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

BEND3 Gene

protein-coding   GIFtS: 42
GCID: GC06M107386

BEN Domain Containing 3

(Previous name: KIAA1553)
(Previous symbol: KIAA1553)
  Search for BEND3
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
BEN Domain Containing 31 2
KIAA15531 2 3
RP11-59I9.22
BEN Domain-Containing Protein 32

External Ids:    HGNC: 230401   Entrez Gene: 576732   Ensembl: ENSG000001784097   UniProtKB: Q5T5X73   

Export aliases for BEND3 gene to outside databases

Previous GC identifers: GC06M107494 GC06M104957


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

GeneCards Summary for BEND3 Gene: 
BEND3 (BEN domain containing 3) is a protein-coding 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_025741.15  NC_018917.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the BEND3 gene promoter:
         RFX1   p53   POU6F1 (c2)   MEF-2A   CBF-A   CP1A   aMEF-2   NF-Y   RSRFC4   CBF(2)   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for BEND3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat BEND3


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

BEND3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BEND3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M107386:  view genomic region     (about GC identifiers)

Start:
107,386,385 bp from pter      End:
107,436,473 bp from pter
Size:
50,089 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: BEND3_HUMAN, Q5T5X7 (See protein sequence)
Recommended Name: BEN domain-containing protein 3  
Size: 828 amino acids; 94475 Da
Secondary accessions: A2RRH2 Q9HCL9

Explore the universe of human proteins at neXtProt for BEND3: NX_Q5T5X7

Explore proteomics data for BEND3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5T5X7

  • BEND3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    BEND3 Protein Expression
    REFSEQ proteins: NP_001073919.1  
    ENSEMBL proteins: 
     ENSP00000358038   ENSP00000411268  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    BEND: BEN domain containing

    1 InterPro protein domain:
     IPR018379 BEN_domain

    Graphical View of Domain Structure for InterPro Entry Q5T5X7

    ProtoNet protein and cluster: Q5T5X7

    UniProtKB/Swiss-Prot: BEND3_HUMAN, Q5T5X7
    Similarity: Contains 4 BEN domains


    BEND3 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Phenotypes:
         2 GenomeRNAi human phenotypes for BEND3:
     Decreased Wnt reporter activit  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for BEND3 
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BEND3


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for BEND3

    5/35 Interacting proteins for BEND3 (Q5T5X72, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 35)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SUMO1P631652, 3MINT-8173832 I2D: score=1 
    USP21Q9UK803I2D: score=2 
    SALL4Q9UJQ43I2D: score=1 
    SUMO3P558543I2D: score=1 
    CHAMP1Q96JM32MINT-8173832
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 BEND3

    Search CenterWatch for drugs/clinical trials and news about BEND3

    (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,
    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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for BEND3 gene: 
    NM_001080450.2  

    Unigene Cluster for BEND3:

    BEN domain containing 3
    Hs.418045  [show with all ESTs]
    Unigene Representative Sequence: NM_001080450
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369042 ENST00000429433(uc003prs.2)
    miRNA
    Products:
         
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    8/83 QIAGEN miScript miRNA Assays for microRNAs that regulate BEND3 (see all 83):
    hsa-miR-3938 hsa-miR-3607-3p hsa-miR-642a hsa-miR-128 hsa-miR-485-3p hsa-miR-200a hsa-miR-219-5p hsa-miR-30d
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for BEND3
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat BEND3
    Clone
    Products:
         
    OriGene clones in human, mouse for BEND3 (see all 7)
    OriGene ORF clones in mouse, rat for BEND3
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: BEND3 (NM_001080450)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for BEND3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat BEND3
    Sirion Biotech Customized lentivirus for stable overexpression of BEND3 
                         Customized lentivirus expression plasmids for stable overexpression of BEND3 
    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat BEND3

    Additional mRNA sequence: 

    AB046773.1 AK026996.1 BC131628.1 

    2 DOTS entries:

    DT.312546  DT.121355460 

    24/55 AceView cDNA sequences (see all 55):

    AI733269 BU179685 BU624353 BQ686361 Z42590 Z38770 AI793293 AI792975 
    AB046773 T32552 F10007 AA604028 CD656239 AA935776 BX506710 BF590912 
    BU150080 AA779361 AI671193 AA931780 BQ686987 D25551 AA931779 AA927520 

    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™, 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

    BEND3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCTGCATTTT
    BEND3 Expression
    About this image


    See BEND3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for BEND3

    SOURCE GeneReport for Unigene cluster: Hs.418045
        SABiosciences Custom PCR Arrays for BEND3
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat BEND3
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BEND3

    (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 chordates.

    Orthologs for BEND3 gene from 4/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Bend31 , 5 BEN domain containing 31, 5 86.34(n)1
    91.15(a)1
      10 (23.00 cM)5
    3316231  NM_199028.21  NP_950193.11 
     434791405 
    chicken
    (Gallus gallus)
    Aves BEND31 BEN domain containing 3 71.11(n)
    77.72(a)
      421778  XM_003641010.1  XP_003641058.1 
    lizard
    (Anolis carolinensis)
    Reptilia BEND36
    BEN domain containing 3
    66(a)
    1 ↔ 1
    1(189635345-189644176)
    zebrafish
    (Danio rerio)
    Actinopterygii bend31 BEN domain containing 3 62.58(n)
    62.34(a)
      565716  NM_001145591.1  NP_001139063.1 


    ENSEMBL Gene Tree for BEND3 (if available)
    TreeFam Gene Tree for BEND3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for BEND3 gene

    BEND3 for paralogs           About GeneDecksing


    3 Pseudogenes.org Pseudogenes for BEND3
    PGOHUM00000238795 PGOHUM00000238853 PGOHUM00000236706


    (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) 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

    10/1268 SNPs in BEND3 are shown (see all 1268)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1397020891,2
    --105008787(+) GCGGCA/GAGGGT 1 -- us2k10--------
    rs788949981,2
    C,F--105008816(+) TGGGTT/GTACCG 1 -- us2k11Minor allele frequency- G:0.03NA 120
    rs93866111,2
    C,H--105008820(+) TTTACC/GGTACC 1 -- us2k1 tfbs33Minor allele frequency- G:0.06NS EA 358
    rs1452308481,2
    --105008875(+) TCCCCC/TCCTTC 1 -- us2k10--------
    rs94865271,2
    C,F--105008892(+) GAAATC/GAAAAG 1 -- us2k11Minor allele frequency- G:0.03WA 118
    rs1151731791,2
    F--107385989(+) GCGGCG/AGGAAA 1 -- ds50011Minor allele frequency- A:0.04WA 118
    rs762050191,2
    C,F--107386004(+) AACCCG/ATTTGA 1 -- ds50011Minor allele frequency- A:0.50WA 2
    rs1462404041,2
    --107386127(+) CTACAC/TGGCCA 1 -- ds50010--------
    rs1379407131,2
    --107386162(+) TTGGAA/GGATTT 1 -- ds50010--------
    rs94865131,2
    C,F,A,H--107386233(+) TGACAC/TGTAGA 1 -- ds500117Minor allele frequency- T:0.15NS EA NA WA 2230

    HapMap Linkage Disequilibrium report for BEND3 (107386385 - 107436473 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for BEND3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2732547CNV Deletion23290073
    esv2732546CNV Deletion23290073
    esv2732548CNV Deletion23290073
    esv1657137CNV Deletion17803354
    dgv87n68CNV Loss17160897
    esv27390CNV Loss19812545
    nsv521601CNV Loss19592680
    dgv1063n67CNV Gain20364138

    SABiosciences Cancer Mutation PCR Assays
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    (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.)
    About This Section

    BEND3 for disorders           About MalaCards

    BEND3 for disorders           About GeneDecksing

    Human Genome Epidemiology (HuGE) Navigator: BEND3 (1 document)

    Export disorders for BEND3 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 BEND3 gene, integrated from 9 sources (see all 21):
    (articles sorted by number of sources associating them with BEND3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10997877)1, 2 Nagase T.... Ohara O. (2000)
    2. Interlaboratory reproducibility of large-scale human p rotein-complex analysis by standardized AP-MS. (PubMed id 23455922)1 Varjosalo M....Superti-Furga G. (2013)
    3. The functional interactome landscape of the human hist one deacetylase family. (PubMed id 23752268)1 Joshi P....Cristea I.M. (2013)
    4. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
    5. Human CCAAT/enhancer-binding protein b interacts with chromatin remodeling complexes of the imitation switch subfamily. (PubMed id 22242598)1 Steinberg X.P....Gutierrez J.L. (2012)
    6. 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)
    7. Maintenance of silent chromatin through replication r equires SWI/SNF-like chromatin remodeler SMARCAD1. (PubMed id 21549307)1 Rowbotham S.P....Mermoud J.E. (2011)
    8. A BEN-domain-containing protein associates with heter ochromatin and represses transcription. (PubMed id 21914818)1 Sathyan K.M....Prasanth S.G. (2011)
    9. 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)
    10. Comparative proteomic analysis identifies a role for S UMO in protein quality control. (PubMed id 21693764)1 Tatham M.H....Hay R.T. (2011)

    (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: 57673 HGNC: 23040 AceView: KIAA1553 Ensembl:ENSG00000178409 euGenes: HUgn57673
    ECgene: BEND3 H-InvDB: BEND3

    (According to HUGE)
    About This Section
    HUGE: KIAA1553

    (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 BEND3 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 BEND3 gene:
    Search GeneIP for patents involving BEND3

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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