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APOBEC4 Gene

protein-coding   GIFtS: 44
GCID: GC01M183615

Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like...

(Previous name: chromosome 1 open reading frame 169)
(Previous symbol: C1orf169)
  Search for APOBEC4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Apolipoprotein B MRNA Editing Enzyme, Catalytic Polypeptide-Like 4
(Putative)1 2
C1orf1691 2 3
Apolipoprotein B MRNA-Editing Enzyme Catalytic Polypeptide-Like 42 3
Chromosome 1 Open Reading Frame 1691
Putative C->U-Editing Enzyme APOBEC-42
EC 3.5.4.-3

External Ids:    HGNC: 321521   Entrez Gene: 4033142   Ensembl: ENSG000001736277   OMIM: 6099085   UniProtKB: Q8WW273   
ORGUL members:         

Export aliases for APOBEC4 gene to outside databases

Previous GC identifers: GC01M180349 GC01M181882 GC01M154851


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for APOBEC4 Gene:
This gene encodes a member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases, which convert
cytidine to uridine. Other AID/APOBEC family members are involved in mRNA editing, somatic hypermutation and
recombination of immunoglobulin genes, and innate immunity to retroviral infection. (provided by RefSeq, Jul
2008)

GeneCards Summary for APOBEC4 Gene:
APOBEC4 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)) is a protein-coding gene. GO annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines.

UniProtKB/Swiss-Prot: ABEC4_HUMAN, Q8WW27
Function: Putative C to U editing enzyme whose physiological substrate is not yet known (By similarity)

Gene Wiki entry for APOBEC4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the APOBEC4 gene promoter:
         USF1   Sox5   MEF-2A   FAC1   SREBP-1a   USF-1   FOXJ2 (long isoform)   ZID   aMEF-2   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidAPOBEC4 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat APOBEC4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q25.3   Ensembl cytogenetic band:  1q25.3   HGNC cytogenetic band: 1q25.3

APOBEC4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
APOBEC4 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M183615:  view genomic region     (about GC identifiers)

Start:
183,615,410 bp from pter      End:
183,622,451 bp from pter
Size:
7,042 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: ABEC4_HUMAN, Q8WW27 (See protein sequence)
Recommended Name: Putative C->U-editing enzyme APOBEC-4  
Size: 367 amino acids; 41581 Da
Cofactor: Zinc (By similarity)
Secondary accessions: Q8N7F6

Explore the universe of human proteins at neXtProt for APOBEC4: NX_Q8WW27

Explore proteomics data for APOBEC4 at MOPED


See APOBEC4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_982279.1  
ENSEMBL proteins: 
 ENSP00000310622  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
APOBEC: Apolipoprotein B mRNA editing enzymes

1 InterPro protein domain:
 IPR013158 APOBEC_N

Graphical View of Domain Structure for InterPro Entry Q8WW27

ProtoNet protein and cluster: Q8WW27

1 Blocks protein domain: IPB002125 Cytidine/deoxycytidylate deaminase

UniProtKB/Swiss-Prot: ABEC4_HUMAN, Q8WW27
Similarity: Belongs to the cytidine and deoxycytidylate deaminase family


Find genes that share domains with APOBEC4           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: ABEC4_HUMAN, Q8WW27
Function: Putative C to U editing enzyme whose physiological substrate is not yet known (By similarity)

     Enzyme Number (IUBMB): EC 3.5.4.-1

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008270zinc ion binding IEA--
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines IEA--
     
Find genes that share ontologies with APOBEC4           About GenesLikeMe


Animal Models:
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miRNA
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miRTarBase miRNAs that target APOBEC4:
hsa-mir-335-5p (MIRT016856)

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Selected qRT-PCR Assays for microRNAs that regulate APOBEC4 (see all 10):
hsa-miR-2052 hsa-miR-374b hsa-miR-4306 hsa-miR-374a hsa-miR-29b-1* hsa-miR-223 hsa-miR-4261 hsa-miR-185
SwitchGear 3'UTR luciferase reporter plasmidAPOBEC4 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
peroxisome2
cytoskeleton1

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for APOBEC4
Interactions:

    Search GeneGlobe Interaction Network for APOBEC4

STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

Selected Interacting proteins for APOBEC4 (ENSP000003106224) via UniProtKB, MINT, STRING, and/or I2D (see all 14)
InteractantInteraction Details
GeneCardExternal ID(s)
CACYBPENSP000003566524STRING: ENSP00000356652
COL11A1ENSP000003511634STRING: ENSP00000351163
CTSKENSP000002716514STRING: ENSP00000271651
ENSG00000236342ENSP000004125534STRING: ENSP00000412553
HORMAD1ENSP000003551674STRING: ENSP00000355167
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006397mRNA processing IEA--

Find genes that share ontologies with APOBEC4           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for APOBEC4 (ABEC4)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for APOBEC4 gene: 
NM_203454.2  

Unigene Cluster for APOBEC4:

Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)
Hs.97335  [show with all ESTs]
Unigene Representative Sequence: NM_203454
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000308641(uc001gqn.3) ENST00000481562
miRNA
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Selected qRT-PCR Assays for microRNAs that regulate APOBEC4 (see all 10):
hsa-miR-2052 hsa-miR-374b hsa-miR-4306 hsa-miR-374a hsa-miR-29b-1* hsa-miR-223 hsa-miR-4261 hsa-miR-185
SwitchGear 3'UTR luciferase reporter plasmidAPOBEC4 3' UTR sequence
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat APOBEC4

Additional mRNA sequence: 

AK098557.1 BC021711.2 

1 DOTS entry:

DT.40224150 

17 AceView cDNA sequences:

BU676426 BX094690 NM_203454 AI961390 AA382354 BC021711 AA292880 BI770442 
BI828948 AK098557 AA496090 AA406043 BG722665 AA401696 CD710557 CD684537 
BI770969 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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APOBEC4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AATAAAAATT
APOBEC4 Expression
About this image

APOBEC4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

APOBEC4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.97335

UniProtKB/Swiss-Prot: ABEC4_HUMAN, Q8WW27
Tissue specificity: Predominantly expressed in testis

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for APOBEC4

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for APOBEC4 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Apobec41 , 5 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like more1, 5 74.76(n)1
64(a)1
  1 (65.01 cM)5
712811  NM_001081197.11  NP_001074666.11 
 1527505515 
chicken
(Gallus gallus)
Aves APOBEC41 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like more 57.56(n)
50.31(a)
  100858926  XM_004943280.1  XP_004943337.1 
lizard
(Anolis carolinensis)
Reptilia APOBEC46
apolipoprotein B mRNA editing enzyme, catalytic po...
54(a)
1 ↔ 1
GL343203.1(4021684-4022733)
tropical clawed frog
(Xenopus tropicalis)
Amphibia apobec41 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like more 56.6(n)
47.58(a)
  100495844  XM_002933765.2  XP_002933811.2 


ENSEMBL Gene Tree for APOBEC4 (if available)
TreeFam Gene Tree for APOBEC4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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6 SNPs for APOBEC4    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs11746571,2,4
----see VAR_0266422 mis40--------
rs168613941,2,4
----see VAR_0266392 mis40--------
rs11746581,2,4
----see VAR_0266402 mis40--------
rs109113911,2,4
----see VAR_0266412 mis40--------
rs109113901,2,4
----see VAR_0266432 mis40--------
rs168613811,2,4
----see VAR_0487242 mis40--------

HapMap Linkage Disequilibrium report for APOBEC4 (183615410 - 183622451 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for APOBEC4:    About this table    
Variant IDTypeSubtypePubMed ID
nsv872582CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 609908    OMIM disorders: --


Find genes that share disorders with APOBEC4           About GenesLikeMe


Export disorders for APOBEC4 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for APOBEC4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with APOBEC4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. (PubMed id 16082223)1, 2, 3 Rogozin I.B.... Koonin E.V. (Cell Cycle 2005)
  2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. (PubMed id 23273568)1 Yang W....Lau Y.L. (Am. J. Hum. Genet. 2013)
  6. APOBEC deaminases-mutases with defensive roles for immunity. (PubMed id 19911124)1 Prochnow C....Chen X.S. (Sci. China, C, Life Sci. 2009)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 403314 HGNC: 32152 AceView: MGC26594 Ensembl:ENSG00000173627 euGenes: HUgn403314
ECgene: APOBEC4 H-InvDB: APOBEC4

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for APOBEC4 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for APOBEC4 gene:
Search GeneIP for patents involving APOBEC4

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Block miRNA regulation of human, mouse, rat APOBEC4 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing APOBEC4
 DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat APOBEC4 Predesigned siRNA for gene silencing in human, mouse, rat APOBEC4
 QuantiFast Probe-based Assays in human, mouse, rat APOBEC4 QuantiTect SYBR Green Assays in human, mouse, rat APOBEC4
 Custom PCR Arrays for APOBEC4 Search Chromatin IP Primers for APOBEC4
 Pre-validated RT2 qPCR Primer Assay in human, mouse, rat APOBEC4  Search GeneGlobe Interaction Network for APOBEC4
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 GenScript Custom Purified and Recombinant Proteins Services for APOBEC4 GenScript cDNA clones with any tag delivered in your preferred vector for APOBEC4
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 Search Tocris compounds for APOBEC4 (ABEC4)
 Browse Sino Biological Proteins
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 See all of Abcam's Antibodies, Kits and Proteins for APOBEC4
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 Browse ESI BIO Cell Lines and PureStem Progenitors for APOBEC4
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for APOBEC4
 SwitchGear 3'UTR luciferase reporter plasmids for APOBEC4
 SwitchGear Promoter luciferase reporter plasmids for APOBEC4
 Search ThermoFisher Antibodies for APOBEC4
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat APOBEC4
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for APOBEC4
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for APOBEC4
 LSBio Antibodies in human, mouse, rat for APOBEC4
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 Browse compounds at ApexBio
 Search Addgene for plasmids for APOBEC4
  Search eBioscience for proteins for APOBEC4
  Search eBioscience for elisas for APOBEC4
  eBioscience FlowRNA Probe Sets
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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