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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ATAD2B Gene

protein-coding   GIFtS: 46
GCID: GC02M023971

ATPase family, AAA domain containing 2B

 Explore 4 diseases affiliated with
ATAD2B via our new
 Human Malady Compendium 
Biological research products
for ATAD2B
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
ATPase Family, AAA Domain Containing 2B1 2
KIAA12401 3
ATPase Family AAA Domain-Containing Protein 2B2
EC 3.5.1.158
EC 3.6.1.38

External Ids:    HGNC: 292301   Entrez Gene: 544542   Ensembl: ENSG000001197787   UniProtKB: Q9ULI03   
ORGUL members:         
NONCODE:n338700    

Export aliases for ATAD2B gene to outside databases

Previous GC identifers: GC02M023825 GC02M023711


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for ATAD2B:
The protein encoded by this gene belongs to the AAA ATPase family, CDC48 subfamily. This subfamily members in
eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the
Golgi apparatus. The exact function of this protein is not known. (provided by RefSeq, May 2011)




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_022184.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ATAD2B gene promoter:
         TBP   AhR   HOXA9   HOXA9B   AML1a   MIF-1   Meis-1b   AREB6   TFIID   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for ATAD2B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ATAD2B


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

Entrez Gene cytogenetic band: 2p24.1-p23.3   Ensembl cytogenetic band:  2p23.3   HGNC cytogenetic band: 2p24.1-p23.3

ATAD2B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATAD2B gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M023971:  view genomic region     (about GC identifiers)

Start:
23,971,534 bp from pter      End:
24,149,984 bp from pter
Size:
178,451 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ATD2B_HUMAN, Q9ULI0 (See protein sequence)
Recommended Name: ATPase family AAA domain-containing protein 2B  
Size: 1458 amino acids; 164914 Da
Subunit: Binds acetylated lysine residues in histone H1.4, H2A, H2B, H3 and H4 (in vitro)
Sequence caution: Sequence=BAD18469.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
2 PDB 3D structures from and Proteopedia for ATAD2B:
2DKW (3D)        3LXJ (3D)    
Secondary accessions: B9ZVQ5 Q6ZNA6 Q8N9E7
Alternative splicing: 2 isoforms:  Q9ULI0-1   Q9ULI0-2   

Explore the universe of human proteins at neXtProt for ATAD2B: NX_Q9ULI0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9ULI0

  • 2 DME Specific Peptides for ATAD2B (Q9ULI0)
     LFYGPPG  TLILEDS 

    ATAD2B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001229267.1  NP_060022.1  

    ENSEMBL proteins: 
     ENSP00000238789   ENSP00000370412   ENSP00000392764   ENSP00000415926   ENSP00000403177  

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    Uscn Proteins for ATAD2B


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    Uscn ELISAs and CLIAs for ATAD2B


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ATAD2B for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR003959 ATPase_AAA_core
     IPR003960 ATPase_AAA_CS
     IPR018359 Bromodomain_CS
     IPR001487 Bromodomain
     IPR003593 AAA+_ATPase

    Graphical View of Domain Structure for InterPro Entry Q9ULI0

    ProtoNet protein and cluster: Q9ULI0

    UniProtKB/Swiss-Prot: ATD2B_HUMAN, Q9ULI0
    Similarity: Belongs to the AAA ATPase family
    Similarity: Contains 1 bromo domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Enzyme Numbers (IUBMB): EC 3.6.1.32 EC 3.5.1.152

    miRNA
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    hsa-miR-3607-3p hsa-miR-411 hsa-miR-199a-3p hsa-miR-4272 hsa-miR-218-1* hsa-miR-30d hsa-miR-578 hsa-miR-30a
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005524ATP binding IEA--
    GO:0017111nucleoside-triphosphatase activity IEA--
    GO:0070577histone acetyl-lysine binding IDA--


    ATAD2B for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ATAD2B:
     Synthetic lethal with Ras 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ATAD2B

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

    5/6 Interacting proteins for ATAD2B (Q9ULI03 ENSP000002387894) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RBL1P287493I2D: score=1 
    SIRT7ENSP000003294664STRING: ENSP00000329466
    SUPT16HENSP000002162974STRING: ENSP00000216297
    POLR2LENSP000003241244STRING: ENSP00000324124
    BTAF1ENSP000002659904STRING: ENSP00000265990
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ATAD2B
    Search CenterWatch for drugs/clinical trials and news about ATAD2B / ATD2B 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for ATAD2B gene (2 alternative transcripts): 
    NM_001242338.1  NM_017552.2  

    Unigene Cluster for ATAD2B:

    ATPase family, AAA domain containing 2B
    Hs.467862  [show with all ESTs]
    Unigene Representative Sequence: NM_017552
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000238789(uc002rej.4 uc002rei.4 uc002rek.4 uc010yki.2)
    ENST00000381024 ENST00000474583 ENST00000486610 ENST00000478885 ENST00000498006
    ENST00000458510 ENST00000366438 ENST00000439915(uc010exx.2)

    miRNA
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    8/91 QIAGEN miScript miRNA Assays for microRNAs that regulate ATAD2B (see all 91):
    hsa-miR-3607-3p hsa-miR-411 hsa-miR-199a-3p hsa-miR-4272 hsa-miR-218-1* hsa-miR-30d hsa-miR-578 hsa-miR-30a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Additional cDNA sequence: 

    AB033066.1 AF038204.1 AK023705.1 AK094821.1 AK125718.1 AK131301.1 BC037408.1 BC171846.1 

    11 DOTS entries:

    DT.99967671  DT.101956844  DT.97776105  DT.91650686  DT.40231078  DT.95261658  DT.91845828  DT.102842507 
    DT.425591  DT.86850973  DT.91836153 

    1 AceView cDNA sequence:

    CB988926 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for ATAD2B    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b
    SP1:              -                                         -                 -                                                         
    SP2:              -           -     -     -                 -           -     -                                                         
    SP3:              -           -     -     -                 -                 -                                                         
    SP4:                          -                                                                                                         
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for ATAD2B

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    ATAD2B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATGTCTACT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See ATAD2B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ATAD2B

    SOURCE GeneReport for Unigene cluster: Hs.467862
        SABiosciences Custom PCR Arrays for ATAD2B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ATAD2B

    (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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for ATAD2B gene from 8/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ATAD2B1 ATPase family, AAA domain containing 2B 80.69(n)
    85.91(a)
      421972  XM_419982.3  XP_419982.3 
    lizard
    (Anolis carolinensis)
    Reptilia ATAD2B6
    --
    90(a)
    1 ↔ 1
    1(140457852-140514679)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.70802 Transcribed sequence with weak similarity to protein more 76.43(n)    AL872229.2 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch73-97d3.26
    si:ch73-97d3.2
    55(a)
    1 ↔ 1
    20(44788086-44994715)
    honey bee
    (Apis mellifera)
    Insecta --
    --
    --
    41(a)
    33(a)
    many ↔ many
    many ↔ many
    GroupUn.10(47904-52304)
    GroupUn.10(57119-63763)
    worm
    (Caenorhabditis elegans)
    Secernentea lex-16
    Tat-binding homolog 7
    32(a)
    1 → many
    IV(12079449-12084338)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G059101 cell division cycle protein 48-like protein 52.39(n)
    47.01(a)
      837101  NM_100472.1  NP_563753.1 
    rice
    (Oryza sativa)
    Liliopsida Os09g05151001 hypothetical protein 50.68(n)
    45.02(a)
      4347572  NM_001070199.1  NP_001063664.1 


    ENSEMBL Gene Tree for ATAD2B (if available)
    TreeFam Gene Tree for ATAD2B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ATAD2B gene
    ATAD22  
    12 SIMAP similar genes for ATAD2B using alignment to 6 protein entries:     ATD2B_HUMAN (see all proteins):
    VCP    PSMC5    PSMC1    KATNAL2    PSMC6    PSMC3
    NVL    ATAD2    DKFZp434E0418    PSMC2    DKFZp434K0126    ATAD1

    ATAD2B for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2803 NCBI SNPs in ATAD2B are shown (see all 2803    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs562618421,2
    C,F,--23711043(+) GCCAAG/TAACAT 2 -- ds50011Minor allele frequency- T:0.13NA 120
    rs25513211,2
    C,F,O,H,--23711268(+) TAGACA/GATCTT 2 -- ds500116Minor allele frequency- G:0.03NS EA NA CSA WA 906
    rs102218251,2
    C,--23711774(+) AGGTAC/GAAGCC 2 -- ut31 ese30--------
    rs23033021,2
    H--23711999(+) AAAAAA/CAAAAA 2 -- ut31 trp31Minor allele frequency- C:0.00NS 120
    rs767040981,2
    --23712449(+) CATTAG/AATTGA 2 -- ut311Minor allele frequency- A:0.01WA 118
    rs27120641,2
    C,F,O,H,--23712797(+) AAAAAC/TCCTTT 2 -- ut31 ese321Minor allele frequency- T:0.03NS EA NA 2538
    rs174617511,2
    C,F,H,--23713584(+) CAAATT/CTGTAG 2 -- ut31 ese35Minor allele frequency- C:0.01NA NS 368
    rs1146875871,2
    C,F,--23713761(+) AGCTCG/ATTTGC 2 -- ut311Minor allele frequency- A:0.04NA 120
    rs773622551,2
    --23714238(+) ATTTCT/AAATTT 2 -- ut311Minor allele frequency- A:0.01WA 118
    rs763319801,2
    --23714486(+) ATTCAA/GCACAG 2 -- ut310--------

    HapMap Linkage Disequilibrium report for ATAD2B (23971534 - 24149984 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for ATAD2B
         2 CNVs: 7255 5972
         1 Indel: 26609

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ATAD2B
    DNA2.0 Custom Variant and Variant Library Synthesis for ATAD2B

    (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.)
    About This Section

    ATAD2B for disorders           About GeneDecksing

    4 diseases for ATAD2B:    About MalaCards
    oligodendroglioma    tuberculosis    neuronitis    mycobacterium tuberculosis


    Export disorders for ATAD2B 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)
    About This Section

    PubMed articles for ATAD2B gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with ATAD2B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10574462)1, 2 Nagase T.... Ohara O. (1999)
    3. Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
    4. Histone recognition and large-scale structural analysis of the human bromodomain family. (PubMed id 22464331)2 Filippakopoulos P.... Knapp S. (2012)
    5. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    6. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    7. ATAD2B is a phylogenetically conserved nuclear protei n expressed during neuronal differentiation and tumorigenesis. (PubMed id 21158754)1 Leachman N.T....Tucker R.P. (2010)
    8. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    9. 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. (2002)
    10. Large-scale concatenation cDNA sequencing. (PubMed id 9110174)1 Yu W.... Gibbs R.A. (1997)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 54454 HGNC: 29230 AceView: KIAA1240.2 Ensembl:ENSG00000119778 euGenes: HUgn54454
    ECgene: ATAD2B H-InvDB: ATAD2B

    (According to HUGE)
    About This Section
    HUGE: KIAA1240

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for ATAD2B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for ATAD2B gene:
    Search GeneIP for patents involving ATAD2B

    GeneCards and IP:
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