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DENND4B Gene

protein-coding   GIFtS: 41
GCID: GC01M153901

DENN/MADD Domain Containing 4B

(Previous name: KIAA0476)
(Previous symbol: KIAA0476)
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(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
DENN/MADD Domain Containing 4B1 2
KIAA04761 2 3
DENN Domain-Containing Protein 4B2

External Ids:    HGNC: 290441   Entrez Gene: 99092   Ensembl: ENSG000001988377   UniProtKB: O750643   

Export aliases for DENND4B gene to outside databases

Previous GC identifers: GC01M150716 GC01M152168 GC01M125264


(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 DENND4B Gene:
DENND4B (DENN/MADD domain containing 4B) is a protein-coding gene. GO annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is ST5.

UniProtKB/Swiss-Prot: DEN4B_HUMAN, O75064
Function: Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP,
converting inactive GDP-bound Rab proteins into their active GTP-bound form




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the DENND4B gene promoter:
         Nkx2-5   CUTL1   Tal-1beta   CREB   N-Myc   deltaCREB   ITF-2   ATF6   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for DENND4B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DENND4B


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

Entrez Gene cytogenetic band: 1q21   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21.3

DENND4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DENND4B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M153901:  view genomic region     (about GC identifiers)

Start:
153,901,977 bp from pter      End:
153,919,172 bp from pter
Size:
17,196 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: DEN4B_HUMAN, O75064 (See protein sequence)
Recommended Name: DENN domain-containing protein 4B  
Size: 1496 amino acids; 163847 Da
Sequence caution: Sequence=BAA32321.3; Type=Erroneous initiation; Sequence=CAI14016.1; Type=Erroneous gene model
prediction; Sequence=EAW53268.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5T4K0

Explore the universe of human proteins at neXtProt for DENND4B: NX_O75064

Explore proteomics data for DENND4B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys610
  • Modification sites at PhosphoSitePlus

  • See DENND4B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055671.2  
    ENSEMBL proteins: 
     ENSP00000354597   ENSP00000357635   ENSP00000435709  

    DENND4B Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for DENND4B

     
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    Cloud-Clone Corp. ELISAs for DENND4B
    Cloud-Clone Corp. CLIAs for DENND4B
    Search eBioscience for ELISAs for DENND4B 


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

    5 InterPro protein domains:
     IPR005112 dDENN_dom
     IPR023341 MABP
     IPR005113 uDENN_dom
     IPR001194 DENN_dom
     IPR002885 Pentatricopeptide_repeat

    Graphical View of Domain Structure for InterPro Entry O75064

    ProtoNet protein and cluster: O75064

    UniProtKB/Swiss-Prot: DEN4B_HUMAN, O75064
    Similarity: Contains 1 dDENN domain
    Similarity: Contains 1 DENN domain
    Similarity: Contains 1 MABP domain
    Similarity: Contains 2 PPR (pentatricopeptide) repeats
    Similarity: Contains 1 uDENN domain


    Find genes that share domains with DENND4B           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DEN4B_HUMAN, O75064
    Function: Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP,
    converting inactive GDP-bound Rab proteins into their active GTP-bound form

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0017112Rab guanyl-nucleotide exchange factor activity IDA--
         
    Find genes that share ontologies with DENND4B           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DENND4B
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    miRNA
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    miRTarBase miRNAs that target DENND4B:
    hsa-mir-500a-3p (MIRT041150), hsa-let-7b-5p (MIRT051981), hsa-mir-193b-3p (MIRT041379), hsa-mir-28-5p (MIRT050007), hsa-mir-320a (MIRT044839), hsa-mir-501-3p (MIRT037992), hsa-mir-151a-3p (MIRT043613), hsa-mir-92a-3p (MIRT049787)

    Block miRNA regulation of human, mouse, rat DENND4B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DENND4B (see all 25):
    hsa-miR-137 hsa-miR-25 hsa-miR-500a hsa-miR-1323 hsa-miR-548x hsa-miR-3662 hsa-miR-24 hsa-miR-92b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DENND4B

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DENND4B


    (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
    DEN4B_HUMAN, O75064: Golgi apparatus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus5
    plasma membrane3
    extracellular2
    peroxisome2
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005794Golgi apparatus IDA--

    Find genes that share ontologies with DENND4B           About GenesLikeMe


    (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 DENND4B
    Interactions:

        Search GeneGlobe Interaction Network for DENND4B

    1 Interacting protein for DENND4B (O750643) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATG10Q9H0Y03I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity IDA--
    GO:0032483regulation of Rab protein signal transduction IDA--

    Find genes that share ontologies with DENND4B           About GenesLikeMe



    (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 DENND4B (DEN4B)



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for DENND4B gene: 
    NM_014856.2  

    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000480340 ENST00000361217(uc001fdd.1) ENST00000492898 ENST00000474386
    ENST00000462423 ENST00000531748 ENST00000368646 ENST00000477746 ENST00000485359
    ENST00000494683 ENST00000483561 ENST00000472932 ENST00000464048
    miRNA
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    Block miRNA regulation of human, mouse, rat DENND4B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DENND4B (see all 25):
    hsa-miR-137 hsa-miR-25 hsa-miR-500a hsa-miR-1323 hsa-miR-548x hsa-miR-3662 hsa-miR-24 hsa-miR-92b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DENND4B
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for DENND4B
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat DENND4B
      QuantiTect SYBR Green Assays in human, mouse, rat DENND4B
      QuantiFast Probe-based Assays in human, mouse, rat DENND4B

    Selected AceView cDNA sequences (see all 193):

    BM726458 BM553560 BU429176 BU741973 BM665466 AW612598 BU741739 AA282492 
    AI912242 BU164923 BM725073 AB007945 CB053403 T30930 AA129131 BU789829 
    AW589797 AI656551 BE888086 BE672949 BG150491 T32415 BU194877 AI287998 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DENND4B (see all 18)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 17a · 17b · 17c ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b · 22c · 22d ^ 23 ^ 24 ^ 25a · 25b ^ 26 ^ 27 ^ 28a · 28b · 28c · 28d
    SP1:                                                                                -                       -                                       
    SP2:                                                                                                                                                
    SP3:                                                                                                                                                
    SP4:                                                  -                             -                                                               
    SP5:                                                  -                             -                                                               


    ECgene alternative splicing isoforms for DENND4B

    (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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    DENND4B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTCCGGTGGT
    DENND4B Expression
    About this image

    DENND4B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DENND4B Protein Expression
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DENND4B

    (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 animals.

    Orthologs for DENND4B gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dennd4b1 , 5 DENN/MADD domain containing 4B1, 5 88.71(n)1
    94.11(a)1
      3 (39.21 cM)5
    2295411  NM_201407.31  NP_958809.31 
     902651855 
    lizard
    (Anolis carolinensis)
    Reptilia DENND4B6
    DENN/MADD domain containing 4B
    64(a)
    1 ↔ 1
    GL343864.1(4870-48030)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7985281 uncharacterized LOC798528 61.12(n)
    57.94(a)
      798528  XM_002665070.3  XP_002665116.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta Crag6
    Calmodulin-binding protein related to a Rab3 GDP/G...
    31(a)
    1 → many
    X(8486086-8495264)
    worm
    (Caenorhabditis elegans)
    Secernentea denn-46
    --
    30(a)
    1 → many
    IV(1924008-1948040) WBGene00018681


    ENSEMBL Gene Tree for DENND4B (if available)
    TreeFam Gene Tree for DENND4B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DENND4B gene
    ST52  DENND5A2  DENND2D2  DENND2A2  DENND32  DENND1C2  DENND4A2  DENND1B2  
    DENND1A2  DENND5B2  DENND2C2  DENND4C2  
    2 SIMAP similar genes for DENND4B using alignment to 3 protein entries:     DEN4B_HUMAN (see all proteins):
    DENND4A    DENND4C

    Find genes that share paralogs with DENND4B           About GenesLikeMe



    (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 DENND4B (see all 412)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2005466451,2
    C--153901498(+) AGGCTA/GAGACC 1 -- ds50010--------
    rs1822757911,2
    --153901764(+) CCACAC/TGGACT 1 -- ds50010--------
    rs1156571321,2
    F--153901794(+) CCAGAT/CTCACC 1 -- ds50011Minor allele frequency- C:0.03NA 120
    rs1849483141,2
    --153901798(+) ATTCAC/TCCTTC 1 -- ds50010--------
    rs762458141,2
    --153901861(+) GGGGAC/TGCAGG 1 -- ds50010--------
    rs1919960381,2
    --153901933(+) TGAAAG/TGTATC 1 -- ds50010--------
    rs120331861,2
    C,H--153901969(+) CAGGAG/CGCCGA 1 -- ds50014Minor allele frequency- C:0.00NS EA 420
    rs1838685221,2
    --153902035(+) GAACAA/GTCCTT 1 -- ut310--------
    rs1887728211,2
    --153902264(+) GTGGCA/TCCAGA 1 -- ut310--------
    rs775557431,2
    C,F--153902485(+) GGTACC/GCTGGA 1 -- ut311Minor allele frequency- G:0.06WA 118

    HapMap Linkage Disequilibrium report for DENND4B (153901977 - 153919172 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for DENND4B:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv872450CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DENND4B
    DNA2.0 Custom Variant and Variant Library Synthesis for DENND4B

    (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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      --

    (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 DENND4B gene integrated from 10 sources:
    (articles sorted by number of sources associating them with DENND4B)
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    1. Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges. (PubMed id 12906859)1, 2, 3 Semova N....Semov A. (Genomics 2003)
    2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PubMed id 9455484)1, 2, 3 Seki N.... Ohara O. (DNA Res. 1997)
    3. Genome-wide association identifies genetic variants associated with lentiform nucleus volume in Na88=a881345 young and elderly subjects. (PubMed id 22903471)1 Hibar D.P....Thompson P.M. (Brain Imaging Behav 2013)
    4. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. (PubMed id 20937701)2 Yoshimura S.... Barr F.A. (J. Cell Biol. 2010)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)
    8. Novel triplet repeat containing genes in human brain: cloning, expression, and length polymorphisms. (PubMed id 8325628)1 Li S.H....Ross C.A. (Genomics 1993)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9909 HGNC: 29044 AceView: KIAA0476 Ensembl:ENSG00000198837 euGenes: HUgn9909
    ECgene: DENND4B H-InvDB: DENND4B

    (According to HUGE)
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    HUGE: KIAA0476

    (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 DENND4B 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 DENND4B gene:
    Search GeneIP for patents involving DENND4B

    GeneCards and IP:
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