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Aliases for APOBEC3B Gene

Aliases for APOBEC3B Gene

  • Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 3B 2 3
  • Phorbolin-1-Related Protein 3 4
  • Phorbolin-2/3 3 4
  • Phorbolin 3 2 3
  • PHRBNL 3 6
  • A3B 3 4
  • Apolipoprotein B MRNA Editing Enzyme Catalytic Polypeptide-Like 3B 3
  • Probable DNA DC->DU-Editing Enzyme APOBEC-3B 3
  • DNA DC->DU-Editing Enzyme APOBEC-3B 3
  • Cytidine Deaminase 3
  • Phorbolin 2 3
  • DJ742C19.2 3
  • EC 3.5.4.- 4
  • BK150C2.2 3
  • APOBEC1L 3
  • EC 3.5.4 64
  • ARCD3 3
  • Arp4 3

External Ids for APOBEC3B Gene

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 Polypeptide-Like 3B) is a Protein Coding gene. Diseases associated with APOBEC3B include human t-cell leukemia virus type 1 and hiv-1. GO annotations related to this gene include RNA binding and deoxycytidine deaminase activity. An important paralog of this gene is AICDA.

UniProtKB/Swiss-Prot 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC3B Gene

Genomics for APOBEC3B Gene

Genomic Location for APOBEC3B Gene

Start:
38,982,347 bp from pter
End:
38,992,804 bp from pter
Size:
10,458 bases
Orientation:
Plus strand

Genomic View for APOBEC3B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for APOBEC3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for APOBEC3B Gene

Regulatory Elements for APOBEC3B Gene

Proteins for APOBEC3B Gene

  • 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};

    Alternative splice isoforms for APOBEC3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for APOBEC3B Gene

Proteomics data for APOBEC3B Gene at MOPED

Selected DME Specific Peptides for APOBEC3B Gene

Post-translational modifications for APOBEC3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for APOBEC3B Gene

Domains for APOBEC3B Gene

Gene Families for APOBEC3B Gene

HGNC:
  • APOBEC :Apolipoprotein B mRNA editing enzymes

UniProtKB/Swiss-Prot:

ABC3B_HUMAN
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.:
    • Q9UH17
  • Contains 2 CMP/dCMP-type deaminase domains.:
    • Q9UH17
Family:
  • Belongs to the cytidine and deoxycytidylate deaminase family.:
    • Q9UH17
genes like me logo Genes that share domains with APOBEC3B: view

Function for APOBEC3B Gene

Molecular function for APOBEC3B Gene

UniProtKB/Swiss-Prot CatalyticActivity: Cytidine + H(2)O = uridine + NH(3)
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 Induction: Phorbol 12-myristate 13-acetate (PMA) induces overexpression in keratinocytes. Up-regulated by IFN-alpha.

Enzyme Numbers (IUBMB) for APOBEC3B Gene

Gene Ontology (GO) - Molecular Function for APOBEC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity --
GO:0008270 zinc ion binding IEA --
GO:0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines --
GO:0044822 poly(A) RNA binding IDA 22681889
GO:0047844 deoxycytidine deaminase activity IMP 22457529
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:

miRNA for APOBEC3B Gene

miRTarBase miRNAs that target APOBEC3B

No data available for Transcription Factor Targeting and HOMER Transcription for APOBEC3B Gene

Localization for APOBEC3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for APOBEC3B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for APOBEC3B Gene COMPARTMENTS Subcellular localization image for APOBEC3B gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for APOBEC3B Gene

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

Pathways for APOBEC3B Gene

SuperPathways for APOBEC3B Gene

No Data Available

Interacting Proteins for APOBEC3B Gene

Gene Ontology (GO) - Biological Process for APOBEC3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008152 metabolic process IMP 22457529
GO:0010529 negative regulation of transposition IDA 16527742
GO:0045087 innate immune response IEA --
GO:0051607 defense response to virus IDA 22457529
genes like me logo Genes that share ontologies with APOBEC3B: view

No data available for Pathways by source for APOBEC3B Gene

Transcripts for APOBEC3B Gene

Unigene Clusters for APOBEC3B Gene

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

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

mRNA expression in normal human tissues for APOBEC3B Gene

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

This gene is overexpressed in Whole Blood (16.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for APOBEC3B Gene

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.
genes like me logo Genes that share expressions with APOBEC3B: view

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 36
  • 97.73 (n)
  • 94.5 (a)
APOBEC3B 37
  • 73 (a)
OneToOne
cow
(Bos Taurus)
Mammalia APOBEC3A 37
  • 48 (a)
OneToMany
APOBEC3B 36
  • 60.74 (n)
  • 44.17 (a)
dog
(Canis familiaris)
Mammalia -- 37
  • 46 (a)
ManyToMany
-- 37
  • 30 (a)
ManyToMany
APOBEC3H 36
  • 53.3 (n)
  • 36.16 (a)
mouse
(Mus musculus)
Mammalia Apobec3 36
  • 56.82 (n)
  • 39.2 (a)
Apobec3 16
rat
(Rattus norvegicus)
Mammalia Apobec3b 36
  • 58.59 (n)
  • 40.28 (a)
Species with no ortholog for APOBEC3B:
  • 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)

Paralogs for APOBEC3B Gene

Selected SIMAP similar genes for APOBEC3B Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for APOBEC3B Gene

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

Variants for APOBEC3B Gene

Sequence variations from dbSNP and Humsavar for APOBEC3B Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type MAF
rs1807558 -- 38,988,748(+) TTCTT(C/T)CTTTC intron-variant
rs2009151 -- 38,987,479(+) CCTGT(A/C)TATGC intron-variant
rs2072864 -- 38,986,805(+) TCCTG(G/T)GGGGA intron-variant
rs2072865 -- 38,989,658(+) TCCAG(A/G)GACAC intron-variant
rs2072866 -- 38,989,804(+) GTTGA(C/G)TCTGC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv915079 CNV Gain 21882294
nsv3627 CNV Loss 18451855
nsv198 CNV Loss 15895083
nsv915080 CNV Loss 21882294
esv28999 CNV Loss 19812545
dgv770n67 CNV Loss 20364138
dgv833e199 CNV Deletion 23128226
esv2495318 CNV Deletion 19546169
esv2724238 CNV Deletion 23290073
dgv36n47 CNV Loss 21111241
nsv9907 CNV Loss 18304495
esv2604392 CNV Loss 19546169
esv33846 CNV Gain+Loss 17666407
esv29947 CNV Loss 18421352
nsv438346 CNV Loss 16468122
nsv915081 CNV Gain 21882294
nsv482077 CNV Gain 20164927
nsv915082 CNV Gain 21882294
nsv9908 CNV Loss 18304495

Relevant External Links for APOBEC3B Gene

HapMap Linkage Disequilibrium report
APOBEC3B
Human Gene Mutation Database (HGMD)
APOBEC3B

Disorders for APOBEC3B Gene

Relevant External Links for APOBEC3B

Genetic Association Database (GAD)
APOBEC3B
Human Genome Epidemiology (HuGE) Navigator
APOBEC3B
genes like me logo Genes that share disorders with APOBEC3B: view

No data available for UniProtKB/Swiss-Prot 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.P. … Celis J.E. (J. Invest. Dermatol. 1999) 2 3 4 23
  2. Population stratification of a common APOBEC gene deletion polymorphism. (PMID: 17447845) Kidd J.M. … Eichler E.E. (PLoS Genet. 2007) 3 23 49
  3. APOBEC3B deletion and risk of HIV-1 acquisition. (PMID: 19698078) An P. … Winkler C.A. (J. Infect. Dis. 2009) 3 23 49
  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
  5. APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T- lymphotropic virus type 1. (PMID: 22457529) Ooms M. … Muenk C. (J. Virol. 2012) 3 4

Products for APOBEC3B Gene

Sources for APOBEC3B Gene

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