Human Gene PLEKHG1 (uc003qnz.2)
  Description: Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 1 (PLEKHG1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr6:151,042,069-151,153,341 Size: 111,273 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr6:151,054,818-151,153,340 Size: 98,523 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:151,042,069-151,153,341)mRNA (may differ from genome)Protein (1031 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIneXtProtPubMed
TreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PKHG1_HUMAN
DESCRIPTION: RecName: Full=Pleckstrin homology domain-containing family G member 1;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 DH (DBL-homology) domain.
SIMILARITY: Contains 1 PH 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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PLEKHG1
CDC HuGE Published Literature: PLEKHG1
Positive Disease Associations: Alcoholism , Cholesterol, HDL , Coronary Artery Disease , Metabolism , panic disorder , Triglycerides
Related Studies:
  1. Alcoholism
    Lingjun Zuo et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2012, Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 22488850]
  2. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Coronary Artery Disease
    , , . [PubMed 0]
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-  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: 14.67 RPKM in Spleen
Total median expression: 167.67 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 -110.56366-0.302 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
IPR000219 - DH-domain
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology

Pfam Domains:
PF00621 - RhoGEF domain

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

ModBase Predicted Comparative 3D Structure on Q9ULL1
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005089 Rho guanyl-nucleotide exchange factor activity

Biological Process:
GO:0035023 regulation of Rho protein signal transduction

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AK293288 - Homo sapiens cDNA FLJ61588 partial cds, highly similar to Pleckstrin homology domain-containing family G member 1.
AK307631 - Homo sapiens cDNA, FLJ97579.
AB384583 - Synthetic construct DNA, clone: pF1KA1209, Homo sapiens PLEKHG1 gene for pleckstrin homology domain-containing protein, family G member 1, complete cds, without stop codon, in Flexi system.
AK294798 - Homo sapiens cDNA FLJ52092 complete cds, highly similar to Pleckstrin homology domain-containing family G member 1.
AK056300 - Homo sapiens cDNA FLJ31738 fis, clone NT2RI2007096, highly similar to Pleckstrin homology domain-containing family G member 1.
BC140864 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 1, mRNA (cDNA clone MGC:176541 IMAGE:9021732), complete cds.
BC151134 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 1, mRNA (cDNA clone MGC:184046 IMAGE:9057034), complete cds.
AJ420468 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2072853.
BC089428 - Homo sapiens pleckstrin homology domain containing, family G (with RhoGef domain) member 1, mRNA (cDNA clone IMAGE:3066302), partial cds.
AB033035 - Homo sapiens mRNA for KIAA1209 protein, partial cds.
JD192254 - Sequence 173278 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AK056300, KIAA1209, NM_001029884, NP_001025055, PKHG1_HUMAN, Q5T1F2, Q9ULL1
UCSC ID: uc003qnz.2
RefSeq Accession: NM_001029884
Protein: Q9ULL1 (aka PKHG1_HUMAN or PHG1_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK056300.1
exon count: 15CDS single in 3' UTR: no RNA size: 2749
ORF size: 3093CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 5125.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: no 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.