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ZBED1 Gene

protein-coding   GIFtS: 47

GC0XM000346
zinc finger, BED-type containing 1
(Previous name: Ac-like transposable element )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: ALTE)
Products    

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

Aliases & Descriptions
zinc finger, BED-type containing 11 2     Putative Ac-like transposable element2 3
KIAA07851 2 3 5     dREF homolog2 3
TRAMP1 2 3 5     OTTHUMP000002148632
DREF1 2 3     putative Ac-like transposon2
ALTE2 3 5     zinc finger BED domain-containing protein 12
Ac-like transposable element1 2     BED-type zinc finger domain-containing protein 12
hDREF1 2     DNA replication-related element binding factor2

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

Export aliases for ZBED1 gene to outside databases

Previous GC identifers: GC0XM001999 GC0YM002320 GC0XM002320 GC0XM002148


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
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)

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

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ZBED1
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for ZBED1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 


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 gene densities for chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM000346:  view genomic region     (about GC identifiers)

Start:
346,909 bp from pter
End:
361,036 bp from pter
Size:
14,128 bases
Orientation:
minus strand

2 alternative locations:
ChrX- 2,404,477-2,419,008      ChrY- 2,354,455-2,369,008     

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
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;
PDB structures from and Proteopedia :
2CT5 (3D)    
Secondary accessions: Q96BY4

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

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


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


    ENSEMBL proteins: 
    ENSP00000419148 ENSP00000370620 ENSP00000370616 


    Human Recombinant Proteins 
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    2 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228 nuclear chromosome TAS9887332
    GO:0005634 nucleus IEA--
    About this table

    ZBED1 for ontologies           About GeneDecksing



    Antibodies for ZBED1: 
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    (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
     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


    (According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
    About This Section

    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

    Inhib.
    RNA:
        
    Browse for Gene Knock-down Tools from Millipore
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    Sigma-Aldrich siRNA for ZBED1
    Sigma-Aldrich shRNA for ZBED1
    OriGene 29mer shRNA kits in GFP-retroviral vector (see all 3): ZBED1
    OriGene shRNA RFP (see all 3): ZBED1
    OriGene basic RS shRNA (see all 3): ZBED1
    OriGene siRNA (see all 3): ZBED1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of ZBED1 
    miRNA:Sigma-Aldrich microRNA Mimics for ZBED1
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of ZBED1 
    Search SABiosciences for Assays for microRNAs that regulate ZBED1

    Gene
    Editing:
    Browse CompoZr Knockout ZFN at Sigma-Aldrich 

    Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
    Browse iPSC Reprogramming Factors at Sigma-Aldrich
    OriGene GFP tagged cDNA clones in CMV expression vector (see all 3): ZBED1
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 3): ZBED1
    OriGene untagged cDNA clones in CMV expression vector: ZBED1
    OriGene 3'-UTR clone: ZBED1 
    Browse MicroRNA Expression Plasmids 
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    Browse Sino Biological Human cDNA Clones

    Cell
    Lines:
      
    GenScript Custom overexpressing Cell Line Services for ZBED1 

    5 Gene Ontology (GO) molecular function terms (GO ID links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677 DNA binding IEA--
    GO:0004803 transposase activity TAS9887332
    GO:0005515 protein binding IPI16189514
    GO:0046872 metal ion binding IEA--
    GO:0046983 protein dimerization activity IEA--
    About this table

    ZBED1 for ontologies           About GeneDecksing


    (Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
    About This Section

        SABiosciences Custom Pathway-Focused PCR Arrays for ZBED1 

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZBED1

    5/11 Interacting proteins for ZBED1 (O960061, 2) via UniProtKB, MINT, and/or STRING (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FANCGO152871, 2EBI-740037,EBI-81610 MINT-66922
    GPN1Q9HCN42MINT-66624
    GPSM1Q86YR52MINT-67402
    NIF3L1Q9GZT82MINT-66440
    NIP7Q9Y2212MINT-67408
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section
    Browse Small Molecules at Sigma-Aldrich
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ZBED1


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Millipore,
    siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
    Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
    About This Section

    Inhib.
    RNA:
         
    Browse for Gene Knock-down Tools from Millipore
    Browse Nano Scale siRNA at Sigma-Aldrich
    Sigma-Aldrich siRNA for ZBED1
    Sigma-Aldrich shRNA for ZBED1
    OriGene 29mer shRNA kits in GFP-retroviral vector (see all 3): ZBED1
    OriGene shRNA RFP (see all 3): ZBED1
    OriGene basic RS shRNA (see all 3): ZBED1
    OriGene siRNA (see all 3): ZBED1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of ZBED1 
    miRNA: Sigma-Aldrich microRNA Mimics for ZBED1
    Browse microRNA target validation systems at Sigma-Aldrich 
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of ZBED1 
    Search SABiosciences for Assays for microRNAs that regulate ZBED1
    Clones: Browse FLAG tag genes at Sigma-Aldrich
    OriGene GFP tagged cDNA clones in CMV expression vector (see all 3): ZBED1
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 3): ZBED1
    OriGene untagged cDNA clones in CMV expression vector: ZBED1
    OriGene 3'-UTR Clone: ZBED1 
    Browse OriGene MicroRNA Expression Plasmids 
    GenScript cDNA clone with any tag delivered in your preferred vector: ZBED1 
    Primers: OriGene genome-wide validated SYBR primer pairs: ZBED1
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for ZBED1: PPH22286A

    REFSEQ mRNAs for ZBED1 gene (3 alternative transcripts): 

    NM_001171135.1  NM_001171136.1  NM_004729.3  

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

    AI752969 BE899456 BF940271 M78108 AW196831 CR597100 BE269286 BQ674932 
    CR613724 AV655439 BM837900 AI682592 BU509734 AL705875 BM549506 AI494595 
    AA302814 AA496808 BG747354 BF970891 AI560640 BV199713 AI953192 AI272762 

    highest scoring ESTs for ZBED1:

    AA216160 AA496808 BE296471 BE741290 BF837834 BG386894 BI114791 BM788079 BM907310 BQ062092 


    GeneLoc Exon Structure

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


    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Primers from OriGene and/or SABiosciences )
    About This Section

    ZBED1 expression in normal and diseased human tissues

    1  / 2  / 3

    5 probe-sets matching ZBED1 gene

    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    39168_at2, 3 U95-A 1 0.88 1.00 0.98 0.94 AB018328 0.80 0.70 0.75 1
    44978_at2, 3 U95-B 1 0.88 1.00 0.98 1.06 AI979194 0.40 0.67 0.55 1
    203043_at2, 3 U133-A 1 0.73 1.00 -- -- NM_004729 0.40 0.67 0.55 1
    1554821_a_at2 U133Plus2 1 0.82 1.00 -- -- -- -- -- -- --
    203043_at2 U133Plus2 1 0.73 1.00 -- -- -- -- -- -- --
    About this table

    ZBED1 for expression           About GeneDecksing

    Data from Genenote  (Publications) and GNF BioGPS
        About these images
    ZBED1 gene expression
    ZBED1 gene electronic northern expression
    ZBED1 gene sage expression
    About these images

    CGAP SAGE TAG: --

    Expression variation in blood from EXPOLDB 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

    Primers: OriGene genome-wide validated SYBR primer pairs: ZBED1
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for ZBED1: PPH22286A
        SABiosciences Custom PCR Arrays for ZBED1 


    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section

    Orthologs for ZBED1 gene from 5/6 species (see all 6)
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    ZBED11   -- zinc finger, BED-type containing 1 87.9(n)
    89.48(a)
    491715  XM_548835.2  XP_548835.2 
    chimpanzee
    (Pan troglodytes)
    ZBED11   -- zinc finger, BED-type containing 1 76.37(n)
    62.03(a)
    471273  XM_001137235.1  XP_001137235.1 
    cow
    (Bos taurus)
    ZBED11   -- zinc finger, BED-type containing 1 84.25(n)
    81.56(a)
    539266  XM_586037.3  XP_586037.3 
    chicken
    (Gallus gallus)
    ZBED11   -- zinc finger, BED-type containing 1 74.46(n)
    84.13(a)
    418663  XM_416859.2  XP_416859.1 
    zebrafish
    (Danio rerio)
    LOC7945971   -- similar to ZBED1 protein 42.48(n)
    29.03(a)
    794597  XM_001334552.1  XP_001334588.1 
    About this table        Species with no ortholog for ZBED1

    ENSEMBL Gene Tree for ZBED1 (if available)

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

    ZBED1 for paralogs           About GeneDecksing


    Pseudogenes
    1 related pseudogene



    (SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
    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
    QIAGEN SeqTarget long-range PCR primers for resequencing ZBED1 

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    ZBED1 for disorders           About GeneDecksing

    OMIM: 300178

    Locus Specific Mutation Databases (LSDB): ZBED1

    Export disorders and mutations for ZBED1 gene to outside databases

    (Possibly Related Articles in Doctor's Guide)
    About This Section
      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6UniProtKB/TrEMBL, and/or 7Novoseek)
    About This Section

    10/49 PubMed articles for ZBED1 gene, integrated from 7 sources (see all 49):
    (articles sorted by number of sources associating them with ZBED1)
    1. A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases. (PubMed id 9887332)1, 2, 3, 7 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, 7 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, 7 Yamashita D....Hirose F. (2007)
    6. Shifted Transversal Design smart-pooling for high cov erage interactome mapping. (PubMed id 19447967)1 Xin X....Thierry-Mieg N. (2009)
    7. Human DNA replication-related element binding factor (hDREF) self- association via hATC domain is necessary for its nuclear accumulation and DNA binding. (PubMed id 17209048)1 Yamashita D....Hirose F. (2007)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (2006)
    10. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)

    (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)

    (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

    (According to HUGE)
    About This Section
    HUGE: KIAA0785

    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
      --

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from XenneX, Inc.)
    About This Section
    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 by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
    Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
    About This Section

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    GeneCards Homepage - Last full update: 31 Dec 2010 - Incremental updates: 10 Jan 2011 , 10 Jan 2011

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