Human Gene PLEKHG4 (uc010ceg.3)
  Description: Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4 (PLEKHG4), transcript variant 5, mRNA.
RefSeq Summary (NM_001129731): The protein encoded by this gene can function as a guanine nucleotide exchange factor (GEF) and may play a role in intracellular signaling and cytoskeleton dynamics at the Golgi apparatus. Polymorphisms in the region of this gene have been found to be associated with spinocerebellar ataxia in some study populations. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015].
Transcript (Including UTRs)
   Position: hg19 chr16:67,313,492-67,323,403 Size: 9,912 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr16:67,313,948-67,322,711 Size: 8,764 Coding Exon Count: 20 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:67,313,492-67,323,403)mRNA (may differ from genome)Protein (1110 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PLEKHG4
CDC HuGE Published Literature: PLEKHG4
Positive Disease Associations: Glucose , Lipoproteins, HDL
Related Studies:
  1. Glucose
    , , . [PubMed 0]
  2. Glucose
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  3. Glucose
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           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: PLEKHG4
Diseases sorted by gene-association score: spinocerebellar ataxia 4* (103), indian tick typhus (17), queensland tick typhus (17), israeli tick typhus (16), flinders island spotted fever (12), deafness, autosomal recessive 89 (12), japanese spotted fever (11), spinocerebellar ataxia 31 (10), spinocerebellar ataxia 18 (9), endemic typhus (8), autosomal dominant cerebellar ataxia (7), cerebellar disease (7), ataxia (6), robinow syndrome, autosomal recessive (5), cerebellar ataxia (2), robinow syndrome (1)
* = Manually curated disease association

-  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: 30.51 RPKM in Testis
Total median expression: 137.29 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 -239.56456-0.525 Picture PostScript Text
3' UTR -246.51692-0.356 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
  Pfam Domains:
PF00621 - RhoGEF domain

SCOP Domains:
48065 - DBL homology domain (DH-domain)
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q58EX7-2
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  Descriptions from all associated GenBank mRNAs
  AB197663 - Homo sapiens prtphn1 mRNA for puratrophin-1, complete cds.
AB197664 - Homo sapiens prtphn1 mRNA for puratrophin-1 short-form, complete cds.
BC082974 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4, mRNA (cDNA clone MGC:99705 IMAGE:6291175), complete cds.
AK024475 - Homo sapiens FLJ00068 mRNA for FLJ00068 protein.
BC001520 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4, mRNA (cDNA clone IMAGE:2987958).
AK308298 - Homo sapiens cDNA, FLJ98246.
BC063501 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4, mRNA (cDNA clone MGC:75210 IMAGE:5527705), complete cds.
BC054486 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 4, mRNA (cDNA clone MGC:51096 IMAGE:4820741), complete cds.
JD282133 - Sequence 263157 from Patent EP1572962.
BC115390 - Homo sapiens cDNA clone IMAGE:40038545.
JD158536 - Sequence 139560 from Patent EP1572962.
JD122730 - Sequence 103754 from Patent EP1572962.
JD106378 - Sequence 87402 from Patent EP1572962.
AB463179 - Synthetic construct DNA, clone: pF1KF0068, Homo sapiens PLEKHG4 gene for pleckstrin homology domain containing, family G (with RhoGef domain) member 4, without stop codon, in Flexi system.
AK304723 - Homo sapiens cDNA FLJ54470 complete cds, highly similar to Puratrophin-1.
AL117435 - Homo sapiens mRNA; cDNA DKFZp434I216 (from clone DKFZp434I216).
JD215388 - Sequence 196412 from Patent EP1572962.
JD193775 - Sequence 174799 from Patent EP1572962.
JD463998 - Sequence 445022 from Patent EP1572962.
JD073570 - Sequence 54594 from Patent EP1572962.
JD168925 - Sequence 149949 from Patent EP1572962.
JD282871 - Sequence 263895 from Patent EP1572962.
JD239911 - Sequence 220935 from Patent EP1572962.
JD477148 - Sequence 458172 from Patent EP1572962.
JD283161 - Sequence 264185 from Patent EP1572962.
JD493253 - Sequence 474277 from Patent EP1572962.
JD431741 - Sequence 412765 from Patent EP1572962.
JD432733 - Sequence 413757 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001129731, NP_001123203, PRTPHN1, Q58EX7-2
UCSC ID: uc010ceg.3
RefSeq Accession: NM_001129731
Protein: Q58EX7-2, splice isoform of Q58EX7 CCDS: CCDS45512.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001129731.1
exon count: 20CDS single in 3' UTR: no RNA size: 4496
ORF size: 3333CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6555.00frame shift in genome: no % Coverage: 99.67
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.