against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 2'-deoxycytidine in a single-stranded DNA + H(+) + H2O = a 2'-deoxyuridine in a single-stranded DNA + NH4(+); Xref=Rhea:RHEA:50948, Rhea:RHEA-COMP:12846, Rhea:RHEA-COMP:12847, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:85452, ChEBI:CHEBI:133902; EC=3.5.4.38;.
UniProtKB/Swiss-Prot Induction:
Phorbol 12-myristate 13-acetate (PMA) induces overexpression in keratinocytes. Up-regulated by IFN-alpha.

Enzyme Numbers (IUBMB) for APOBEC3B Gene

Phenotypes From GWAS Catalog for APOBEC3B Gene

Gene Ontology (GO) - Molecular Function for APOBEC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0003824 catalytic activity IEA --
GO:0004126 cytidine deaminase activity IBA 21873635
GO:0008270 zinc ion binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with APOBEC3B: view
genes like me logo Genes that share phenotypes with APOBEC3B: view

Animal Models for APOBEC3B Gene

MGI Knock Outs for APOBEC3B:

Animal Model Products

CRISPR Products

miRNA for APOBEC3B Gene

miRTarBase miRNAs that target APOBEC3B

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for APOBEC3B Gene

Localization for APOBEC3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC3B Gene

Nucleus.

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 APOBEC3B gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for APOBEC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 16699599
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with APOBEC3B: view

Pathways & Interactions for APOBEC3B Gene

genes like me logo Genes that share pathways with APOBEC3B: view

Pathways by source for APOBEC3B Gene

1 KEGG pathway for APOBEC3B Gene

Gene Ontology (GO) - Biological Process for APOBEC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009972 cytidine deamination IEA --
GO:0010529 negative regulation of transposition IDA 16527742
GO:0016554 cytidine to uridine editing IBA 21873635
GO:0045087 innate immune response IEA --
GO:0051607 defense response to virus IEA,IDA 22457529
genes like me logo Genes that share ontologies with APOBEC3B: view

No data available for SIGNOR curated interactions for APOBEC3B Gene

Drugs & Compounds for APOBEC3B Gene

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  1. Drug

(4) Drugs for APOBEC3B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Ammonia Approved Pharma 0
Cytarabine Approved, Experimental, Investigational Pharma 1294
Water Approved Pharma 0
Uridine Experimental, Investigational Pharma 0
genes like me logo Genes that share compounds with APOBEC3B: view

Transcripts for APOBEC3B Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
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mRNA/cDNA for APOBEC3B Gene

(2) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(55) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for APOBEC3B Gene

No ASD Table

Relevant External Links for APOBEC3B Gene

GeneLoc Exon Structure for
APOBEC3B
ECgene alternative splicing isoforms for
APOBEC3B

Expression for APOBEC3B Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for APOBEC3B Gene

mRNA expression in normal human tissues for APOBEC3B Gene
mRNA expression by BioGPS for APOBEC3B GenemRNA expression by GTEx for APOBEC3B Gene

mRNA differential expression in normal tissues according to GTEx for APOBEC3B Gene

This gene is overexpressed in Whole Blood (x16.7).

Protein differential expression in normal tissues from HIPED for APOBEC3B Gene

This gene is overexpressed in Blymphocyte (30.5), Heart (26.9), and Peripheral blood mononuclear cells (11.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for APOBEC3B Gene



Protein tissue co-expression partners for APOBEC3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of APOBEC3B Gene:

APOBEC3B

SOURCE GeneReport for Unigene cluster for APOBEC3B Gene:

Hs.226307

mRNA Expression by UniProt/SwissProt for APOBEC3B Gene:

Q9UH17-ABC3B_HUMAN
Tissue specificity: Expressed at high and moderate levels in peripheral blood leukocytes, spleen, testes, heart, thymus, prostate and ovary. Also expressed at low levels in several other tissues.

Evidence on tissue expression from TISSUES for APOBEC3B Gene

  • Skin(4)
genes like me logo Genes that share expression patterns with APOBEC3B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for APOBEC3B Gene

Orthologs for APOBEC3B Gene

This gene was present in the common ancestor of mammals.

Orthologs for APOBEC3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia APOBEC3B 33 32
  • 97.73 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia APOBEC3B 32
  • 60.74 (n)
APOBEC3A 33
  • 48 (a)
 OneToMany
rat
(Rattus norvegicus)
 Mammalia Apobec3b 32
  • 58.59 (n)
mouse
(Mus musculus)
 Mammalia Apobec3 17 32
  • 56.82 (n)
dog
(Canis familiaris)
 Mammalia APOBEC3H 32
  • 53.3 (n)
-- 33
  • 46 (a)
 ManyToMany
-- 33
  • 30 (a)
 ManyToMany
Species where no ortholog for APOBEC3B 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)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 APOBEC3B Gene

ENSEMBL:
Gene Tree for APOBEC3B (if available)
TreeFam:
Gene Tree for APOBEC3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for APOBEC3B: view image

Paralogs for APOBEC3B Gene

Paralogs for APOBEC3B Gene

(10) SIMAP similar genes for APOBEC3B Gene using alignment to 3 proteins:

  • ABC3B_HUMAN
  • B0QYD3_HUMAN
  • W0HJ78_HUMAN

Pseudogenes.org Pseudogenes for APOBEC3B Gene

genes like me logo Genes that share paralogs with APOBEC3B: view

Variants for APOBEC3B Gene

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Sequence variations from dbSNP and Humsavar for APOBEC3B Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000852159 -- 38,985,105(+) G/A intron_variant
rs1000947215 -- 38,991,436(+) T/C coding_sequence_variant, synonymous_variant
rs1001509097 -- 38,985,419(+) G/A intron_variant
rs1001538797 -- 38,988,523(+) A/C/G intron_variant
rs1001877588 -- 38,989,999(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for APOBEC3B Gene

Variant ID Type Subtype PubMed ID
dgv172n111 CNV deletion 26073780
dgv36n47 CNV loss 21111241
dgv4571n100 CNV loss 25217958
dgv770n67 CNV loss 20364138
dgv8106n54 CNV loss 21841781
dgv8107n54 CNV loss 21841781
dgv833e199 CNV deletion 23128226
esv2495318 CNV deletion 19546169
esv2604392 CNV loss 19546169
esv2724238 CNV deletion 23290073
esv2760711 CNV loss 21179565
esv2763703 CNV loss 21179565
esv28999 CNV loss 19812545
esv29947 CNV loss 18421352
esv33846 CNV gain+loss 17666407
esv3568392 CNV loss 25503493
esv3584501 CNV gain 24956385
esv3584781 CNV loss 24956385
esv3647746 CNV loss 21293372
esv3647747 CNV loss 21293372
esv3647748 CNV gain 21293372
nsv1055716 CNV loss 25217958
nsv1056597 CNV loss 25217958
nsv1061176 CNV gain+loss 25217958
nsv198 CNV deletion 15895083
nsv3627 CNV deletion 18451855
nsv438346 CNV loss 16468122
nsv472943 CNV novel sequence insertion 20440878
nsv482077 CNV gain 20164927
nsv589021 CNV loss 21841781
nsv589030 CNV loss 21841781
nsv589031 CNV loss 21841781
nsv964630 OTHER complex 23825009
nsv979676 CNV duplication 23825009
nsv9907 CNV loss 18304495
nsv9908 CNV loss 18304495

Variation tolerance for APOBEC3B Gene

Residual Variation Intolerance Score: 99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.98; 74.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for APOBEC3B Gene

Human Gene Mutation Database (HGMD)
APOBEC3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
APOBEC3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC3B Gene

Disorders for APOBEC3B Gene

Additional Disease Information for APOBEC3B

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

No disorders were found for APOBEC3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APOBEC3B Gene

Publications for APOBEC3B Gene

  1. Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1. (PMID: 10469298) Madsen P … Celis JE (The Journal of investigative dermatology 1999) 2 3 4 23 56
  2. APOBEC3B deletion and risk of HIV-1 acquisition. (PMID: 19698078) An P … Winkler CA (The Journal of infectious diseases 2009) 3 23 43 56
  3. Population stratification of a common APOBEC gene deletion polymorphism. (PMID: 17447845) Kidd JM … Eichler EE (PLoS genetics 2007) 3 23 43 56
  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 56
  5. APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T-lymphotropic virus type 1. (PMID: 22457529) Ooms M … Münk C (Journal of virology 2012) 3 4 56

ExternalLinks

View latest publications for APOBEC3B gene in Mastermind

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