Human Gene PRPF3 (ENST00000324862.7_4) from GENCODE V47lift37
  Description: pre-mRNA processing factor 3, transcript variant 6 (from RefSeq NR_146769.1)
Gencode Transcript: ENST00000324862.7_4
Gencode Gene: ENSG00000117360.13_7
Transcript (Including UTRs)
   Position: hg19 chr1:150,293,982-150,325,709 Size: 31,728 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr1:150,297,401-150,325,455 Size: 28,055 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:150,293,982-150,325,709)mRNA (may differ from genome)Protein (683 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PRPF3_HUMAN
DESCRIPTION: RecName: Full=U4/U6 small nuclear ribonucleoprotein Prp3; AltName: Full=Pre-mRNA-splicing factor 3; Short=hPrp3; AltName: Full=U4/U6 snRNP 90 kDa protein;
FUNCTION: Participates in pre-mRNA splicing. May play a role in the assembly of the U4/U5/U6 tri-snRNP complex.
SUBUNIT: Interacts directly with PRPF4. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. This complex interacts with the U4/U5/U6 tri-snRNP complex.
INTERACTION: Q92997:DVL3; NbExp=2; IntAct=EBI-744322, EBI-739789;
SUBCELLULAR LOCATION: Nucleus speckle. Note=Colocalizes with spliceosomal snRNPs.
TISSUE SPECIFICITY: Highly expressed in retina, liver, kidney and blood. Detected at lower levels in heart and brain.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in PRPF3 are the cause of retinitis pigmentosa type 18 (RP18) [MIM:601414]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP18 inheritance is autosomal dominant.
SIMILARITY: Contains 1 PWI domain.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PRPF3";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PRPF3
Diseases sorted by gene-association score: retinitis pigmentosa 18* (1258), prpf3-related retinitis pigmentosa* (100), retinitis pigmentosa* (72), retinitis (16), retinitis pigmentosa 13 (10), retinitis pigmentosa 29 (8)
* = 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: 23.08 RPKM in Thyroid
Total median expression: 645.12 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 -27.40108-0.254 Picture PostScript Text
3' UTR -49.40254-0.194 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
IPR010541 - DUF1115
IPR013881 - Pre-mRNA_splic_Prp3
IPR002483 - PWI

Pfam Domains:
PF01480 - PWI domain
PF06544 - Protein of unknown function (DUF1115)
PF08572 - pre-mRNA processing factor 3 (PRP3)

SCOP Domains:
101233 - PWI domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1X4Q - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O43395
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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 orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0016607 nuclear speck
GO:0032991 macromolecular complex
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome


-  Descriptions from all associated GenBank mRNAs
  CU674950 - Synthetic construct Homo sapiens gateway clone IMAGE:100017769 5' read PRPF3 mRNA.
KJ892694 - Synthetic construct Homo sapiens clone ccsbBroadEn_02088 PRPF3 gene, encodes complete protein.
KR709756 - Synthetic construct Homo sapiens clone CCSBHm_00005696 PRPF3 (PRPF3) mRNA, encodes complete protein.
KR709757 - Synthetic construct Homo sapiens clone CCSBHm_00005697 PRPF3 (PRPF3) mRNA, encodes complete protein.
KR709758 - Synthetic construct Homo sapiens clone CCSBHm_00005698 PRPF3 (PRPF3) mRNA, encodes complete protein.
LF383812 - JP 2014500723-A/191315: Polycomb-Associated Non-Coding RNAs.
AK297139 - Homo sapiens cDNA FLJ55983 complete cds, highly similar to U4/U6 small nuclear ribonucleoprotein Prp3.
LF352567 - JP 2014500723-A/160070: Polycomb-Associated Non-Coding RNAs.
AK309330 - Homo sapiens cDNA, FLJ99371.
AK311653 - Homo sapiens cDNA, FLJ18695.
AK299980 - Homo sapiens cDNA FLJ50652 complete cds, highly similar to U4/U6 small nuclear ribonucleoprotein Prp3.
AK297265 - Homo sapiens cDNA FLJ50575 complete cds, highly similar to U4/U6 small nuclear ribonucleoprotein Prp3.
AK222825 - Homo sapiens mRNA for PRP3 pre-mRNA processing factor 3 homolog, clone: HEP06906.
AK312891 - Homo sapiens cDNA, FLJ93335, highly similar to Homo sapiens PRP3 pre-mRNA processing factor 3 homolog (yeast) (PRPF3), mRNA.
AK310241 - Homo sapiens cDNA, FLJ17283.
AF016370 - Homo sapiens U4/U6 small nuclear ribonucleoprotein hPrp3 mRNA, complete cds.
AF001947 - Homo sapiens U4/U6-associated RNA splicing factor (PRP3) mRNA, complete cds.
BC001954 - Homo sapiens PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:4388 IMAGE:2905308), complete cds.
BC000184 - Homo sapiens PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:2026 IMAGE:3351519), complete cds.
JD346061 - Sequence 327085 from Patent EP1572962.
DQ892853 - Synthetic construct clone IMAGE:100005483; FLH190313.01X; RZPDo839G1175D PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae) (PRPF3) gene, encodes complete protein.
DQ896100 - Synthetic construct Homo sapiens clone IMAGE:100010560; FLH190309.01L; RZPDo839G1165D PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae) (PRPF3) gene, encodes complete protein.
LF352565 - JP 2014500723-A/160068: Polycomb-Associated Non-Coding RNAs.
LF352562 - JP 2014500723-A/160065: Polycomb-Associated Non-Coding RNAs.
LF352561 - JP 2014500723-A/160064: Polycomb-Associated Non-Coding RNAs.
LF352559 - JP 2014500723-A/160062: Polycomb-Associated Non-Coding RNAs.
LF352558 - JP 2014500723-A/160061: Polycomb-Associated Non-Coding RNAs.
JD390484 - Sequence 371508 from Patent EP1572962.
JD390485 - Sequence 371509 from Patent EP1572962.
JD440726 - Sequence 421750 from Patent EP1572962.
LF352557 - JP 2014500723-A/160060: Polycomb-Associated Non-Coding RNAs.
MA619389 - JP 2018138019-A/191315: Polycomb-Associated Non-Coding RNAs.
MA588144 - JP 2018138019-A/160070: Polycomb-Associated Non-Coding RNAs.
MA588142 - JP 2018138019-A/160068: Polycomb-Associated Non-Coding RNAs.
MA588139 - JP 2018138019-A/160065: Polycomb-Associated Non-Coding RNAs.
MA588138 - JP 2018138019-A/160064: Polycomb-Associated Non-Coding RNAs.
MA588136 - JP 2018138019-A/160062: Polycomb-Associated Non-Coding RNAs.
MA588135 - JP 2018138019-A/160061: Polycomb-Associated Non-Coding RNAs.
MA588134 - JP 2018138019-A/160060: Polycomb-Associated Non-Coding RNAs.
MA880082 - JP 2019500347-A/3: COMPOSITIONS AND METHODS FOR TREATMENT OF RETINITIS PIGMENTOSA 18 AND RETINITIS PIGMENTOSA 13.

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

Protein O43395 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B4DSY9, ENST00000324862.1, ENST00000324862.2, ENST00000324862.3, ENST00000324862.4, ENST00000324862.5, ENST00000324862.6, HPRP3 , NR_146769, O43395, O43446, PRP3, PRPF3_HUMAN, Q5VT54, uc317rth.1, uc317rth.2
UCSC ID: ENST00000324862.7_4
RefSeq Accession: NM_004698.4
Protein: O43395 (aka PRPF3_HUMAN or PRP3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PRPF3:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
  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.