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

DENND2D Gene

protein-coding   GIFtS: 44
GCID: GC01M111729

DENN/MADD domain containing 2D

 Explore 1 disease affiliated with
DENND2D via our new
 Human Malady Compendium 
Biological research products
for DENND2D
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
DENN/MADD Domain Containing 2D1 2
RP5-1180E21.21 2
FLJ224571
DENN Domain-Containing Protein 2D2

External Ids:    HGNC: 261921   Entrez Gene: 799612   Ensembl: ENSG000001627777   UniProtKB: Q9H6A03   

Export aliases for DENND2D gene to outside databases

Previous GC identifers: GC01M111442 GC01M111531 GC01M109601


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

UniProtKB/Swiss-Prot: DEN2D_HUMAN, Q9H6A0
Function: Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DENND2D gene promoter:
         POU2F2 (Oct-2.1)   Oct-B1   oct-B3   oct-B2   POU2F2   AREB6   POU2F2C   POU2F1   POU2F1a   POU2F2B   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDENND2D promoter sequence
   Search SABiosciences Chromatin IP Primers for DENND2D

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DENND2D


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

Entrez Gene cytogenetic band: 1p13.3   Ensembl cytogenetic band:  1p13.3   HGNC cytogenetic band: 1p13.3

DENND2D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DENND2D gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M111729:  view genomic region     (about GC identifiers)

Start:
111,729,796 bp from pter      End:
111,747,157 bp from pter
Size:
17,362 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: DEN2D_HUMAN, Q9H6A0 (See protein sequence)
Recommended Name: DENN domain-containing protein 2D  
Size: 471 amino acids; 53672 Da
Secondary accessions: Q5T5V6 Q9BSU0
Alternative splicing: 2 isoforms:  Q9H6A0-1   Q9H6A0-2   

Explore the universe of human proteins at neXtProt for DENND2D: NX_Q9H6A0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H6A0

  • DENND2D Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001258762.1  NP_079177.2  

    ENSEMBL proteins: 
     ENSP00000350266   ENSP00000358767  

    Human Recombinant Protein Products: 
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    Uscn Proteins for DENND2D


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    Uscn ELISAs and CLIAs for DENND2D


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    DENND2D for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR005113 uDENN_dom
     IPR005112 dDENN_dom
     IPR001194 DENN_dom

    Graphical View of Domain Structure for InterPro Entry Q9H6A0

    ProtoNet protein and cluster: Q9H6A0

    UniProtKB/Swiss-Prot: DEN2D_HUMAN, Q9H6A0
    Similarity: Contains 1 dDENN domain
    Similarity: Contains 1 DENN domain
    Similarity: Contains 1 uDENN domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: DEN2D_HUMAN, Q9H6A0
    Function: Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. Promotes the exchange of GDP to
    GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form

    miRNA
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    3 QIAGEN miScript miRNA Assays for microRNAs that regulate DENND2D:
    hsa-miR-140-3p hsa-miR-597 hsa-miR-197
    SwitchGear 3'UTR luciferase reporter plasmidDENND2D 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DENND2D

    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0017112Rab guanyl-nucleotide exchange factor activity IDA--


    DENND2D for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for DENND2D:
     Decreased nuclei size in G2M  Increased circadian rhythm amp 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for DENND2D

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 DENND2D
    Search CenterWatch for drugs/clinical trials and news about DENND2D / DEN2D 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for DENND2D gene (2 alternative transcripts): 
    NM_001271833.1  NM_024901.4  

    Unigene Cluster for DENND2D:

    DENN/MADD domain containing 2D
    Hs.557850  [show with all ESTs]
    Unigene Representative Sequence: NM_024901
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000468692 ENST00000357640(uc001eak.1) ENST00000369752(uc001eal.1)
    ENST00000473682 ENST00000463713 ENST00000477586 ENST00000473822 ENST00000488786


    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat DENND2D
    3 QIAGEN miScript miRNA Assays for microRNAs that regulate DENND2D:
    hsa-miR-140-3p hsa-miR-597 hsa-miR-197
    SwitchGear 3'UTR luciferase reporter plasmidDENND2D 3' UTR sequence
    Inhib. RNA
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    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for DENND2D (see all 7)
    OriGene shRNA RFP: DENND2D
    OriGene siRNA: DENND2D
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat DENND2D
    Clone
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    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for DENND2D (see all 4)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for DENND2D (see all 2)
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector: DENND2D (NM_024901)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for DENND2D
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DENND2D 
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat DENND2D
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat DENND2D

    Additional cDNA sequence: 

    AK026110.1 AK301583.1 BC004557.2 

    15 DOTS entries:

    DT.410602  DT.95272114  DT.100873339  DT.95272110  DT.444662  DT.91906248  DT.121409399  DT.92430109 
    DT.97845084  DT.92430107  DT.100800397  DT.97844567  DT.100697992  DT.121409460  DT.91963607 

    24/218 AceView cDNA sequences (see all 218):

    BC004557 BF062413 BM747627 BX415728 CR612515 AW235262 CR590904 BQ055967 
    BU188391 BI834164 BU188661 CA436842 BM542835 BM834263 AK026110 BF939031 
    BP341117 BX096184 CA311009 BE672876 AA808567 BQ065832 N95028 BF794684 

    GeneLoc Exon Structure

    5/14 Alternative Splicing Database (ASD) splice patterns (SP) for DENND2D (see all 14)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c · 10d · 10e · 10f ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^
    SP1:                                      -     -     -     -     -     -                                   -     -     -     -                             -   
    SP2:                                                        -     -     -                                   -     -     -     -                             -   
    SP3:                                      -     -     -     -     -     -                                   -     -     -     -           -                     
    SP4:                    -     -     -     -           -     -     -     -                                   -     -     -     -                                 
    SP5:                                            -     -     -     -     -                                   -     -     -     -                                 

    ExUns: 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b
    SP1:                    -                                 
    SP2:                    -                                 
    SP3:                                                      
    SP4:                                                      
    SP5:                                                      


    ECgene alternative splicing isoforms for DENND2D

    (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

    DENND2D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TAAGGACGAG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See DENND2D Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DENND2D

    SOURCE GeneReport for Unigene cluster: Hs.557850
        SABiosciences Custom PCR Arrays for DENND2D
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DENND2D

    (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 DENND2D gene from 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves DENND2D1 DENN/MADD domain containing 2D 70.58(n)
    71.13(a)
      421153  XM_419235.3  XP_419235.3 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    73(a)
    71(a)
    1 ↔ many
    1 ↔ many
    4(133080756-133087348)
    4(133062210-133076020)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia BG512350.12   -- 73.44(n)    BG512350.1 
    zebrafish
    (Danio rerio)
    Actinopterygii dennd2da1 DENN/MADD domain containing 2Da 59.12(n)
    55.6(a)
      768151  NM_001077294.1  NP_001070762.1 


    ENSEMBL Gene Tree for DENND2D (if available)
    TreeFam Gene Tree for DENND2D (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DENND2D gene
    ST52  DENND5A2  DENND2A2  DENND32  DENND4A2  DENND1C2  DENND4B2  DENND1B2  
    DENND1A2  DENND5B2  DENND4C2  DENND2C2  
    4 SIMAP similar genes for DENND2D using alignment to 1 protein entry:     DEN2D_HUMAN:
    DKFZp667I053    ST5    DENND2A    DENND2C

    DENND2D for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/342 NCBI SNPs in DENND2D are shown (see all 342    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1380146281,2
    --111729312(+) CGATCC/GCTTCA 1 -- int10--------
    rs6263391,2
    C,F,O,A,H,--111729325(-) CTTTAA/GCTAAA 1 -- int120Minor allele frequency- G:0.41NA EA NS WA CSA 1147
    rs121406241,2
    H--111729398(+) AAGGAC/TTAGTG 1 -- int14Minor allele frequency- T:0.00NS EA 418
    rs759166441,2
    --111729419(+) GTGATG/AGGGAA 1 -- int11Minor allele frequency- A:0.50NA 2
    rs1460075271,2
    --111729503(+) CTCTAA/GACTGA 1 -- int10--------
    rs1399627461,2
    --111729508(+) GACTGA/CAGCTG 1 -- int10--------
    rs1418945571,2
    --111729542(+) CCTCCC/TAGGAT 1 -- int10--------
    rs1446769731,2
    --111729584(+) ACTTAA/GATGCC 1 -- int10--------
    rs1857555421,2
    --111729637(+) CTTCCA/GGTTAG 1 -- int10--------
    rs770306691,2
    F,--111729663(+) TGCCCC/TCCATG 1 -- int11Minor allele frequency- T:0.08WA 118

    HapMap Linkage Disequilibrium report for DENND2D (111729796 - 111747157 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for DENND2D: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing DENND2D
    DNA2.0 Custom Variant and Variant Library Synthesis for DENND2D

    (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.)
    About This Section

    DENND2D for disorders           About GeneDecksing

    1 disease for DENND2D:    About MalaCards
    melanoma

    1 disease from the University of Copenhagen DISEASES database for DENND2D:
    Lung squamous cell carcinoma

    Export disorders for DENND2D 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 DENND2D gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with DENND2D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. (PubMed id 20937701)1, 2 Yoshimura S.... Barr F.A. (2010)
    2. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    6. Suppression of non-small cell lung cancer proliferatio n and tumorigenicity by DENND2D. (PubMed id 23182661)1 Ling B....Zhang K. (2013)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    8. Genome-wide association study identifies loci influenc ing concentrations of liver enzymes in plasma. (PubMed id 22001757)1 Chambers J.C....Kooner J.S. (2011)
    9. Identification of ARHGEF17, DENND2D, FGFR3, and RB1 mutations in melanoma by inhibition of nonsense-mediated mRNA decay. (PubMed id 18677770)1 Bloethner S....Hayward N.K. (2008)
    10. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)

    (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)
    About This Section
    Entrez Gene: 79961 HGNC: 26192 AceView: FLJ22457 Ensembl:ENSG00000162777 euGenes: HUgn79961
    ECgene: DENND2D H-InvDB: DENND2D

    (According to HUGE)
    About This Section
      --

    (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 DENND2D 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 DENND2D gene:
    Search GeneIP for patents involving DENND2D

    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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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