Human Gene DENND6B (ENST00000413817.8_8) from GENCODE V47lift37
  Description: DENN domain containing 6B (from RefSeq NM_001001794.4)
Gencode Transcript: ENST00000413817.8_8
Gencode Gene: ENSG00000205593.12_10
Transcript (Including UTRs)
   Position: hg19 chr22:50,747,459-50,765,441 Size: 17,983 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr22:50,750,568-50,765,417 Size: 14,850 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:50,747,459-50,765,441)mRNA (may differ from genome)Protein (585 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DEN6B_HUMAN
DESCRIPTION: RecName: Full=Protein DENND6B; AltName: Full=DENN domain-containing protein 6B;
FUNCTION: Guanine nucleotide exchange factor (GEF) for RAB14. Also has some, lesser GEF activity towards RAB35.
SUBCELLULAR LOCATION: Recycling endosome (Potential). Cytoplasm (Potential).
SIMILARITY: Belongs to the DENND6 family.
CAUTION: Identified as having similarity to the core DENN family and referred to as DENN6B (PubMed:21330364). Prediction methods do not indicate a DENN domain for this sequence and, the exact role of the DENN or this DENN-like domain in GEF activity needs to be clarified.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.99 RPKM in Brain - Cerebellum
Total median expression: 276.18 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.2024-0.258 Picture PostScript Text
3' UTR -1420.803109-0.457 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
IPR012860 - Afi1_N
IPR024224 - Uncharacterised_FAM116

Pfam Domains:
PF02141 - DENN (AEX-3) domain
PF08616 - Stabilization of polarity axis
PF09794 - Transport protein Avl9

ModBase Predicted Comparative 3D Structure on Q8NEG7
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 DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

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

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0055037 recycling endosome


-  Descriptions from all associated GenBank mRNAs
  LF210401 - JP 2014500723-A/17904: Polycomb-Associated Non-Coding RNAs.
MA445978 - JP 2018138019-A/17904: Polycomb-Associated Non-Coding RNAs.
LF337629 - JP 2014500723-A/145132: Polycomb-Associated Non-Coding RNAs.
BC031069 - Homo sapiens family with sequence similarity 116, member B, mRNA (cDNA clone MGC:33692 IMAGE:5296726), complete cds.
AK054743 - Homo sapiens cDNA FLJ30181 fis, clone BRACE2001143.
KJ900760 - Synthetic construct Homo sapiens clone ccsbBroadEn_10154 FAM116B gene, encodes complete protein.
LF337633 - JP 2014500723-A/145136: Polycomb-Associated Non-Coding RNAs.
AK022407 - Homo sapiens cDNA FLJ12345 fis, clone MAMMA1002294.
MA573206 - JP 2018138019-A/145132: Polycomb-Associated Non-Coding RNAs.
MA573210 - JP 2018138019-A/145136: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8NEG7 (Reactome details) participates in the following event(s):

R-HSA-8876616 DENND6A,B exchange GTP for GDP on RAB14
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: A6X8I5, DEN6B_HUMAN, ENST00000413817.1, ENST00000413817.2, ENST00000413817.3, ENST00000413817.4, ENST00000413817.5, ENST00000413817.6, ENST00000413817.7, FAM116B, NM_001001794, Q8NEG7, uc319jsh.1, uc319jsh.2
UCSC ID: ENST00000413817.8_8
RefSeq Accession: NM_001001794.4
Protein: Q8NEG7 (aka DEN6B_HUMAN)

-  Gene Model Information
  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.