Human Gene DENND2A (uc010lnk.3) Description and Page Index
  Description: Homo sapiens DENN/MADD domain containing 2A (DENND2A), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:140,218,220-140,340,576 Size: 122,357 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr7:140,218,507-140,302,197 Size: 83,691 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:140,218,220-140,340,576)mRNA (may differ from genome)Protein (1009 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
PubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: DEN2A_HUMAN
DESCRIPTION: RecName: Full=DENN domain-containing protein 2A;
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. May play a role in late endosomes back to trans-Golgi network/TGN transport.
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton, actin patch.
SIMILARITY: Contains 1 dDENN domain.
SIMILARITY: Contains 1 DENN domain.
SIMILARITY: Contains 1 uDENN domain.
SEQUENCE CAUTION: Sequence=BAA86591.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DENND2A
CDC HuGE Published Literature: DENND2A
Positive Disease Associations: Eye
Related Studies:
  1. Eye
    Stuart Macgregor et al. Human molecular genetics 2010, Genome-wide association identifies ATOH7 as a major gene determining human optic disc size., Human molecular genetics. [PubMed 20395239]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.63 RPKM in Fallopian Tube
Total median expression: 320.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -259.64520-0.499 Picture PostScript Text
3' UTR -113.20287-0.394 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR005112 - dDENN_dom
IPR001194 - DENN_dom
IPR005113 - uDENN_dom

Pfam Domains:
PF02141 - DENN (AEX-3) domain
PF03455 - dDENN domain
PF03456 - uDENN domain

ModBase Predicted Comparative 3D Structure on Q9ULE3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0017112 Rab guanyl-nucleotide exchange factor activity

Biological Process:
GO:0015031 protein transport
GO:0042147 retrograde transport, endosome to Golgi

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0015629 actin cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  BC049193 - Homo sapiens DENN/MADD domain containing 2A, mRNA (cDNA clone IMAGE:4445131), partial cds.
AK297959 - Homo sapiens cDNA FLJ54496 complete cds, highly similar to DENN domain-containing protein 2A.
AB033103 - Homo sapiens KIAA1277 mRNA for KIAA1277 protein.
BC132875 - Homo sapiens DENN/MADD domain containing 2A, mRNA (cDNA clone MGC:164506 IMAGE:40146897), complete cds.
BC144190 - Homo sapiens cDNA clone IMAGE:9052710, containing frame-shift errors.
AK290056 - Homo sapiens cDNA FLJ76768 complete cds.
AB384168 - Synthetic construct DNA, clone: pF1KSDA1277, Homo sapiens DENND2A gene for DENN domain-containing protein 2A, complete cds, without stop codon, in Flexi system.
BC115004 - Homo sapiens DENN/MADD domain containing 2A, mRNA (cDNA clone MGC:131568 IMAGE:7470138), complete cds.
KJ902454 - Synthetic construct Homo sapiens clone ccsbBroadEn_11848 DENND2A gene, encodes complete protein.
JD182341 - Sequence 163365 from Patent EP1572962.
JD526788 - Sequence 507812 from Patent EP1572962.
JD298490 - Sequence 279514 from Patent EP1572962.
JD305116 - Sequence 286140 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9ULE3 (Reactome details) participates in the following event(s):

R-HSA-8876191 RAB9 GEFs exchange GTP for GDP on RAB9
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: AK290056, C9JUI3, DEN2A_HUMAN, KIAA1277, NM_015689, NP_056504, Q1RMD5, Q86XY0, Q9ULE3
UCSC ID: uc010lnk.3
RefSeq Accession: NM_015689
Protein: Q9ULE3 (aka DEN2A_HUMAN)
CCDS: CCDS43659.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK290056.1
exon count: 20CDS single in 3' UTR: no RNA size: 3562
ORF size: 3030CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 5678.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.