Human Gene GSPT2 (uc004dpl.3)
  Description: Homo sapiens G1 to S phase transition 2 (GSPT2), mRNA.
RefSeq Summary (NM_018094): This gene encodes a GTPase that belongs to the GTP-binding elongation factor family. The encoded protein is a polypeptide release factor that complexes with eukaryotic peptide chain release factor 1 to mediate translation termination. This protein may also be involved in mRNA stability.[provided by RefSeq, Mar 2010].
Transcript (Including UTRs)
   Position: hg19 chrX:51,486,481-51,489,326 Size: 2,846 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg19 chrX:51,486,723-51,488,609 Size: 1,887 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:51,486,481-51,489,326)mRNA (may differ from genome)Protein (628 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ERF3B_HUMAN
DESCRIPTION: RecName: Full=Eukaryotic peptide chain release factor GTP-binding subunit ERF3B; Short=Eukaryotic peptide chain release factor subunit 3b; Short=eRF3b; AltName: Full=G1 to S phase transition protein 2 homolog;
FUNCTION: Involved in translation termination in response to the termination codons UAA, UAG and UGA. May play a role as a potent stimulator of the release factor activity of ETF1. Exhibits GTPase activity, which is ribosome- and ETF1-dependent. May play a role in cell cycle progression. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.
SUBUNIT: Interacts with ETF1 (By similarity). Component of the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. Interacts with UPF1 and PABPC1.
INTERACTION: P11940:PABPC1; NbExp=3; IntAct=EBI-3869637, EBI-81531; Q92900:UPF1; NbExp=3; IntAct=EBI-3869637, EBI-373471;
SUBCELLULAR LOCATION: Cytoplasm (Probable).
TISSUE SPECIFICITY: Highly expressed in IUCC stage II colorectal cancer (CRC).
SIMILARITY: Belongs to the GTP-binding elongation factor family. ERF3 subfamily.

-  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): GSPT2
CDC HuGE Published Literature: GSPT2
Positive Disease Associations: prostate cancer
Related Studies:
  1. prostate cancer
    Gudmundsson ,et al. 2008, Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer, Nature genetics 2008 40- 3 : 281-3. [PubMed 18264098]

-  MalaCards Disease Associations
  MalaCards Gene Search: GSPT2
Diseases sorted by gene-association score: autistic disorder* (231), visual epilepsy* (126), seizure disorder* (121), syndromic x-linked intellectual disability (11)
* = Manually curated disease association

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

+  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: 13.37 RPKM in Testis
Total median expression: 211.72 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 -96.20242-0.398 Picture PostScript Text
3' UTR -150.59717-0.210 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
IPR009818 - Ataxin-2_C
IPR000795 - ProtSyn_GTP-bd
IPR009001 - Transl_elong_EF1A/Init_IF2_C
IPR004161 - Transl_elong_EFTu/EF1A_2
IPR004160 - Transl_elong_EFTu/EF1A_C
IPR009000 - Transl_elong_init/rib_B-barrel

Pfam Domains:
PF00009 - Elongation factor Tu GTP binding domain
PF03143 - Elongation factor Tu C-terminal domain
PF03144 - Elongation factor Tu domain 2
PF07145 - Ataxin-2 C-terminal region

SCOP Domains:
50447 - Translation proteins
50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3KUJ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8IYD1
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003747 translation release factor activity
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding

Biological Process:
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0002184 cytoplasmic translational termination
GO:0006412 translation
GO:0007049 cell cycle

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0018444 translation release factor complex


-  Descriptions from all associated GenBank mRNAs
  AK225671 - Homo sapiens mRNA for peptide chain release factor 3 variant, clone: STM07487.
LF211576 - JP 2014500723-A/19079: Polycomb-Associated Non-Coding RNAs.
BC036077 - Homo sapiens G1 to S phase transition 2, mRNA (cDNA clone MGC:33729 IMAGE:5313878), complete cds.
AK298868 - Homo sapiens cDNA FLJ55563 complete cds, highly similar to Homo sapiens G1 to S phase transition 2 (GSPT2), mRNA.
AK023155 - Homo sapiens cDNA FLJ13093 fis, clone NT2RP3002151.
AK001303 - Homo sapiens cDNA FLJ10441 fis, clone NT2RP1000733, highly similar to Human mRNA for GSPT1-TK protein.
JD523521 - Sequence 504545 from Patent EP1572962.
JD054964 - Sequence 35988 from Patent EP1572962.
JD475942 - Sequence 456966 from Patent EP1572962.
JD389875 - Sequence 370899 from Patent EP1572962.
JD125048 - Sequence 106072 from Patent EP1572962.
JD247565 - Sequence 228589 from Patent EP1572962.
JD269356 - Sequence 250380 from Patent EP1572962.
JD189047 - Sequence 170071 from Patent EP1572962.
KJ898533 - Synthetic construct Homo sapiens clone ccsbBroadEn_07927 GSPT2 gene, encodes complete protein.
AJ251548 - Homo sapiens mRNA for polypeptide chain release factor 3b (GSPT2 gene).
LF381483 - JP 2014500723-A/188986: Polycomb-Associated Non-Coding RNAs.
LF381484 - JP 2014500723-A/188987: Polycomb-Associated Non-Coding RNAs.
LF381485 - JP 2014500723-A/188988: Polycomb-Associated Non-Coding RNAs.
LF381486 - JP 2014500723-A/188989: Polycomb-Associated Non-Coding RNAs.
JD369760 - Sequence 350784 from Patent EP1572962.
JD265635 - Sequence 246659 from Patent EP1572962.
JD501613 - Sequence 482637 from Patent EP1572962.
JD555655 - Sequence 536679 from Patent EP1572962.
JD367145 - Sequence 348169 from Patent EP1572962.
JD280110 - Sequence 261134 from Patent EP1572962.
JD561953 - Sequence 542977 from Patent EP1572962.
MA447153 - JP 2018138019-A/19079: Polycomb-Associated Non-Coding RNAs.
MA617060 - JP 2018138019-A/188986: Polycomb-Associated Non-Coding RNAs.
MA617061 - JP 2018138019-A/188987: Polycomb-Associated Non-Coding RNAs.
MA617062 - JP 2018138019-A/188988: Polycomb-Associated Non-Coding RNAs.
MA617063 - JP 2018138019-A/188989: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8IYD1 (Reactome details) participates in the following event(s):

R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex
R-HSA-927789 Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
R-HSA-6800138 N6AMT1:TRMT112 transfers CH3 group from AdoMet to ETF1 dimer
R-HSA-141691 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
R-HSA-141671 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
R-HSA-141673 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-376176 Signaling by ROBO receptors
R-HSA-72764 Eukaryotic Translation Termination
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-422475 Axon guidance
R-HSA-72766 Translation
R-HSA-8953854 Metabolism of RNA
R-HSA-1266738 Developmental Biology
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ERF3B, ERF3B_HUMAN, NM_018094, NP_060564, Q8IYD1, Q9H909, Q9NVY0, Q9NY44
UCSC ID: uc004dpl.3
RefSeq Accession: NM_018094
Protein: Q8IYD1 (aka ERF3B_HUMAN)
CCDS: CCDS14336.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018094.4
exon count: 1CDS single in 3' UTR: no RNA size: 2861
ORF size: 1887CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2045.00frame shift in genome: no % Coverage: 99.48
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
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.