Human Gene PGGT1B (uc003kqw.4) Description and Page Index
  Description: Homo sapiens protein geranylgeranyltransferase type I, beta subunit (PGGT1B), mRNA.
RefSeq Summary (NM_005023): Protein geranylgeranyltransferase type I (GGTase-I) transfers a geranylgeranyl group to the cysteine residue of candidate proteins containing a C-terminal CAAX motif in which 'A' is an aliphatic amino acid and 'X' is leucine (summarized by Zhang et al., 1994 [PubMed 8106351]). The enzyme is composed of a 48-kD alpha subunit (FNTA; MIM 134635) and a 43-kD beta subunit, encoded by the PGGT1B gene. The FNTA gene encodes the alpha subunit for both GGTase-I and the related enzyme farnesyltransferase.[supplied by OMIM, Mar 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660803.41166.1, SRR3476690.950674.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000419445.6/ ENSP00000404676.1 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:114,546,527-114,598,569 Size: 52,043 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr5:114,548,099-114,598,548 Size: 50,450 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:114,546,527-114,598,569)mRNA (may differ from genome)Protein (377 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PGTB1_HUMAN
DESCRIPTION: RecName: Full=Geranylgeranyl transferase type-1 subunit beta; EC=2.5.1.59; AltName: Full=Geranylgeranyl transferase type I subunit beta; Short=GGTase-I-beta; AltName: Full=Type I protein geranyl-geranyltransferase subunit beta;
FUNCTION: Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to a cysteine at the fourth position from the C-terminus of proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. Acts on the Rac1, Rac2, Rap1A and Rap1B proteins. The beta subunit is responsible for peptide-binding.
CATALYTIC ACTIVITY: Geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate.
COFACTOR: Binds 1 zinc ion per subunit (By similarity).
SUBUNIT: Heterodimer of an alpha and a beta subunit.
SIMILARITY: Belongs to the protein prenyltransferase subunit beta family.
SIMILARITY: Contains 4 PFTB repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PGGT1B
CDC HuGE Published Literature: PGGT1B

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 192.73 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 -2.6021-0.124 Picture PostScript Text
3' UTR -372.601572-0.237 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
IPR001330 - Prenyltrans
IPR008930 - Terpenoid_cyclase/PrenylTrfase

Pfam Domains:
PF00432 - Prenyltransferase and squalene oxidase repeat

SCOP Domains:
48239 - Terpenoid cyclases/Protein prenyltransferases

ModBase Predicted Comparative 3D Structure on P53609
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004659 prenyltransferase activity
GO:0004661 protein geranylgeranyltransferase activity
GO:0004662 CAAX-protein geranylgeranyltransferase activity
GO:0008144 drug binding
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0019840 isoprenoid binding
GO:0042277 peptide binding
GO:0046872 metal ion binding

Biological Process:
GO:0008284 positive regulation of cell proliferation
GO:0018344 protein geranylgeranylation
GO:0034097 response to cytokine
GO:0045787 positive regulation of cell cycle
GO:0051771 negative regulation of nitric-oxide synthase biosynthetic process

Cellular Component:
GO:0005953 CAAX-protein geranylgeranyltransferase complex


-  Descriptions from all associated GenBank mRNAs
  L25441 - Human geranylgeranyltransferase type I beta-subunit mRNA, complete cds.
AY780790 - Homo sapiens geranylgeranyltransferase type I beta subunit (PGGT1B) mRNA, complete cds, alternatively spliced.
AB590094 - Synthetic construct DNA, clone: pFN21AE0555, Homo sapiens PGGT1B gene for protein geranylgeranyltransferase type I, beta subunit, without stop codon, in Flexi system.
BC111924 - Synthetic construct Homo sapiens clone IMAGE:40080750, MGC:133463 PGGT1B protein (PGGT1B) mRNA, encodes complete protein.
BC118496 - Synthetic construct Homo sapiens clone IMAGE:40080759, MGC:155332 PGGT1B protein (PGGT1B) mRNA, encodes complete protein.
JD562996 - Sequence 544020 from Patent EP1572962.
JD437534 - Sequence 418558 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_005023, NP_005014, P53609, PGTB1_HUMAN, Q5MJP9
UCSC ID: uc003kqw.4
RefSeq Accession: NM_005023
Protein: P53609 (aka PGTB1_HUMAN)
CCDS: CCDS4116.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005023.3
exon count: 9CDS single in 3' UTR: no RNA size: 2727
ORF size: 1134CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2099.00frame 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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.