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

ZBED1 Gene

protein-coding   GIFtS: 45
GCID: GC0XM002320

zinc finger, BED-type containing 1

(Previous name: Ac-like transposable element )
(Previous symbol: ALTE)
 Explore 6 diseases affiliated with
ZBED1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for ZBED1    

Aliases
for ZBED1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Zinc Finger, BED-Type Containing 11 2     HDREF1
ALTE1 2 3 5     DREF Homolog2 3
TRAMP1 2 3 5     BED-Type Zinc Finger Domain-Containing Protein 12
DREF1 2 3     DNA Replication-Related Element Binding Factor2
KIAA07851 3 5     Zinc Finger BED Domain-Containing Protein 12
Ac-Like Transposable Element1 2     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


Summaries
for ZBED1 gene

(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 ZBED1:
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)

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


Genomic Views
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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
 Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ZBED1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: ZBED1 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZBED1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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     

Proteins
for ZBED1 gene

(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: ZBED1_HUMAN, O96006 (See protein sequence)
Recommended Name: Zinc finger BED domain-containing protein 1  
Size: 694 amino acids; 78156 Da
Subunit: Homodimer (Potential)
Subcellular location: Nucleus. Note=In granular structures
Miscellaneous: The gene encoding 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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O96006

    • ZBED1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

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

    ENSEMBL proteins: 
     ENSP00000370620   ENSP00000370616   ENSP00000419148   ENSP00000370621  

    Human Recombinant Protein Products: 
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    Uscn Proteins for ZBED1

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228nuclear chromosome TAS9887332


    ZBED1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for ZBED1

    Protein Domains /
    Families
    for ZBED1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ZBED1 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR008906 HATC
     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 family: IPB008906 HAT dimerisation

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


    Function
    for ZBED1 gene

    (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
    Function Summary:

         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
    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

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for ZBED1 (see all 3)
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    Cell Line
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    Search LifeMap BioReagents cell lines for ZBED1

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZBED1

    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0004803transposase activity TAS9887332
    GO:0046872metal ion binding IEA--
    GO:0046983protein dimerization activity IEA--


    ZBED1 for ontologies           About GeneDecksing



    Pathways & Interactions
    for ZBED1 gene

    (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 ZBED1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 18)

    5/26 Interacting proteins for ZBED1 (O960062, 3 ENSP000003706164) via UniProtKB, MINT, STRING, and/or I2D (see all 26)
    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

    Drugs & Compounds
    for ZBED1 gene

    (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 ZBED1
    Search CenterWatch for drugs/clinical trials and news about ZBED1 

    Transcripts
    for ZBED1 gene

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

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


    miRNA
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    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ZBED1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ZBED1

    24/192 AceView cDNA sequences (see all 192):

    AA302814 AI494595 CR597100 AL705875 M78108 BE899456 BE269286 BF940271 
    AW196831 AV655439 AI752969 BM549506 BU509734 CR613724 BQ674932 BM837900 
    AI682592 BV199713 BM665016 BI161369 BQ669498 CA391211 AW067840 AB018328 

    GeneLoc Exon Structure


    Expression
    for ZBED1 gene

    (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

    ZBED1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See ZBED1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZBED1

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

        SABiosciences Custom PCR Arrays for ZBED1
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZBED1

    Orthologs
    for ZBED1 gene

    (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 animals.

    Orthologs for ZBED1 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves ZBED11 zinc finger, BED-type containing 1 74.46(n)
    84.13(a)    		   418663  XM_416859.3  XP_416859.1 
    lizard
    (Anolis carolinensis)    		 Reptilia ZBED16
    		 --
    		 80(a)
    		 1 ↔ 1
    		 3(113709404-113711491)
    zebrafish
    (Danio rerio)    		 Actinopterygii BX908745.16
    CR847563.26
    (see all 11)    		 --
    		 29(a)
    28(a)
    (see all 11)    		 possible ortholog
    possible ortholog
    (see all 11)    		 7(71312740-71314530)
    11(8660848-8663129)
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG137756
    		 --
    		 19(a)
    		 possible ortholog
    		 2L(6954585-6956872)
    worm
    (Caenorhabditis elegans)    		 Secernentea K09A11.16
    C10A4.16
    (see all 4)    		 --
    		 19(a)
    18(a)
    (see all 4)    		 possible ortholog
    possible ortholog
    (see all 4)    		 X(13262431-13264518)
    X(7415794-7418582)
            Species with no ortholog for ZBED1

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

    Paralogs
    for ZBED1 gene

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

    ZBED1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for ZBED1
    PGOHUM00000246025


    Genomic Variants
    for ZBED1 gene

    (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

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for ZBED1
         3 CNVs: 31578 4142 31543
    Locus Specific Mutation Databases (LSDB): ZBED1
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ZBED1
    DNA2.0 Custom Variant and Variant Library Synthesis for ZBED1

    Disorders / Diseases
    for ZBED1 gene

    (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
    ZBED1 for disorders           About GeneDecksing

    OMIM gene information: 300178    OMIM disorders: --

    6 diseases for ZBED1:    About MalaCards
    sudden infant death syndrome    munchausen by proxy    gastroesophageal reflux disease    myeloid leukemia
    ataxia    leukemia


    Export disorders for ZBED1 gene to outside databases

    Publications
    for ZBED1 gene

    (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 ZBED1 gene, integrated from 9 sources (see all 58):
    (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. (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. (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. (2003)
    4. 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. (2004)
    5. hDREF regulates cell proliferation and expression of ribosomal protein genes. (PubMed id 17220279)1, 9 Yamashita D....Hirose F. (2007)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    7. XNP/dATRX interacts with DREF in the chromatin to regu late gene expression. (PubMed id 22021382)1 Valadez-Graham V....Zurita M. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)

    External Searches for ZBED1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing ZBED1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 9189 HGNC: 447 AceView: ZBED1.1 Ensembl:ENSG00000214717 euGenes: HUgn9189
    ECgene: ZBED1 H-InvDB: ZBED1

    Other Databases showing ZBED1 gene

    (According to HUGE)
    About This Section
    HUGE: KIAA0785

    Specialized Databases showing ZBED1 gene

    (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 ZBED1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for ZBED1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for ZBED1 gene:
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     ZBED1 Proteins, Antibodies, CLIAs, and ELISAs
     Search LifeMap BioReagents cell lines for ZBED1
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