Human Gene PRPF4 (ENST00000374198.5_9) from GENCODE V47lift37
  Description: pre-mRNA processing factor 4, transcript variant 6 (from RefSeq NR_136266.2)
Gencode Transcript: ENST00000374198.5_9
Gencode Gene: ENSG00000136875.13_11
Transcript (Including UTRs)
   Position: hg19 chr9:116,037,938-116,055,185 Size: 17,248 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr9:116,038,024-116,053,940 Size: 15,917 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:116,037,938-116,055,185)mRNA (may differ from genome)Protein (521 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  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: PRPF4
Diseases sorted by gene-association score: retinitis pigmentosa 70* (1229), prpf4-related retinitis pigmentosa* (500), retinitis pigmentosa* (49), retinitis pigmentosa 18 (8), retinitis pigmentosa 13 (7)
* = 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: 20.37 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 410.13 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 -39.7086-0.462 Picture PostScript Text
3' UTR -348.201245-0.280 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
IPR020472 - G-protein_beta_WD-40_rep
IPR014906 - PRP4
IPR003648 - SFM
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR019775 - WD40_repeat_CS
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF00400 - WD domain, G-beta repeat
PF08799 - pre-mRNA processing factor 4 (PRP4) like

SCOP Domains:
158230 - PRP4-like
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q5T1M7
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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 DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK225056 - Homo sapiens mRNA for Splice isoform 2 of O43172 variant, clone: adSE01169.
U82756 - Homo sapiens WD splicing factor Hprp4p (HPRP4) mRNA, complete cds.
BC007424 - Homo sapiens PRP4 pre-mRNA processing factor 4 homolog (yeast), mRNA (cDNA clone MGC:3611 IMAGE:3029831), complete cds.
AF016369 - Homo sapiens U4/U6 small nuclear ribonucleoprotein hPrp4 mRNA, complete cds.
AB209797 - Homo sapiens mRNA for PRPF4 protein variant protein.
AK313131 - Homo sapiens cDNA, FLJ93619, highly similar to Homo sapiens PRP4 pre-mRNA processing factor 4 homolog (yeast) (PRPF4), mRNA.
BC001588 - Homo sapiens PRP4 pre-mRNA processing factor 4 homolog (yeast), mRNA (cDNA clone MGC:1501 IMAGE:2988225), complete cds.
KJ892693 - Synthetic construct Homo sapiens clone ccsbBroadEn_02087 PRPF4 gene, encodes complete protein.
KJ901945 - Synthetic construct Homo sapiens clone ccsbBroadEn_11339 PRPF4 gene, encodes complete protein.
EU176673 - Synthetic construct Homo sapiens clone IMAGE:100011473; FLH184210.01L; RZPDo839A02255D PRP4 pre-mRNA processing factor 4 homolog (yeast) (PRPF4) gene, encodes complete protein.
EU176331 - Synthetic construct Homo sapiens clone IMAGE:100006441; FLH184214.01X; RZPDo839F07251D PRP4 pre-mRNA processing factor 4 homolog (yeast) (PRPF4) gene, encodes complete protein.
AB590453 - Synthetic construct DNA, clone: pFN21AB5305, Homo sapiens PRPF4 gene for PRP4 pre-mRNA processing factor 4 homolog, without stop codon, in Flexi system.
CR457105 - Homo sapiens full open reading frame cDNA clone RZPDo834H0814D for gene PRPF4, PRP4 pre-mRNA processing factor 4 homolog (yeast); complete cds, incl. stopcodon.
AY572489 - Homo sapiens 60 kDa U4/U6 snRNP-specific spliceosomal protein (PRPF4) mRNA, complete cds.
JD044334 - Sequence 25358 from Patent EP1572962.
JD430406 - Sequence 411430 from Patent EP1572962.
JD055471 - Sequence 36495 from Patent EP1572962.
JD546696 - Sequence 527720 from Patent EP1572962.
JD386586 - Sequence 367610 from Patent EP1572962.
JD372556 - Sequence 353580 from Patent EP1572962.
JD458147 - Sequence 439171 from Patent EP1572962.
JD139179 - Sequence 120203 from Patent EP1572962.
JD532616 - Sequence 513640 from Patent EP1572962.
JD463493 - Sequence 444517 from Patent EP1572962.
JD206417 - Sequence 187441 from Patent EP1572962.
JD286856 - Sequence 267880 from Patent EP1572962.
JD425349 - Sequence 406373 from Patent EP1572962.
JD277643 - Sequence 258667 from Patent EP1572962.
JD083892 - Sequence 64916 from Patent EP1572962.
JD145432 - Sequence 126456 from Patent EP1572962.
JD343488 - Sequence 324512 from Patent EP1572962.
JD138446 - Sequence 119470 from Patent EP1572962.
JD092359 - Sequence 73383 from Patent EP1572962.
JD537931 - Sequence 518955 from Patent EP1572962.
JD367066 - Sequence 348090 from Patent EP1572962.
JD523856 - Sequence 504880 from Patent EP1572962.
JD523857 - Sequence 504881 from Patent EP1572962.
JD106141 - Sequence 87165 from Patent EP1572962.
JD106142 - Sequence 87166 from Patent EP1572962.
JD508468 - Sequence 489492 from Patent EP1572962.
JD163922 - Sequence 144946 from Patent EP1572962.
JD174421 - Sequence 155445 from Patent EP1572962.
JD091587 - Sequence 72611 from Patent EP1572962.
JD067327 - Sequence 48351 from Patent EP1572962.
JD540151 - Sequence 521175 from Patent EP1572962.
JD458178 - Sequence 439202 from Patent EP1572962.
JD273678 - Sequence 254702 from Patent EP1572962.
JD260055 - Sequence 241079 from Patent EP1572962.
JD228710 - Sequence 209734 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000374198.1, ENST00000374198.2, ENST00000374198.3, ENST00000374198.4, hCG_29193 , NR_136266, PRPF4 , Q5T1M7, Q5T1M7_HUMAN, uc318ljp.1, uc318ljp.2
UCSC ID: ENST00000374198.5_9
RefSeq Accession: NM_001244926.2
Protein: Q5T1M7

-  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.