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ZBED1 Gene

protein-coding   GIFtS: 48
GCID: GC0XM002320

Zinc Finger, BED-Type Containing 1

(Previous name: Ac-like transposable element)
(Previous symbol: ALTE)
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(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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Aliases
Zinc Finger, BED-Type Containing 11 2     KIAA07853 5
ALTE1 2 3 5     BED-Type Zinc Finger Domain-Containing Protein 12
TRAMP2 3 5     DNA Replication-Related Element Binding Factor2
Ac-Like Transposable Element1 2     hDREF2
DREF2 3     Zinc Finger BED Domain-Containing Protein 12
DREF Homolog2 3     Putative Ac-Like Transposable Element3

External Ids:    HGNC: 4471   Entrez Gene: 91892   Ensembl: ENSG000002147177   OMIM: 3001785   UniProtKB: O960063   

Export aliases for ZBED1 gene to outside databases

Previous GC identifers: GC0XM001999 GC0YM002320 GC0XM002148 GC0XM000346


(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 ZBED1 Gene:
This gene is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. It was earlier identified as a
gene with similarity to Ac transposable elements, however, was found not to have transposase activity. Later
studies show that this gene product is localized in the nucleus and functions as a transcription factor. It binds
to DNA elements found in the promoter regions of several genes related to cell proliferation, such as histone H1,
hence may have a role in regulating genes related to cell proliferation. Alternatively spliced transcript
variants with different 5' untranslated region have been found for this gene. (provided by RefSeq, Jan 2010)

GeneCards Summary for ZBED1 Gene:
ZBED1 (zinc finger, BED-type containing 1) is a protein-coding gene. GO annotations related to this gene include transposase activity and protein dimerization activity. An important paralog of this gene is ZBED4.

UniProtKB/Swiss-Prot: ZBED1_HUMAN, O96006
Function: Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related
to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as
gene weakly similar to Ac transposable elements, but does not code for any transposase activity

Gene Wiki entry for ZBED1 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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Regulatory elements:
   Search for regulatory transcription factor binding sites for ZBED1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZBED1 promoter sequence
   Search Chromatin IP Primers for ZBED1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZBED1


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

Entrez Gene cytogenetic band: Xp22.33;Yp11   Ensembl cytogenetic band:  Xp22.33   HGNC cytogenetic band: Xp22.33 and Yp11

ZBED1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZBED1 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM002320:  view genomic region     (about GC identifiers)

Start:
2,404,455 bp from pter      End:
2,419,008 bp from pter
Size:
14,554 bases      Orientation:
minus strand

1 alternative location:
ChrY- 2,354,455-2,369,008     

(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,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ZBED1_HUMAN, O96006 (See protein sequence)
Recommended Name: Zinc finger BED domain-containing protein 1  
Size: 694 amino acids; 78156 Da
Subunit: Homodimer (Potential)
Miscellaneous: The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y
chromosomes
Sequence caution: Sequence=BAA34505.2; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for ZBED1:
2CT5 (3D)    
Secondary accessions: Q96BY4

Explore the universe of human proteins at neXtProt for ZBED1: NX_O96006

Explore proteomics data for ZBED1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys113, Lys607
  • Modification sites at PhosphoSitePlus

  • See ZBED1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001164606.1  NP_001164607.1  NP_004720.1  

    ENSEMBL proteins: 
     ENSP00000370620   ENSP00000370616   ENSP00000419148   ENSP00000370621  

    ZBED1 Human Recombinant Protein Products:

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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:
    ZBED: Zinc fingers, BED-type
    PAR1: Pseudoautosomal regions / PAR1

    3 InterPro protein domains:
     IPR008906 HATC_dom_C
     IPR012337 RNaseH-like_dom
     IPR003656 Znf_BED_prd

    Graphical View of Domain Structure for InterPro Entry O96006

    ProtoNet protein and cluster: O96006

    1 Blocks protein domain: IPB008906 HAT dimerisation

    UniProtKB/Swiss-Prot: ZBED1_HUMAN, O96006
    Similarity: Contains 1 BED-type zinc finger


    Find genes that share domains with ZBED1           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: ZBED1_HUMAN, O96006
    Function: Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related
    to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as
    gene weakly similar to Ac transposable elements, but does not code for any transposase activity
    Induction: Expression is linked to the cell cycle: low in serum-starved fibroblasts, increasing during the G1/S
    phase, highest during the S/G2 phase and then decreasing again

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0004803transposase activity TAS9887332
    GO:0046872metal ion binding IEA--
    GO:0046983protein dimerization activity IEA--
         
    Find genes that share ontologies with ZBED1           About GenesLikeMe


    Animal Models:
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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 UniProtKB/Swiss-Prot
    ZBED1_HUMAN, O96006: Nucleus. Note=In granular structures
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    golgi apparatus2
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228nuclear chromosome TAS9887332

    Find genes that share ontologies with ZBED1           About GenesLikeMe


    (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 ZBED1
    Interactions:

        Search GeneGlobe Interaction Network for ZBED1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for ZBED1 (O960062, 3 ENSP000003706164) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FANCGO152872, 3, ENSP000003679104MINT-66922 I2D: score=5 STRING: ENSP00000367910
    GPN1Q9HCN42, 3, ENSP000002647184MINT-66624 I2D: score=5 STRING: ENSP00000264718
    NIP7Q9Y2212, 3, ENSP000002549404MINT-67408 I2D: score=5 STRING: ENSP00000254940
    RENBPP516062, 3, ENSP000003773034MINT-68359 I2D: score=5 STRING: ENSP00000377303
    SPEF1Q9Y4P92, 3, ENSP000003690804MINT-66054 I2D: score=5 STRING: ENSP00000369080
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008152metabolic process TAS9887332

    Find genes that share ontologies with ZBED1           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 ZBED1



    (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 ZBED1 gene (3 alternative transcripts): 
    NM_001171135.1  NM_001171136.1  NM_004729.3  

    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381222 ENST00000515319 ENST00000381218 ENST00000461691 ENST00000381223(uc004cqh.2 uc004cqg.2 uc022brw.1)

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      QuantiTect SYBR Green Assays in human, mouse, rat ZBED1
      QuantiFast Probe-based Assays in human, mouse, rat ZBED1

    Selected AceView cDNA sequences (see all 192):

    BF940271 AI682592 AV655439 AL705875 BE269286 BM837900 AA302814 BM549506 
    CR613724 M78108 BE899456 BQ674932 CR597100 BU509734 AI494595 AI752969 
    AW196831 BM695367 BX483798 AA367492 BE886788 AI953192 BQ671369 BI161369 

    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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    ZBED1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    ZBED1 Expression
    About this image


    ZBED1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
    ZBED1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZBED1 Protein Expression

    UniProtKB/Swiss-Prot: ZBED1_HUMAN, O96006
    Tissue specificity: Ubiquitously expressed at low levels. Expression is highest in skeletal muscle, heart, spleen
    and placenta

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    (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 animals.

    Orthologs for ZBED1 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia ZBED11 zinc finger, BED-type containing 1 87.9(n)
    89.48(a)
      491715  XM_005641065.1  XP_005641122.1 
    chicken
    (Gallus gallus)
    Aves ZBED11 zinc finger, BED-type containing 1 74.46(n)
    84.13(a)
      418663  XM_004938445.1  XP_004938502.1 
    lizard
    (Anolis carolinensis)
    Reptilia ZBED16
    zinc finger, BED-type containing 1
    72(a)
    1 ↔ 1
    3(113708106-113711543)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004950881 zinc finger BED domain-containing protein 1-like 67.87(n)
    78.87(a)
      100495088  XM_004911743.1  XP_004911800.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1018842851 zinc finger BED domain-containing protein 1-like 42.7(n)
    29.72(a)
      101884285  XM_005167801.1  XP_005167858.1 
    worm
    (Caenorhabditis elegans)
    Secernentea B0545.46
    Protein B0545.4 (B0545.4) mRNA, complete cds
    15(a)
    1 ↔ 1
    IV(109054-109684) WBGene00015247


    ENSEMBL Gene Tree for ZBED1 (if available)
    TreeFam Gene Tree for ZBED1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZBED1 gene
    ZBED42  ZBED62  

    Find genes that share paralogs with ZBED1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for ZBED1
    PGOHUM00000246025


    (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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    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for ZBED1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv29996CNV Loss17803354
    nsv10010CNV Gain18304495
    nsv9930CNV Gain18304495
    dgv2432e1CNV Complex17122850

    Locus Specific Mutation Databases (LSDB): ZBED1

    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: 300178    OMIM disorders: --


    Find genes that share disorders with ZBED1           About GenesLikeMe


    Export disorders for ZBED1 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 ZBED1 gene, integrated from 10 sources (see all 60):
    (articles sorted by number of sources associating them with ZBED1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases. (PubMed id 9887332)1, 2, 3, 9 Esposito T.... Forabosco A. (Hum. Mol. Genet. 1999)
    2. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 9872452)1, 2, 3 Nagase T.... Ohara O. (DNA Res. 1998)
    3. Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene. (PubMed id 12663651)1, 2, 9 Ohshima N.... Hirose F. (J. Biol. Chem. 2003)
    4. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PubMed id 23533661)1, 3 Hayward A.... Jern P. (PLoS ONE 2013)
    5. 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)
    6. hDREF regulates cell proliferation and expression of ribosomal protein genes. (PubMed id 17220279)1, 9 Yamashita D....Hirose F. (Mol. Cell. Biol. 2007)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    8. XNP/dATRX interacts with DREF in the chromatin to regulate gene expression. (PubMed id 22021382)1 Valadez-Graham V....Zurita M. (Nucleic Acids Res. 2012)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    10. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)

    (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: 9189 HGNC: 447 AceView: ZBED1.1 Ensembl:ENSG00000214717 euGenes: HUgn9189
    ECgene: ZBED1 H-InvDB: ZBED1

    (According to HUGE)
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    HUGE: KIAA0785

    (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 ZBED1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for ZBED1 gene:
    Search GeneIP for patents involving ZBED1

    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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