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BEX4 Gene

protein-coding   GIFtS: 48
GCID: GC0XP102470

Brain Expressed, X-Linked 4

(Previous names: brain expressed X-linked-like 1, BEX family member 4)
(Previous symbol: BEXL1)
  Search for BEX4
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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Aliases
Brain Expressed, X-Linked 41 2     BEX1-Like Protein 12 3
BEXL11 2 3     Protein BEX42
BEX Family Member 41 2     NADE33
Brain Expressed X-Linked-Like 11 2     Brain-Expressed X-Linked Protein 43
Nerve Growth Factor Receptor-Associated Protein 32 3     

External Ids:    HGNC: 254751   Entrez Gene: 562712   Ensembl: ENSG000001024097   OMIM: 3006925   UniProtKB: Q9NWD93   

Export aliases for BEX4 gene to outside databases

Previous GC identifers: GC0XP102357 GC0XP092133


(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 BEX4 Gene:
This gene is a member of the brain expressed X-linked gene family. The proteins encoded by some of the other
members of this family act as transcription elongation factors which allow RNA polymerase II to escape pausing
during elongation. Multiple alternatively spliced variants, encoding the same protein, have been identified.
(provided by RefSeq, Aug 2011)

GeneCards Summary for BEX4 Gene:
BEX4 (brain expressed, X-linked 4) is a protein-coding gene. An important paralog of this gene is BEX1.




(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:
NC_000023.11  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the BEX4 gene promoter:
         GR   GR-beta   POU3F1   C/EBPalpha   POU2F1   POU2F1a   Sox9   GR-alpha   En-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for BEX4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BEX4


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

Entrez Gene cytogenetic band: Xq22.1-q22.3   Ensembl cytogenetic band:  Xq22.1   HGNC cytogenetic band: Xq22.1-q22.3

BEX4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BEX4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP102470:  view genomic region     (about GC identifiers)

Start:
102,470,020 bp from pter      End:
102,472,174 bp from pter
Size:
2,155 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: BEX4_HUMAN, Q9NWD9 (See protein sequence)
Recommended Name: Protein BEX4  
Size: 120 amino acids; 14067 Da

Explore the universe of human proteins at neXtProt for BEX4: NX_Q9NWD9

Explore proteomics data for BEX4 at MOPED

Post-translational modifications: 

  • Ubiquitinated. Degraded by the proteasome (By similarity)1
  • Ubiquitination2 at Lys91
  • Modification sites at PhosphoSitePlus

  • See BEX4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001073894.1  NP_001121160.1  

    ENSEMBL proteins: 
     ENSP00000361780   ENSP00000361776  

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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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    2 InterPro protein domains:
     IPR021156 TF_A-like/BEX-like
     IPR007623 BEX

    Graphical View of Domain Structure for InterPro Entry Q9NWD9

    ProtoNet protein and cluster: Q9NWD9

    UniProtKB/Swiss-Prot: BEX4_HUMAN, Q9NWD9
    Similarity: Belongs to the BEX family


    BEX4 for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         1 GenomeRNAi human phenotype for BEX4:
     Increased G1 DNA content 

         1 MGI phenotypic allele for Bex4 (no phenotypes)

    BEX4 for phenotypes           About GeneDecksing

    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
    BEX4_HUMAN, Q9NWD9: Nucleus (By similarity). Cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular2
    nucleus2
    cytosol1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    BEX4 for ontologies           About GeneDecksing


    (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 BEX4
    Interactions:

        Search GeneGlobe Interaction Network for BEX4

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    2 Interacting proteins for BEX4 (Q9NWD93 ENSP000003617764) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTK2Q053973I2D: score=2 
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    (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 BEX4



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for BEX4 gene (2 alternative transcripts): 
    NM_001080425.3  NM_001127688.2  

    Unigene Cluster for BEX4:

    Brain expressed, X-linked 4
    Hs.184736  [show with all ESTs]
    Unigene Representative Sequence: NM_001080425
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372695(uc004ejv.4 uc004ejw.4) ENST00000372691
    miRNA
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    hsa-miR-100*
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    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat BEX4

    Additional mRNA sequence: 

    AK000959.1 AY833563.1 BC015794.2 BC068069.1 

    13 DOTS entries:

    DT.442377  DT.100031998  DT.100785667  DT.97813298  DT.100785664  DT.100785670  DT.121305800  DT.95217724 
    DT.100739054  DT.121305818  DT.92462691  DT.97773413  DT.121305835 

    Selected AceView cDNA sequences (see all 181):

    BQ786933 BE463664 AA031771 BE350256 AW338036 BI324844 AI679387 CR624132 
    CR598850 AA404255 AI955137 AU117899 BQ719299 BX463776 AI199874 CR617571 
    BQ432530 AL045947 AA404705 BM674357 AL544124 AL517301 AA256688 CR598194 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for BEX4    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c · 3d
    SP1:                    -                                 
    SP2:                    -                                 
    SP3:                    -     -                           
    SP4:                                                      


    ECgene alternative splicing isoforms for BEX4

    (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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    BEX4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAATTCACC
    BEX4 Expression
    About this image


    BEX4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 18) fully expand
     
     Gonad (Reproductive System)
             Primordial Germ Cells Primitive Gonad
     
     Eye (Sensory Organs)
             Mature Rod Bipolar Cells Inner Nuclear Layer
     
     Testis (Reproductive System)
             Pre-Sertoli Cells Testis Cord
     
     Liver (Hepatobiliary System)
             Hematopoietic Stem Cells Liver Bud
     
     Neurons
             Mature Rod Bipolar Cells Inner Nuclear Layer
    BEX4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BEX4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.184736
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    In Situ
    Assay Products:
     

     
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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 human and mouse.

    Orthologs for BEX4 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Bex41 , 5 brain expressed gene 41, 5 75.99(n)1
    60.17(a)1
      X (57.40 cM)5
    4062171  NM_212457.21  NP_997622.11 
     1361389965 


    ENSEMBL Gene Tree for BEX4 (if available)
    TreeFam Gene Tree for BEX4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for BEX4 gene
    BEX12  BEX52  BEX22  NGFRAP12  
    4 SIMAP similar genes for BEX4 using alignment to 1 protein entry:     BEX4_HUMAN:
    NGFRAP1    BEX1    BEX5    BEX2

    BEX4 for paralogs           About GeneDecksing



    (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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    Selected SNPs for BEX4 (see all 72)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1511026691,2
    --102437510(+) CCTACC/TTCAGC 2 -- us2k10--------
    rs1878852771,2
    --102437519(+) GCCCCA/CCAAAT 2 -- us2k10--------
    rs1923152511,2
    --102437935(+) CTAAAA/TTCCCA 2 -- us2k10--------
    rs59877081,2
    C,F,A,H--102437963(+) AGAGTA/CTTTGC 2 -- us2k120Minor allele frequency- C:0.24NS EA WA NA CSA 1968
    rs59877091,2
    --102438049(+) aggaaC/Tcacag 2 -- us2k10--------
    rs1887260221,2
    --102438063(+) AAAGAC/GATAAT 2 -- us2k10--------
    rs1998785891,2
    --102438247(+) CTGTT-/AAAAAA 2 -- us2k10--------
    rs1924172851,2
    C--102438450(+) TTAAGA/GTTGGG 2 -- us2k10--------
    rs1845850741,2
    --102439006(+) TTCTGA/GTGTGG 2 -- us2k10--------
    rs1889034831,2
    --102439037(+) AACAAA/GTACCA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for BEX4 (102470020 - 102472174 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for BEX4: --
    Human Gene Mutation Database (HGMD): BEX4
    Locus Specific Mutation Databases (LSDB): BEX4

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing BEX4
    DNA2.0 Custom Variant and Variant Library Synthesis for BEX4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300692    OMIM disorders: --


    BEX4 for disorders           About GeneDecksing


    Export disorders for BEX4 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 BEX4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with BEX4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of the Bex gene family in humans, mice, and rats. (PubMed id 15958283)1, 2, 3 Alvarez E.... Freed C.R. (Gene 2005)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    3. Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events. (PubMed id 16221301)1, 3 Winter E.E. and Ponting C.P. (BMC Evol. Biol. 2005)
    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. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    6. 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)
    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: 56271 HGNC: 25475 AceView: BEXL1 Ensembl:ENSG00000102409 euGenes: HUgn56271
    ECgene: BEX4 H-InvDB: BEX4

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for BEX4 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 BEX4 gene:
    Search GeneIP for patents involving BEX4

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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