Human Gene PRY (uc004fvh.1)
  Description: Homo sapiens PTPN13-like, Y-linked (PRY), mRNA.
RefSeq Summary (NM_004676): This gene is located in the nonrecombining portion of the Y chromosome, and expressed specifically in testis. It encodes a protein which has a low degree of similarity to protein tyrosine phosphatase, non-receptor type 13. Two nearly identical copies of this gene exist within a palindromic region. This record represents the more telomeric copy. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chrY:24,636,544-24,660,784 Size: 24,241 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chrY:24,647,712-24,660,217 Size: 12,506 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrY:24,636,544-24,660,784)mRNA (may differ from genome)Protein (147 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PRY_HUMAN
DESCRIPTION: RecName: Full=PTPN13-like protein, Y-linked; AltName: Full=Testis-specific PTP-BL-related Y protein;
TISSUE SPECIFICITY: Expressed in testis. Detected in spermatocytes, spermatids and spermatozoa (at protein level).
CAUTION: PRY has multiple identical or highly similar copies on chromosome Y, some of which might be non functional pseudogenes.

-  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


-  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: 0.09 RPKM in Testis
Total median expression: 0.09 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 -60.01227-0.264 Picture PostScript Text
3' UTR -200.71567-0.354 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
  ModBase Predicted Comparative 3D Structure on O14603
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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF000988 - Homo sapiens testis-specific PTP-BL Related Y protein (PRY) mRNA, complete cds.
AF517635 - Homo sapiens testis-specific PTP-BL related Y protein mRNA, complete cds, alternatively spliced.
JD364731 - Sequence 345755 from Patent EP1572962.
JD347786 - Sequence 328810 from Patent EP1572962.
JD266264 - Sequence 247288 from Patent EP1572962.
JD442086 - Sequence 423110 from Patent EP1572962.
JD441523 - Sequence 422547 from Patent EP1572962.
JD329346 - Sequence 310370 from Patent EP1572962.
JD388518 - Sequence 369542 from Patent EP1572962.
JD453975 - Sequence 434999 from Patent EP1572962.
JD556903 - Sequence 537927 from Patent EP1572962.
BC113548 - Homo sapiens PTPN13-like, Y-linked, mRNA (cDNA clone MGC:142108 IMAGE:8322600), complete cds.
BC113550 - Homo sapiens PTPN13-like, Y-linked, mRNA (cDNA clone MGC:142110 IMAGE:8322602), complete cds.
BC143893 - Homo sapiens PTPN13-like, Y-linked, mRNA (cDNA clone MGC:177427 IMAGE:9052410), complete cds.
BC171757 - Homo sapiens PTPN13-like, Y-linked, mRNA (cDNA clone MGC:198471 IMAGE:9053258), complete cds.
GQ901033 - Homo sapiens clone HEL-T-145 epididymis secretory sperm binding protein mRNA, complete cds.
JD096145 - Sequence 77169 from Patent EP1572962.
JD044217 - Sequence 25241 from Patent EP1572962.
AB464107 - Synthetic construct DNA, clone: pF1KB7436, Homo sapiens PRY gene for PTPN13-like, Y-linked, without stop codon, in Flexi system.
BC148536 - Synthetic construct Homo sapiens clone IMAGE:100015521, MGC:183076 PTPN13-like, Y-linked 2 (PRY2) mRNA, encodes complete protein.
BC153128 - Synthetic construct Homo sapiens clone IMAGE:100016506, MGC:184308 PTPN13-like, Y-linked 2 (PRY2) mRNA, encodes complete protein.
JD436168 - Sequence 417192 from Patent EP1572962.
JD222283 - Sequence 203307 from Patent EP1572962.
JD326524 - Sequence 307548 from Patent EP1572962.
JD116496 - Sequence 97520 from Patent EP1572962.
JD113964 - Sequence 94988 from Patent EP1572962.
JD347604 - Sequence 328628 from Patent EP1572962.
JD100301 - Sequence 81325 from Patent EP1572962.
JD441324 - Sequence 422348 from Patent EP1572962.
JD313127 - Sequence 294151 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZLM1, NM_004676, NP_004667, O14603, PRY1, PRY2, PRYP3, PRYP4, PRY_HUMAN, PTPN13LY, PTPN13LY2, Q14D09
UCSC ID: uc004fvh.1
RefSeq Accession: NM_004676
Protein: O14603 (aka PRY_HUMAN)
CCDS: CCDS14799.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004676.2
exon count: 5CDS single in 3' UTR: no RNA size: 1238
ORF size: 444CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 553.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 2
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.