Human Gene PUS7 (uc003vcx.3)
  Description: Homo sapiens pseudouridylate synthase 7 homolog (S. cerevisiae) (PUS7), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:105,096,960-105,162,685 Size: 65,726 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr7:105,098,237-105,148,959 Size: 50,723 Coding Exon Count: 15 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:105,096,960-105,162,685)mRNA (may differ from genome)Protein (661 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PUS7_HUMAN
DESCRIPTION: RecName: Full=Pseudouridylate synthase 7 homolog; EC=5.4.99.-;
CATALYTIC ACTIVITY: tRNA uridine = tRNA pseudouridine.
SIMILARITY: Belongs to the pseudouridine synthase TruD family.
SIMILARITY: Contains 1 TRUD domain.
SEQUENCE CAUTION: Sequence=BAA91203.1; Type=Erroneous initiation;

-  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): PUS7
CDC HuGE Published Literature: PUS7
Positive Disease Associations: Erythrocyte Indices
Related Studies:
  1. Erythrocyte Indices
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.

-  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: 7.91 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 164.53 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 -98.00219-0.447 Picture PostScript Text
3' UTR -316.641277-0.248 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
IPR001656 - PsdUridine_synth_TruD
IPR020119 - PsdUridine_synth_TruD_CS
IPR017091 - PsdUridine_synth_TruD_euk
IPR011760 - PsdUridine_synth_TruD_insert

Pfam Domains:
PF01142 - tRNA pseudouridine synthase D (TruD)

SCOP Domains:
55120 - Pseudouridine synthase

ModBase Predicted Comparative 3D Structure on Q96PZ0
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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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0009982 pseudouridine synthase activity
GO:0016853 isomerase activity
GO:0019899 enzyme binding

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

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AB067484 - Homo sapiens mRNA for KIAA1897 protein, partial cds.
AK091283 - Homo sapiens cDNA FLJ33964 fis, clone CTONG2019029, highly similar to Pseudouridylate synthase 7 homolog (EC 5.4.99.-).
AX746894 - Sequence 419 from Patent EP1308459.
AK128629 - Homo sapiens cDNA FLJ46788 fis, clone TRACH3028855, highly similar to Pseudouridylate synthase 7 homolog (EC 5.4.99.-).
BC011396 - Homo sapiens pseudouridylate synthase 7 homolog (S. cerevisiae), mRNA (cDNA clone MGC:17720 IMAGE:3870711), complete cds.
BC005209 - Homo sapiens pseudouridylate synthase 7 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3686082), partial cds.
AK000492 - Homo sapiens cDNA FLJ20485 fis, clone KAT07835.
JD505632 - Sequence 486656 from Patent EP1572962.
JD466349 - Sequence 447373 from Patent EP1572962.
JD410809 - Sequence 391833 from Patent EP1572962.
JD150147 - Sequence 131171 from Patent EP1572962.
JD535475 - Sequence 516499 from Patent EP1572962.
JD535476 - Sequence 516500 from Patent EP1572962.
JD367646 - Sequence 348670 from Patent EP1572962.
JD536087 - Sequence 517111 from Patent EP1572962.
JD160453 - Sequence 141477 from Patent EP1572962.
JD152892 - Sequence 133916 from Patent EP1572962.
JD229900 - Sequence 210924 from Patent EP1572962.
JD559616 - Sequence 540640 from Patent EP1572962.
CU679922 - Synthetic construct Homo sapiens gateway clone IMAGE:100018565 5' read PUS7 mRNA.
CU675043 - Synthetic construct Homo sapiens gateway clone IMAGE:100016914 5' read PUS7 mRNA.
KJ902655 - Synthetic construct Homo sapiens clone ccsbBroadEn_12049 PUS7 gene, encodes complete protein.
JD045532 - Sequence 26556 from Patent EP1572962.
JD058930 - Sequence 39954 from Patent EP1572962.
JD082773 - Sequence 63797 from Patent EP1572962.
JD317722 - Sequence 298746 from Patent EP1572962.
JD351161 - Sequence 332185 from Patent EP1572962.
JD073760 - Sequence 54784 from Patent EP1572962.
JD178300 - Sequence 159324 from Patent EP1572962.
JD073674 - Sequence 54698 from Patent EP1572962.
JD348595 - Sequence 329619 from Patent EP1572962.
JD072624 - Sequence 53648 from Patent EP1572962.
JD540624 - Sequence 521648 from Patent EP1572962.
JD424627 - Sequence 405651 from Patent EP1572962.

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

Protein Q96PZ0 (Reactome details) participates in the following event(s):

R-HSA-6786583 PUS7 transforms uridine to pseudouridine in tRNAs
R-HSA-6782315 tRNA modification in the nucleus and cytosol
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA1897, NM_019042, NP_061915, PUS7_HUMAN, Q75MG4, Q96PZ0, Q9NX19
UCSC ID: uc003vcx.3
RefSeq Accession: NM_019042
Protein: Q96PZ0 (aka PUS7_HUMAN)
CCDS: CCDS34725.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_019042.3
exon count: 16CDS single in 3' UTR: no RNA size: 3484
ORF size: 1986CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4161.00frame 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: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 1249# 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.