Human Gene DENND4A (ENST00000431932.6) from GENCODE V44
  Description: Homo sapiens DENN domain containing 4A (DENND4A), transcript variant 2, mRNA. (from RefSeq NM_005848)
RefSeq Summary (NM_005848): This gene encodes a DENN domain-containing protein that may function as a guanine nucleotide exchange factor that specifically activates ras-related protein Rab-10. This protein also contains a interferon stimulated response element-binding domain and may be involved in regulating the v-myc avian myelocytomatosis viral (MYC) oncogene. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 8. [provided by RefSeq, Mar 2016].
Gencode Transcript: ENST00000431932.6
Gencode Gene: ENSG00000174485.16
Transcript (Including UTRs)
   Position: hg38 chr15:65,661,777-65,792,124 Size: 130,348 Total Exon Count: 32 Strand: -
Coding Region
   Position: hg38 chr15:65,661,851-65,756,450 Size: 94,600 Coding Exon Count: 30 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:65,661,777-65,792,124)mRNA (may differ from genome)Protein (1863 aa)
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HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MYCPP_HUMAN
DESCRIPTION: RecName: Full=C-myc promoter-binding protein; AltName: Full=DENN domain-containing protein 4A;
FUNCTION: Probable 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 PubMed:8056341, it may bind to ISRE-like element (interferon-stimulated response element) of MYC P2 promoter.
SUBCELLULAR LOCATION: Nucleus (Probable).
TISSUE SPECIFICITY: Expressed ubiquitously. Highest expression in bone marrow, medium in peripheral blood lymphocytes and lowest in spleen. In brain, breast, and prostate, higher expression was seen in normal cells than in tumor cells. Expression is regulated in a growth- and cell cycle-dependent manner.
DEVELOPMENTAL STAGE: Highly expressed in fetal liver.
INDUCTION: By serum in low-passage fibroblasts.
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.

-  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           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.55 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 177.35 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 -73.90209-0.354 Picture PostScript Text
3' UTR -13.8074-0.186 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
IPR023341 - MABP
IPR002885 - Pentatricopeptide_repeat
IPR005113 - uDENN_dom

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

ModBase Predicted Comparative 3D Structure on Q7Z401
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-  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
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0017112 Rab guanyl-nucleotide exchange factor activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated

Cellular Component:
GO:0005634 nucleus
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AL833317 - Homo sapiens mRNA; cDNA DKFZp313L197 (from clone DKFZp313L197).
AF534403 - Homo sapiens c-MYC promoter-binding protein IRLB (IRLB) mRNA, complete cds.
AL832602 - Homo sapiens mRNA; cDNA DKFZp451C1717 (from clone DKFZp451C1717).
AK091268 - Homo sapiens cDNA FLJ33949 fis, clone CTONG2018383, highly similar to IRLB.
AX746884 - Sequence 409 from Patent EP1308459.
AL833384 - Homo sapiens mRNA; cDNA DKFZp667N1914 (from clone DKFZp667N1914).
BC041706 - Homo sapiens DENN/MADD domain containing 4A, mRNA (cDNA clone MGC:48955 IMAGE:5530033), complete cds.
X63417 - Homo sapiens irlB mRNA.
EU446866 - Synthetic construct Homo sapiens clone IMAGE:100070244; IMAGE:100012075; FLH258728.01L DENN/MADD domain containing 4A (DENND4A) gene, encodes complete protein.
AK307411 - Homo sapiens cDNA, FLJ97359.
BC028057 - Homo sapiens DENN/MADD domain containing 4A, mRNA (cDNA clone IMAGE:5139692), partial cds.
AK091368 - Homo sapiens cDNA FLJ34049 fis, clone FCBBF3000110, weakly similar to CRAG protein.
AX746940 - Sequence 465 from Patent EP1308459.
AK290292 - Homo sapiens cDNA FLJ77039 partial cds, highly similar to Homo sapiens c-myc promoter binding protein (MYCPBP), mRNA.
AK299570 - Homo sapiens cDNA FLJ52112 complete cds, highly similar to C-myc promoter-binding protein.
JD499561 - Sequence 480585 from Patent EP1572962.
JD408115 - Sequence 389139 from Patent EP1572962.

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

Protein Q7Z401 (Reactome details) participates in the following event(s):

R-HSA-8876188 DENND4s exchange GTP for GDP on RAB10
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: ENST00000431932.1, ENST00000431932.2, ENST00000431932.3, ENST00000431932.4, ENST00000431932.5, IRLB, MYCPBP, MYCPP_HUMAN, NM_005848, Q14655, Q7Z401, Q86T77, Q8IVX2, Q8NB93, uc002aph.1, uc002aph.2, uc002aph.3, uc002aph.4
UCSC ID: ENST00000431932.6
RefSeq Accession: NM_005848
Protein: Q7Z401 (aka MYCPP_HUMAN)
CCDS: CCDS45285.1, CCDS53949.1

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