Human Gene PUS10 (uc010fci.3)
  Description: Homo sapiens pseudouridylate synthase 10 (PUS10), mRNA.
RefSeq Summary (NM_144709): Pseudouridination, the isomerization of uridine to pseudouridine, is the most common posttranscriptional nucleotide modification found in RNA and is essential for biologic functions such as spliceosome biogenesis. Pseudouridylate synthases, such as PUS10, catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. These enzymes also act as RNA chaperones, facilitating the correct folding and assembly of tRNAs (McCleverty et al., 2007 [PubMed 17900615]).[supplied by OMIM, May 2009]. Sequence Note: The RefSeq transcript and protein were derived from transcript and genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Transcript (Including UTRs)
   Position: hg19 chr2:61,167,548-61,244,328 Size: 76,781 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr2:61,169,530-61,239,025 Size: 69,496 Coding Exon Count: 17 

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 (chr2:61,167,548-61,244,328)mRNA (may differ from genome)Protein (529 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PUS10_HUMAN
DESCRIPTION: RecName: Full=Putative tRNA pseudouridine synthase Pus10; EC=5.4.99.-; AltName: Full=Coiled-coil domain-containing protein 139; AltName: Full=tRNA pseudouridine 55 synthase; Short=Psi55 synthase; AltName: Full=tRNA pseudouridylate synthase; AltName: Full=tRNA-uridine isomerase;
FUNCTION: Pseudouridylate synthases catalyze pseudouridination of structural RNAs, including transfer, ribosomal, and splicing RNAs. PUS10 catalyzes the formation of the universal psi55 in the GC loop of transfer RNAs (Probable). Modulator of TRAIL-induced cell death via activation of procaspase 8 and BID cleavage. Required for the progression of the apoptotic signal through intrinsic mitochondrial cell death.
CATALYTIC ACTIVITY: tRNA uridine = tRNA pseudouridine.
PTM: Proteolytically cleaved during TRAIL-induced cell death. Cleaved, in vitro, either by caspase-3 or caspase-8.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the pseudouridine synthase Pus10 family.
SEQUENCE CAUTION: Sequence=CAI46123.1; Type=Miscellaneous discrepancy; Note=Partially unspliced pre-RNA;

-  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): PUS10
CDC HuGE Published Literature: PUS10
Positive Disease Associations: Celiac Disease , Colitis, Ulcerative , Crohn Disease , Intestinal Diseases , ulcerative colitis
Related Studies:
  1. Celiac Disease
    Patrick C A Dubois et al. Nature genetics 2010, Multiple common variants for celiac disease influencing immune gene expression., Nature genetics. [PubMed 20190752]
  2. Colitis, Ulcerative
    Dermot P B McGovern et al. Nature genetics 2010, Genome-wide association identifies multiple ulcerative colitis susceptibility loci., Nature genetics. [PubMed 20228799]
  3. Colitis, Ulcerative
    Carl A Anderson et al. Nature genetics 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47., Nature genetics. [PubMed 21297633]
           more ... click here to view the complete list

-  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: 3.79 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 61.84 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 -11.6060-0.193 Picture PostScript Text
3' UTR -458.401982-0.231 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
IPR020103 - PsdUridine_synth_cat_dom

SCOP Domains:
55120 - Pseudouridine synthase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2V9K - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q3MIT2
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0009982 pseudouridine synthase activity
GO:0016853 isomerase activity

Biological Process:
GO:0001522 pseudouridine synthesis
GO:0008033 tRNA processing
GO:0009451 RNA modification
GO:0031119 tRNA pseudouridine synthesis


-  Descriptions from all associated GenBank mRNAs
  AL832208 - Homo sapiens mRNA; cDNA DKFZp686K122 (from clone DKFZp686K122).
AK056874 - Homo sapiens cDNA FLJ32312 fis, clone PROST2003210.
AK291729 - Homo sapiens cDNA FLJ77651 complete cds.
BC101680 - Homo sapiens pseudouridylate synthase 10, mRNA (cDNA clone MGC:126729 IMAGE:8069186), complete cds.
BC143480 - Homo sapiens cDNA clone IMAGE:9051988.
BC101706 - Homo sapiens pseudouridylate synthase 10, mRNA (cDNA clone MGC:126755 IMAGE:8069212), complete cds.
KJ900281 - Synthetic construct Homo sapiens clone ccsbBroadEn_09675 PUS10-like gene, encodes complete protein.
JD315854 - Sequence 296878 from Patent EP1572962.
JD554994 - Sequence 536018 from Patent EP1572962.
JD454967 - Sequence 435991 from Patent EP1572962.
BC065197 - Homo sapiens cDNA clone IMAGE:5167882, partial cds.
BC060323 - Homo sapiens cDNA clone IMAGE:3898374, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: AK291729, CCDC139, DOBI, NM_144709, NP_653310, PUS10_HUMAN, Q3MIT2, Q5JPJ5, Q96MI8
UCSC ID: uc010fci.3
RefSeq Accession: NM_144709
Protein: Q3MIT2 (aka PUS10_HUMAN)
CCDS: CCDS1865.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK291729.1
exon count: 18CDS single in 3' UTR: no RNA size: 1815
ORF size: 1590CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 3380.00frame shift in genome: no % Coverage: 99.94
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.