Human Gene PRP4K (ENST00000337659.11_4) from GENCODE V47lift37
  Description: pre-mRNA processing factor 4B, transcript variant 4 (from RefSeq NR_146785.2)
Gencode Transcript: ENST00000337659.11_4
Gencode Gene: ENSG00000112739.17_10
Transcript (Including UTRs)
   Position: hg19 chr6:4,021,534-4,065,217 Size: 43,684 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr6:4,021,660-4,060,850 Size: 39,191 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:4,021,534-4,065,217)mRNA (may differ from genome)Protein (1007 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PRP4B_HUMAN
DESCRIPTION: RecName: Full=Serine/threonine-protein kinase PRP4 homolog; EC=2.7.11.1; AltName: Full=PRP4 kinase; AltName: Full=PRP4 pre-mRNA-processing factor 4 homolog;
FUNCTION: Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SUBUNIT: Identified in the spliceosome C complex. Interacts with Clk1 C-terminus.
INTERACTION: P49407:ARRB1; NbExp=2; IntAct=EBI-395940, EBI-743313; P32121:ARRB2; NbExp=3; IntAct=EBI-395940, EBI-714559; P04590:gag (xeno); NbExp=6; IntAct=EBI-395940, EBI-780156; Q9Y2Y9:KLF13; NbExp=5; IntAct=EBI-395940, EBI-1255893; Q9H1D9:POLR3F; NbExp=2; IntAct=EBI-395940, EBI-710067;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
PTM: Phosphorylated by Clk1.
SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family.
SIMILARITY: Contains 1 protein kinase domain.
SEQUENCE CAUTION: Sequence=AAH09844.1; Type=Frameshift; Positions=432; Sequence=BAA25462.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


+  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: 21.60 RPKM in Ovary
Total median expression: 682.77 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 -36.98126-0.293 Picture PostScript Text
3' UTR -1039.404367-0.238 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
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain
PF07714 - Protein tyrosine and serine/threonine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q13523
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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 DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0004693 cyclin-dependent protein serine/threonine kinase activity

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006468 protein phosphorylation
GO:0008380 RNA splicing
GO:0016310 phosphorylation

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005694 chromosome
GO:0016607 nuclear speck
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AB011108 - Homo sapiens KIAA0536 mRNA for KIAA0536 protein.
AF283465 - Homo sapiens PRP4 kinase (PRP4K) mRNA, complete cds.
BC009844 - Homo sapiens PRP4 pre-mRNA processing factor 4 homolog B (yeast), mRNA (cDNA clone IMAGE:3943395), complete cds.
BC034969 - Homo sapiens PRP4 pre-mRNA processing factor 4 homolog B (yeast), mRNA (cDNA clone MGC:26845 IMAGE:4821304), complete cds.
AK291244 - Homo sapiens cDNA FLJ76831 complete cds, highly similar to Homo sapiens PRP4 pre-mRNA processing factor 4 homolog B (yeast) (PRPF4B), transcript variant 1, mRNA.
AB385345 - Synthetic construct DNA, clone: pF1KA0536, Homo sapiens PRPF4B gene for serine/threonine-protein kinase PRP4 homolog, complete cds, without stop codon, in Flexi system.
KJ897934 - Synthetic construct Homo sapiens clone ccsbBroadEn_07328 PRPF4B gene, encodes complete protein.
AY029347 - Homo sapiens serine/threonine-protein kinase (PRP4) mRNA, complete cds.
AK303047 - Homo sapiens cDNA FLJ51417 complete cds, highly similar to Serine/threonine-protein kinase PRP4 homolog (EC 2.7.11.1).
U48736 - Human serine/threonine-protein kinase PRP4h (PRP4h) mRNA, complete cds.
Z25435 - H.sapiens protein-serine/threonine kinase gene, complete CDS.
JD045793 - Sequence 26817 from Patent EP1572962.
JD022690 - Sequence 3714 from Patent EP1572962.
JD035844 - Sequence 16868 from Patent EP1572962.
JD043360 - Sequence 24384 from Patent EP1572962.
JD499467 - Sequence 480491 from Patent EP1572962.
JD298952 - Sequence 279976 from Patent EP1572962.
JD219825 - Sequence 200849 from Patent EP1572962.
JD070937 - Sequence 51961 from Patent EP1572962.
JD041028 - Sequence 22052 from Patent EP1572962.
JD168584 - Sequence 149608 from Patent EP1572962.
JD303150 - Sequence 284174 from Patent EP1572962.
JD494663 - Sequence 475687 from Patent EP1572962.
JD358678 - Sequence 339702 from Patent EP1572962.
JD311381 - Sequence 292405 from Patent EP1572962.
JD378884 - Sequence 359908 from Patent EP1572962.
JD350485 - Sequence 331509 from Patent EP1572962.
JD538829 - Sequence 519853 from Patent EP1572962.
JD230837 - Sequence 211861 from Patent EP1572962.
JD486143 - Sequence 467167 from Patent EP1572962.
JD304135 - Sequence 285159 from Patent EP1572962.
JD510193 - Sequence 491217 from Patent EP1572962.
JD399749 - Sequence 380773 from Patent EP1572962.
JD418431 - Sequence 399455 from Patent EP1572962.
JD528657 - Sequence 509681 from Patent EP1572962.
JD121218 - Sequence 102242 from Patent EP1572962.
JD080746 - Sequence 61770 from Patent EP1572962.
JD558663 - Sequence 539687 from Patent EP1572962.
JD197454 - Sequence 178478 from Patent EP1572962.
JD295270 - Sequence 276294 from Patent EP1572962.
JD334946 - Sequence 315970 from Patent EP1572962.
JD242238 - Sequence 223262 from Patent EP1572962.
JD045715 - Sequence 26739 from Patent EP1572962.
JD431554 - Sequence 412578 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K5C9, ENST00000337659.1, ENST00000337659.10, ENST00000337659.2, ENST00000337659.3, ENST00000337659.4, ENST00000337659.5, ENST00000337659.6, ENST00000337659.7, ENST00000337659.8, ENST00000337659.9, KIAA0536, NR_146785, PRP4, PRP4B_HUMAN, PRP4H, PRPF4B, Q13523, Q5D0F6, Q5TAY8, Q8IVC3, Q8TDP2, Q96QT7, Q9UEE6, uc317uuz.1, uc317uuz.2
UCSC ID: ENST00000337659.11_4
RefSeq Accession: NM_003913.5
Protein: Q13523 (aka PRP4B_HUMAN or PR4B_HUMAN)

-  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.