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
- 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
- DNA DC->DU-Editing Enzyme APOBEC-3B 3
- Cytidine Deaminase 3
- Phorbolin 2 3
External Ids for APOBEC3B Gene
- HGNC: 17352
- Entrez Gene: 9582
- Ensembl: ENSG00000179750
- OMIM: 607110
- UniProtKB: Q9UH17
Previous GeneCards Identifiers for APOBEC3B Gene
- GC22P035992
- GC22P037621
- GC22P037702
- GC22P039378
- GC22P022346
Summaries 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 mRNA Editing- C to U Conversion and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and deoxycytidine deaminase activity. An important paralog of this gene is APOBEC3D.
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.
No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for APOBEC3B Gene
Genomics for APOBEC3B Gene
Regulatory Elements for APOBEC3B Gene
Enhancers for APOBEC3B Gene
- Elite enhancer and/or Elite enhancer-gene association
Download GeneHancer data dump
Enhancers around APOBEC3B on UCSC Golden Path with GeneCards custom track
Regulatory Element Products
Genomic Location for APOBEC3B Gene
- Chromosome:
- 22
- 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
Genes around APOBEC3B on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- 22q13.1 by Ensembl
- 22q13.1 by Entrez Gene
- 22q13.1 by HGNC
APOBEC3B Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence 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
- 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
Protein Expression for APOBEC3B Gene
Selected DME Specific Peptides for APOBEC3B Gene
- Q9UH17:
-
- EHSQALSGRL
- CFLSWFC
- PFQPWDGL
- WLCYEVK
Post-translational modifications for APOBEC3B Gene
Other Protein References for APOBEC3B Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
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Domains & Families for APOBEC3B Gene
Gene Families for APOBEC3B Gene
Protein Domains for APOBEC3B Gene
Suggested Antigen Peptide Sequences for APOBEC3B Gene
- GenScript: Design optimal peptide antigens:
Graphical View of Domain Structure for InterPro Entry
Q9UH17UniProtKB/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.
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
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0003723 | RNA binding | IDA,IEA | 22681889 |
| GO:0003824 | catalytic activity | IEA | -- |
| GO:0008270 | zinc ion binding | IEA | -- |
| GO:0016787 | hydrolase activity | IEA | -- |
| GO:0016814 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines | IEA | -- |
Phenotypes for APOBEC3B Gene
- MGI mutant phenotypes for APOBEC3B:
- inferred from 4 alleles
- GenomeRNAi human phenotypes for APOBEC3B:
Animal Models for APOBEC3B Gene
- MGI Knock Outs for APOBEC3B:
-
- Apobec3 tm1Msn
Animal Model Products
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-
-
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miRNA for APOBEC3B Gene
- miRTarBase miRNAs that target APOBEC3B
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-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Cell Line Products
-
Horizon Cell Lines for APOBEC3B
-
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-
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-
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Flow Cytometry 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.
| Compartment | Confidence |
|---|---|
| nucleus | 5 |
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0005634 | nucleus | IDA,IEA | 16699599 |
Pathways & Interactions for APOBEC3B Gene
| SuperPathway | Contained pathways | ||
|---|---|---|---|
| 1 | mRNA Editing- C to U Conversion |
.82
|
|
| 2 | Gene Expression |
.48
|
|
Pathways by source for APOBEC3B Gene
4 Reactome pathways for APOBEC3B Gene
Interacting Proteins for APOBEC3B Gene
| GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|---|---|---|
| GO:0010529 | negative regulation of transposition | IDA | 16527742 |
| GO:0045087 | innate immune response | IEA | -- |
| GO:0051607 | defense response to virus | IDA,IEA | 22457529 |
No data available for SIGNOR curated interactions for APOBEC3B Gene
Drugs & Compounds for APOBEC3B Gene
| Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
|---|---|---|---|---|---|---|
| Ammonia |
|
7664-41-7 |
|
Transcripts for APOBEC3B Gene
mRNA/cDNA for APOBEC3B Gene
- (2) REFSEQ mRNAs :
- (9) Additional mRNA sequences :
- (55) Selected AceView cDNA sequences:
- (4) Ensembl transcripts including schematic representations, and UCSC links where relevant :
Unigene Clusters for APOBEC3B Gene
CRISPR Products
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Inhibitory RNA Products
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- VectorBuilder custom plasmid, inducible vectors for APOBEC3B
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for APOBEC3B
-
VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Flow Cytometry Products
Expression for APOBEC3B Gene
mRNA expression in embryonic tissues and stem cells from LifeMap Discovery
- Mesenchymal Stem Cells (Uncategorized)
- Umbilical Cord (Extraembryonic Tissues)
-
Epiblast (Early Embryonic Tissues)
- Epiblast Cells Epiblast
- Epiblast Stem Cell line 5
- Inner Cell Mass (Early Embryonic Tissues)
- Blood (Hematopoietic System)
- Kidney (Urinary System)
- Thymus (Hematopoietic System)
- Adipose (Muscoskeletal System)
- NULL (Uncategorized)
mRNA differential expression in normal tissues according to GTEx for APOBEC3B Gene
This gene is overexpressed in Whole Blood (x16.7).
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
- Elite partner
NURSA nuclear receptor signaling pathways regulating expression of APOBEC3B Gene:
APOBEC3BSOURCE GeneReport for Unigene cluster for APOBEC3B Gene:
Hs.226307mRNA 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)
Primer Products
-
OriGene qPCR primer pairs for APOBEC3B
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.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| chimpanzee (Pan troglodytes) |
Mammalia | APOBEC3B 34 35 |
|
||
| cow (Bos Taurus) |
Mammalia | APOBEC3B 34 |
|
||
| APOBEC3A 35 |
|
OneToMany | |||
| rat (Rattus norvegicus) |
Mammalia | Apobec3b 34 |
|
||
| mouse (Mus musculus) |
Mammalia | Apobec3 34 16 |
|
||
| dog (Canis familiaris) |
Mammalia | APOBEC3H 34 |
|
||
| -- 35 |
|
ManyToMany | |||
| -- 35 |
|
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)
Paralogs for APOBEC3B Gene
Paralogs for APOBEC3B Gene
(10) SIMAP similar genes for APOBEC3B Gene using alignment to 3 proteins:
Pseudogenes.org Pseudogenes for APOBEC3B Gene
Variants for APOBEC3B Gene
| SNP ID | Clin | Chr 22 pos | Sequence Context | AA Info | Type |
|---|---|---|---|---|---|
| rs1000852159 | -- | 38,985,105(+) | ACCAT(A/G)TTGGC | intron-variant | |
| rs1000947215 | -- | 38,991,436(+) | GTCAC(C/T)TGGTT | downstream-variant-500B, reference, synonymous-codon | |
| rs1001509097 | -- | 38,985,419(+) | CCTGG(A/G)ATGTC | intron-variant | |
| rs1001538797 | -- | 38,988,523(+) | TATGA(A/C/G)GAAGC | intron-variant | |
| rs1001877588 | -- | 38,989,999(+) | GATCA(C/G)GGGTT | intron-variant |
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)
Relevant External Links for APOBEC3B Gene
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for APOBEC3B Gene
Disorders for APOBEC3B Gene
Relevant External Links for APOBEC3B
No disorders were found for APOBEC3B Gene.
No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for APOBEC3B Gene
Publications for APOBEC3B Gene
- 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 22 64
- APOBEC3B deletion and risk of HIV-1 acquisition. (PMID: 19698078) An P. … Winkler C.A. (J. Infect. Dis. 2009) 3 22 46 64
- Population stratification of a common APOBEC gene deletion polymorphism. (PMID: 17447845) Kidd J.M. … Eichler E.E. (PLoS Genet. 2007) 3 22 46 64
- 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 64
- APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T- lymphotropic virus type 1. (PMID: 22457529) Ooms M. … Muenk C. (J. Virol. 2012) 3 4 64
Products for APOBEC3B Gene
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- VectorBuilder custom plasmid, inducible vectors for APOBEC3B
- VectorBuilder custom lentivirus, adenovirus, AAV vector/virus packaging for APOBEC3B
- VectorBuilder Other custom vectors
- Mammalian expression: PiggyBac
- Mammalian Tet-on expression: plasmid
- Mammalian conditional (Cre-Lox): plasmid and PiggyBac
- Mammalian shRNA knockdown: lentiviral, adenoviral, AAV, and PiggyBac
- CRISPR: plasmid gRNA, lentiviral gRNA, and donor plasmid
- Bacterial expression: pET, pBAD, and pCS
- Yeast expression
Sources for APOBEC3B Gene
- (1) GeneCards
- (2) HGNC
- (3) EntrezGene
- (4) Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) GO
- (12) TrEMBL
- (13) InterPro
- (14) ProtoNet
- (15) Blocks
- (16) MGI
- (17) IUBMB
- (18) KEGG
- (19) MINT
- (20) STRING
- (21) IntAct
- (22) Novoseek
- (23) PharmGKB
- (24) DrugBank
- (25) HMDB
- (26) UniGene
- (27) AceView
- (28) RNAdb
- (29) ASD
- (30) ECgene
- (31) GeneAnnot
- (32) CGAP SAGE
- (33) SOURCE
- (34) HomoloGene
- (35) PanEnsembl
- (36) euGenes
- (37) SGD
- (38) FlyBase
- (39) WormBase
- (40) Pseudogene
- (41) DGV
- (42) dbSNP
- (43) GenAtlas
- (44) GeneTests
- (45) HGMD
- (46) GAD
- (47) LSDB
- (48) BGMUT
- (49) HuGE
- (50) eBioscience
- (51) Atlas
- (52) Cell Signaling Technology
- (53) GenBank
- (54) H-invDB
- (55) HORDE
- (56) HUGE
- (57) IMGT
- (58) Leiden
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