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BEND4 Gene

protein-coding   GIFtS: 40
GCID: GC04M042112

BEN Domain Containing 4

(Previous name: coiled-coil domain containing 4)
(Previous symbol: CCDC4)
  Search for BEND4
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
BEN Domain Containing 41 2
CCDC41 2 3
Coiled-Coil Domain Containing 41 2
Coiled-Coil Domain-Containing Protein 42 3
BEN Domain-Containing Protein 42

External Ids:    HGNC: 238151   Entrez Gene: 3892062   Ensembl: ENSG000001888487   UniProtKB: Q6ZU673   

Export aliases for BEND4 gene to outside databases

Previous GC identifers: GC04M041808 GC04M041434


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for BEND4 Gene:
BEND4 (BEN domain containing 4) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000004.12  NC_018915.2  NT_006238.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the BEND4 gene promoter:
         SRF   GR   GR-beta   Pax-2   Pax-2a   Nkx2-5   Evi-1   POU2F1   POU2F1a   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): BEND4 promoter sequence
   Search Chromatin IP Primers for BEND4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BEND4


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

Entrez Gene cytogenetic band: 4p13   Ensembl cytogenetic band:  4p13   HGNC cytogenetic band: 4p13

BEND4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BEND4 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M042112:  view genomic region     (about GC identifiers)

Start:
42,112,870 bp from pter      End:
42,154,895 bp from pter
Size:
42,026 bases      Orientation:
minus 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: BEND4_HUMAN, Q6ZU67 (See protein sequence)
Recommended Name: BEN domain-containing protein 4  
Size: 534 amino acids; 58375 Da
Sequence caution: Sequence=AAI28593.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAI28594.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD93191.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAD93192.1; Type=Erroneous
initiation; Note=Translation N-terminally extended;
Secondary accessions: A1A5D6 A1A5D7 C9JQZ5 Q58A26 Q58A27
Alternative splicing: 5 isoforms:  Q6ZU67-1   Q6ZU67-2   Q6ZU67-3   Q6ZU67-4   Q6ZU67-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for BEND4: NX_Q6ZU67

Explore proteomics data for BEND4 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See BEND4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001153019.1  NP_997289.2  

    ENSEMBL proteins: 
     ENSP00000421169   ENSP00000421160  

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    Browse CLIAs at Cloud-Clone Corp.


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

    1 InterPro protein domain:
     IPR018379 BEN_domain

    Graphical View of Domain Structure for InterPro Entry Q6ZU67

    ProtoNet protein and cluster: Q6ZU67

    UniProtKB/Swiss-Prot: BEND4_HUMAN, Q6ZU67
    Similarity: Contains 1 BEN domain


    BEND4 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 BEND4:
     Decreased viability of wild-ty 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BEND4
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for BEND4
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    miRTarBase miRNAs that target BEND4:
    hsa-mir-26b-5p (MIRT029476)

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    hsa-miR-140-5p hsa-miR-26a-2* hsa-miR-376b hsa-miR-146a hsa-miR-128 hsa-miR-342-3p hsa-miR-3622b-3p hsa-miR-508-5p
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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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    (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 BEND4
    Interactions:

        Search GeneGlobe Interaction Network for BEND4

    (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 BEND4



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for BEND4 gene (2 alternative transcripts): 
    NM_001159547.1  NM_207406.3  

    Unigene Cluster for BEND4:

    BEN domain containing 4
    Hs.120591  [show with all ESTs]
    Unigene Representative Sequence: NM_207406
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000502486(uc003gwn.3 uc003gwm.3 uc011byy.1) ENST00000504360

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate BEND4 (see all 139):
    hsa-miR-140-5p hsa-miR-26a-2* hsa-miR-376b hsa-miR-146a hsa-miR-128 hsa-miR-342-3p hsa-miR-3622b-3p hsa-miR-508-5p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat BEND4
      QuantiFast Probe-based Assays in human, mouse, rat BEND4

    Additional mRNA sequence: 

    AB126828.1 AB126829.1 AK092951.1 AK125953.1 BC128592.1 BC128593.1 

    5 DOTS entries:

    DT.100009753  DT.107175  DT.107176  DT.121222397  DT.121222399 

    7 AceView cDNA sequences:

    T25372 AA714025 AK125953 AA810297 NM_207406 BG113872 CF134945 

    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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    BEND4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAAGAAAAT
    BEND4 Expression
    About this image


    BEND4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 6 entries
             hIPS1
    BEND4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BEND4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.120591
        Custom PCR Arrays for BEND4
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BEND4

    (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 chordates.

    Orthologs for BEND4 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Bend41 , 5 BEN domain containing 41, 5 87.23(n)1
    89.81(a)1
      5 (36.06 cM)5
    6669381  NM_001164806.11  NP_001158278.11 
     673921475 
    chicken
    (Gallus gallus)
    Aves BEND41 BEN domain containing 4 84.49(n)
    90.43(a)
      422777  XM_420730.4  XP_420730.3 
    lizard
    (Anolis carolinensis)
    Reptilia BEND46
    BEN domain containing 4
    74(a)
    1 ↔ 1
    5(101160035-101198602)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia bend41 BEN domain containing 4 74.83(n)
    75.9(a)
      100145654  XM_002933452.2  XP_002933498.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5669371 BEN domain-containing protein 4-like 65.38(n)
    69.51(a)
      566937  XM_690223.6  XP_695315.5 


    ENSEMBL Gene Tree for BEND4 (if available)
    TreeFam Gene Tree for BEND4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 BEND4 (see all 854)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1481110281,2
    C--42112425(+) TACTC-/AAATTA 2 -- ds50010--------
    rs793103161,2
    C,F--42112443(+) TGATAA/CTGATT 2 -- ds50011Minor allele frequency- C:0.05NA 120
    rs174459981,2
    C,F,H--42112536(+) TTGTAC/TGCAGA 2 -- ds500123Minor allele frequency- T:0.10NA NS EA WA 2540
    rs1828104081,2
    --42112539(+) TACGCA/GGAACG 2 -- ds50010--------
    rs1878947541,2
    --42112543(+) CAGAAC/TGCTGC 2 -- ds50010--------
    rs1119192481,2
    C,F--42112555(+) CAAAAA/CCCATA 2 -- ds50013Minor allele frequency- C:0.14CSA WA 121
    rs768001921,2
    C--42112576(+) ATCTG-/TTTATTT 2 -- ds50010--------
    rs1924663381,2
    --42112599(+) GGGTAA/GCAGCT 2 -- ds50010--------
    rs1823648521,2
    --42112636(+) AATGGC/TACCAC 2 -- ds50010--------
    rs174460191,2
    C,F,H--42112665(+) CTTTAC/TGTGTG 2 -- ds500110Minor allele frequency- T:0.08NA NS EA WA 798

    HapMap Linkage Disequilibrium report for BEND4 (42112870 - 42154895 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for BEND4:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv527340CNV Loss19592680
    dgv5532n71CNV Loss21882294
    nsv523585CNV Gain19592680
    dgv870n67CNV Gain20364138
    nsv822545CNV Gain20364138

    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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    BEND4 for disorders           About GeneDecksing

    Genetic Association Database (GAD): BEND4

    Export disorders for BEND4 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 BEND4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with BEND4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. 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)
    5. (PubMed id )2 

    (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: 389206 HGNC: 23815 AceView: FLJ43965 Ensembl:ENSG00000188848 euGenes: HUgn389206
    ECgene: BEND4 H-InvDB: BEND4

    (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)
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    NameDescription
    PharmGKB entry for BEND4 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 BEND4 gene:
    Search GeneIP for patents involving BEND4

    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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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