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

DENND4C Gene

protein-coding   GIFtS: 40
GCID: GC09P019289

DENN/MADD domain containing 4C

(Previous names: chromosome 9 open reading frame 55B, chromosome 9 open...)
(Previous symbols: C9orf55B, C9orf55)
  Search for DENND4C
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(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 4C1 2     Chromosome 9 Open Reading Frame 551
C9orf551 2 3     Chromosome 9 Open Reading Frame 55B1
C9orf55B1 2 3     DENN Domain-Containing Protein 4C2
BA513M16.31     DENN/MADD Domain Containing 4A Pseudogene2
FLJ206861     

External Ids:    HGNC: 260791   Entrez Gene: 556672   Ensembl: ENSG000001371457   UniProtKB: Q5VZ893   

Export aliases for DENND4C gene to outside databases

Previous GC identifers: GC09P019281 GC09P019252


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

UniProtKB/Swiss-Prot: DEN4C_HUMAN, Q5VZ89
Function: Guanine nucleotide exchange factor (GEF) activating RAB10. Promotes the exchange of GDP to GTP, converting
inactive GDP-bound RAB10 into its active GTP-bound form. Thereby, stimulates SLC2A4/GLUT4 glucose transporter-enriched
vesicles delivery to the plasma membrane in response to insulin




(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_000009.11  NC_018920.1  NT_008413.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DENND4C gene promoter:
         AREB6   ISGF-3   AML1a   GATA-6   FOXF2   FOXJ2 (long isoform)   HFH-1   FOXJ2   Ik-3   c-Ets-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for DENND4C

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DENND4C


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

Entrez Gene cytogenetic band: 9p22.1   Ensembl cytogenetic band:  9p22.1   HGNC cytogenetic band: 9p22.1

DENND4C Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DENND4C gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P019289:  view genomic region     (about GC identifiers)

Start:
19,288,622 bp from pter      End:
19,374,275 bp from pter
Size:
85,654 bases      Orientation:
plus 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: DEN4C_HUMAN, Q5VZ89 (See protein sequence)
Recommended Name: DENN domain-containing protein 4C  
Size: 1673 amino acids; 186857 Da
Subcellular location: Cytoplasmic vesicle membrane. Cell membrane. Cytoplasm, cytosol. Note=Associates with
SLC2A4/GLUT4 storage vesicles
Sequence caution: Sequence=BAA91294.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAA91478.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA92039.1;
Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB15221.1; Type=Erroneous initiation;
Note=Translation N-terminally extended; Sequence=CAH10466.1; Type=Erroneous initiation; Note=Translation N-terminally
extended; Sequence=CAM21141.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A2A3R1 A2A3R2 A2A3R3 A2A3R9 Q6AI48 Q6ZUB3 Q8NCY7 Q9H6N4 Q9NUT1 Q9NWA5 Q9NWT3
Alternative splicing: 6 isoforms:  Q5VZ89-1   Q5VZ89-2   Q5VZ89-3   Q5VZ89-4   Q5VZ89-5   Q5VZ89-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for DENND4C: NX_Q5VZ89

Post-translational modifications:

  • Phosphorylated in response to insulin (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5VZ89

  • DENND4C Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060395.5  
    ENSEMBL proteins: 
     ENSP00000369802   ENSP00000369797   ENSP00000369792   ENSP00000354301   ENSP00000369789  
     ENSP00000305795   ENSP00000443804  

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    Uscn Proteins for DENND4C

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005829cytosol ISS--
    GO:0005886plasma membrane ISS--
    GO:0016021integral to membrane ----
    GO:0030659cytoplasmic vesicle membrane IEA--
    GO:0030904retromer complex IEA--


    DENND4C for ontologies           About GeneDecksing



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

    DENND4C 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 Q5VZ89

    ProtoNet protein and cluster: Q5VZ89

    UniProtKB/Swiss-Prot: DEN4C_HUMAN, Q5VZ89
    Similarity: Contains 1 dDENN domain
    Similarity: Contains 1 DENN domain
    Similarity: Contains 1 PPR (pentatricopeptide) repeat
    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: DEN4C_HUMAN, Q5VZ89
    Function: Guanine nucleotide exchange factor (GEF) activating RAB10. Promotes the exchange of GDP to GTP, converting
    inactive GDP-bound RAB10 into its active GTP-bound form. Thereby, stimulates SLC2A4/GLUT4 glucose transporter-enriched
    vesicles delivery to the plasma membrane in response to insulin

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    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--


    DENND4C for ontologies           About GeneDecksing



    (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 DENND4C

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

    2 Interacting proteins for DENND4C (Q5VZ893 ENSP000003698024) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAP1LC3CQ9BXW43I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031protein transport IEA--
    GO:0032869cellular response to insulin stimulus ISS--
    GO:0072659protein localization to plasma membrane ISS--


    DENND4C for ontologies           About GeneDecksing



    (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
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    Search CenterWatch for drugs/clinical trials and news about DENND4C / DEN4C 

    (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 DENND4C gene: 
    NM_017925.5  

    Unigene Cluster for DENND4C:

    DENN/MADD domain containing 4C
    Hs.249591  [show with all ESTs]
    Unigene Representative Sequence: NM_017925
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000494124 ENST00000380437 ENST00000380432 ENST00000380427(uc003znt.3)
    ENST00000361024 ENST00000380424 ENST00000307015(uc003znr.3 uc003znq.3 uc011lnc.2 uc011lnd.2 uc003zns.3)
    ENST00000540671

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    hsa-miR-579 hsa-miR-607 hsa-miR-300 hsa-miR-4272 hsa-miR-25 hsa-miR-624* hsa-miR-301a hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidDENND4C 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK000627.1 AK000693.1 AK001046.1 AK002020.1 AK025705.1 AK125842.1 AK127734.1 AK299842.1 
    AK302901.1 AL834521.1 BC144484.1 BC144485.1 CR627367.1 NR_073201.1 

    15 DOTS entries:

    DT.97838739  DT.214521  DT.410018  DT.121149839  DT.100784968  DT.40217577  DT.70101132  DT.121149867 
    DT.121149910  DT.121149931  DT.439289  DT.91972220  DT.92014101  DT.99999363  DT.92047754 

    2 AceView cDNA sequences:

    N28227 BG197754 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for DENND4C (see all 9)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18a · 18b ·
    SP1:                                                                                                                                                  -     -   
    SP2:                                                  -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -   
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                  -         
    SP5:                                                                                                                                                            

    ExUns: 18c ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32
    SP1:  -                                                                       -                                       
    SP2:  -     -     -     -     -     -     -     -                             -                                       
    SP3:                                                                          -                             -         
    SP4:                                                                                                                  
    SP5:                                                                                                                  


    ECgene alternative splicing isoforms for DENND4C

    (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

    DENND4C expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    About this image
    See DENND4C Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DENND4C

    SOURCE GeneReport for Unigene cluster: Hs.249591
        SABiosciences Custom PCR Arrays for DENND4C
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DENND4C

    (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 eukaryotes.

    Orthologs for DENND4C gene from 8/24 species (see all 24)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves DENND4C1 DENN/MADD domain containing 4C 74.78(n)
    77.42(a)
      427236  XM_424821.3  XP_424821.3 
    lizard
    (Anolis carolinensis)
    Reptilia DENND4C6
    --
    64(a)
    1 ↔ 1
    2(62476030-62552438)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.160122 Transcribed sequence with weak similarity to protein more 74.18(n)    142033743 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC5586261 similar to DENN/MADD domain containing 4C 63.34(n)
    66.04(a)
      558626  XM_001919955.3  XP_001919990.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Crag6
    Calmodulin-binding protein related to a Rab3 GDP/G...
    26(a)
    1 → many
    X(8486086-8495264)
    worm
    (Caenorhabditis elegans)
    Secernentea F52C12.41 Protein F52C12.4 49.12(n)
    41.9(a)
      186100  NM_067744.2  NP_500145.2 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SCD16
    stomatal cytokinesis defective / SCD1 protein (SCD...
    10(a)
    possible ortholog
    1(18139234-18148981)
    rice
    (Oryza sativa)
    Liliopsida --
    SCD1, putative, expressed
    10(a)
    possible ortholog
    1(22162051-22179384)


    ENSEMBL Gene Tree for DENND4C (if available)
    TreeFam Gene Tree for DENND4C (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DENND4C gene
    ST52  DENND5A2  DENND2D2  DENND2A2  DENND32  DENND4A2  DENND1C2  DENND4B2  
    DENND1B2  DENND1A2  DENND5B2  DENND2C2  
    2 SIMAP similar genes for DENND4C using alignment to 2 protein entries:     DEN4C_HUMAN (see all proteins):
    DENND4A    DENND4B

    DENND4C 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

    10/3180 NCBI SNPs in DENND4C are shown (see all 3180    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1841801641,2
    --19228909(+) TTTTTC/TTTTTT 2 -- us2k10--------
    rs1861177221,2
    --19229211(+) GCTAAA/GTTTTG 2 -- us2k10--------
    rs1897286931,2
    --19229229(+) AGATCC/TTTTCT 2 -- us2k10--------
    rs123407971,2
    F,--19229240(+) TAAACT/CTTTGC 2 -- us2k11Minor allele frequency- C:0.08WA 118
    rs1820731101,2
    --19229242(+) AACTTC/TTGCTC 2 -- us2k10--------
    rs1866246881,2
    --19229290(+) CCAAAC/TTGGCC 2 -- us2k10--------
    rs109640511,2
    F,--19229472(+) CCCAGG/CTATAA 2 -- us2k11Minor allele frequency- C:0.05NA 120
    rs726983711,2
    C,F,--19229504(+) TACAGA/GTTAAA 2 -- us2k13Minor allele frequency- G:0.06WA NA EA 358
    rs1447516471,2
    --19229556(+) ATACTC/TACCAG 2 -- us2k10--------
    rs1485318341,2
    --19229630(+) TTTTCA/CCCCCA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for DENND4C (19288622 - 19374275 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for DENND4C
         3 CNVs: 65351 95870 52762

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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.)
    About This Section
      --

    (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 DENND4C gene, integrated from 9 sources (see all 19):
    (articles sorted by number of sources associating them with DENND4C)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. 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, 3 Semova N....Semov A. (2003)
    5. Insulin-stimulated GLUT4 protein translocation in adi pocytes requires the Rab10 guanine nucleotide exchange factor Dennd4C. (PubMed id 21454697)1 Sano H....Lienhard G.E. (2011)
    6. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (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. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (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: 55667 HGNC: 26079 AceView: C9orf55.1 Ensembl:ENSG00000137145 euGenes: HUgn55667
    ECgene: DENND4C H-InvDB: DENND4C

    (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 DENND4C 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 DENND4C gene:
    Search GeneIP for patents involving DENND4C

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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