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Protein

U4/U6 small nuclear ribonucleoprotein Prp4

Gene

PRPF4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.1 Publication

GO - Molecular functioni

GO - Biological processi

  • mRNA splicing, via spliceosome Source: BHF-UCL
  • RNA processing Source: ProtInc
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciZFISH:ENSG00000136875-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SignaLinkiO43172.

Names & Taxonomyi

Protein namesi
Recommended name:
U4/U6 small nuclear ribonucleoprotein Prp4
Alternative name(s):
PRP4 homolog
Short name:
hPrp4
U4/U6 snRNP 60 kDa protein
WD splicing factor Prp4
Gene namesi
Name:PRPF4
Synonyms:PRP4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:17349. PRPF4.

Subcellular locationi

  • Nucleus speckle 1 Publication

  • Note: Colocalizes with spliceosomal snRNPs.By similarity

GO - Cellular componenti

  • Cajal body Source: BHF-UCL
  • nuclear speck Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: ProtInc
  • spliceosomal complex Source: UniProtKB
  • spliceosomal snRNP complex Source: UniProtKB
  • U4/U6 snRNP Source: UniProtKB
  • U4/U6 x U5 tri-snRNP complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Involvement in diseasei

Retinitis pigmentosa 70 (RP70)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. 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.
See also OMIM:615922
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074029192R → H in RP70; does not affect nuclear speck localization; disrupts interaction with PRPF3; does not affect interaction with PPIH; does not integrated in spliceosomal snRNP complex. 1 PublicationCorresponds to variant rs41296057dbSNPEnsembl.1
Natural variantiVAR_071872315P → L in RP70. 1 PublicationCorresponds to variant rs587777599dbSNPEnsembl.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi192R → E: Decreases PRPF3 binding. 1 Publication1
Mutagenesisi192R → K: Decreases PRPF3 binding. 1 Publication1
Mutagenesisi192R → W: Decreases PRPF3 binding. 1 Publication1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi9128.
MalaCardsiPRPF4.
MIMi615922. phenotype.
OpenTargetsiENSG00000136875.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA38448.

Chemistry databases

ChEMBLiCHEMBL1163119.

Polymorphism and mutation databases

BioMutaiPRPF4.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000511491 – 522U4/U6 small nuclear ribonucleoprotein Prp4Add BLAST522

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei27N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiO43172.
MaxQBiO43172.
PaxDbiO43172.
PeptideAtlasiO43172.
PRIDEiO43172.

PTM databases

iPTMnetiO43172.
PhosphoSitePlusiO43172.

Expressioni

Gene expression databases

BgeeiENSG00000136875.
CleanExiHS_PRPF4.
ExpressionAtlasiO43172. baseline and differential.
GenevisibleiO43172. HS.

Organism-specific databases

HPAiHPA021794.
HPA022248.

Interactioni

Subunit structurei

Interacts directly with PRPF18, PPIH and PRPF3. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GPKOWQ929172EBI-718395,EBI-746309
PPIHO434472EBI-718395,EBI-1055615

Protein-protein interaction databases

BioGridi114576. 133 interactors.
IntActiO43172. 78 interactors.
MINTiMINT-270624.
STRINGi9606.ENSP00000363313.

Chemistry databases

BindingDBiO43172.

Structurei

Secondary structure

1522
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi108 – 114Combined sources7
Beta strandi119 – 121Combined sources3
Helixi126 – 136Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MZWX-ray2.00B107-137[»]
3JCRelectron microscopy7.00L1-522[»]
ProteinModelPortaliO43172.
SMRiO43172.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43172.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati229 – 268WD 1Add BLAST40
Repeati271 – 318WD 2Add BLAST48
Repeati321 – 360WD 3Add BLAST40
Repeati363 – 402WD 4Add BLAST40
Repeati405 – 444WD 5Add BLAST40
Repeati447 – 487WD 6Add BLAST41
Repeati490 – 521WD 7Add BLAST32

Sequence similaritiesi

Contains 7 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0272. Eukaryota.
ENOG410XNP8. LUCA.
GeneTreeiENSGT00810000125363.
HOGENOMiHOG000157615.
HOVERGENiHBG030892.
InParanoidiO43172.
KOiK12662.
OMAiCWDVRKV.
OrthoDBiEOG091G0HXT.
PhylomeDBiO43172.
TreeFamiTF314922.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR027106. Prp4.
IPR014906. PRP4-like.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PANTHERiPTHR19846. PTHR19846. 1 hit.
PfamiPF08799. PRP4. 1 hit.
PF00400. WD40. 6 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF158230. SSF158230. 1 hit.
SSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O43172-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI
60 70 80 90 100
LGKDGLKAGI EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN
110 120 130 140 150
VSTDDSEVKA CLRALGEPIT LFGEGPAERR ERLRNILSVV GTDALKKTKK
160 170 180 190 200
DDEKSKKSKE EYQQTWYHEG PNSLKVARLW IANYSLPRAM KRLEEARLHK
210 220 230 240 250
EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS PNSKMLATAC
260 270 280 290 300
WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA
310 320 330 340 350
ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW
360 370 380 390 400
DLEAQEEILH QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI
410 420 430 440 450
MFLEGHLKEI YGINFSPNGY HIATGSGDNT CKVWDLRQRR CVYTIPAHQN
460 470 480 490 500
LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP GWSPLKTLAG HEGKVMGLDI
510 520
SSDGQLIATC SYDRTFKLWM AE
Length:522
Mass (Da):58,449
Last modified:May 2, 2002 - v2
Checksum:i08975A26D0B21857
GO
Isoform 2 (identifier: O43172-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     10-10: Missing.

Show »
Length:521
Mass (Da):58,321
Checksum:iB4EF92D9E12C9188
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti78 – 103HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261 (PubMed:9328476).CuratedAdd BLAST26
Sequence conflicti78H → R in AAC51925 (PubMed:9404889).Curated1
Sequence conflicti86V → L in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti134R → K in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti141G → D in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti176Missing in AAC02261 (PubMed:9328476).Curated1
Sequence conflicti275 – 282NVGAIVFH → KKEQLHSI in AAC02261 (PubMed:9328476).Curated8
Sequence conflicti405G → D in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti447A → P in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti510C → Y in AAB87640 (PubMed:9257651).Curated1
Sequence conflicti521A → L in AAB87640 (PubMed:9257651).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_074029192R → H in RP70; does not affect nuclear speck localization; disrupts interaction with PRPF3; does not affect interaction with PPIH; does not integrated in spliceosomal snRNP complex. 1 PublicationCorresponds to variant rs41296057dbSNPEnsembl.1
Natural variantiVAR_071872315P → L in RP70. 1 PublicationCorresponds to variant rs587777599dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_00678510Missing in isoform 2. 2 Publications1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001687 Genomic DNA. Translation: AAB87640.1.
AF016369 mRNA. Translation: AAC51925.1.
U82756 mRNA. Translation: AAC02261.1.
AL449305 Genomic DNA. Translation: CAI10968.1.
CH471090 Genomic DNA. Translation: EAW87362.1.
BC001588 mRNA. Translation: AAH01588.1.
BC007424 mRNA. Translation: AAH07424.1.
CCDSiCCDS59142.1. [O43172-2]
CCDS6791.1. [O43172-1]
RefSeqiNP_001231855.1. NM_001244926.1. [O43172-2]
NP_004688.2. NM_004697.4. [O43172-1]
UniGeneiHs.744014.

Genome annotation databases

EnsembliENST00000374198; ENSP00000363313; ENSG00000136875. [O43172-1]
ENST00000374199; ENSP00000363315; ENSG00000136875. [O43172-2]
GeneIDi9128.
KEGGihsa:9128.
UCSCiuc004bgx.4. human. [O43172-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001687 Genomic DNA. Translation: AAB87640.1.
AF016369 mRNA. Translation: AAC51925.1.
U82756 mRNA. Translation: AAC02261.1.
AL449305 Genomic DNA. Translation: CAI10968.1.
CH471090 Genomic DNA. Translation: EAW87362.1.
BC001588 mRNA. Translation: AAH01588.1.
BC007424 mRNA. Translation: AAH07424.1.
CCDSiCCDS59142.1. [O43172-2]
CCDS6791.1. [O43172-1]
RefSeqiNP_001231855.1. NM_001244926.1. [O43172-2]
NP_004688.2. NM_004697.4. [O43172-1]
UniGeneiHs.744014.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1MZWX-ray2.00B107-137[»]
3JCRelectron microscopy7.00L1-522[»]
ProteinModelPortaliO43172.
SMRiO43172.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114576. 133 interactors.
IntActiO43172. 78 interactors.
MINTiMINT-270624.
STRINGi9606.ENSP00000363313.

Chemistry databases

BindingDBiO43172.
ChEMBLiCHEMBL1163119.

PTM databases

iPTMnetiO43172.
PhosphoSitePlusiO43172.

Polymorphism and mutation databases

BioMutaiPRPF4.

Proteomic databases

EPDiO43172.
MaxQBiO43172.
PaxDbiO43172.
PeptideAtlasiO43172.
PRIDEiO43172.

Protocols and materials databases

DNASUi9128.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000374198; ENSP00000363313; ENSG00000136875. [O43172-1]
ENST00000374199; ENSP00000363315; ENSG00000136875. [O43172-2]
GeneIDi9128.
KEGGihsa:9128.
UCSCiuc004bgx.4. human. [O43172-1]

Organism-specific databases

CTDi9128.
DisGeNETi9128.
GeneCardsiPRPF4.
HGNCiHGNC:17349. PRPF4.
HPAiHPA021794.
HPA022248.
MalaCardsiPRPF4.
MIMi607795. gene.
615922. phenotype.
neXtProtiNX_O43172.
OpenTargetsiENSG00000136875.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA38448.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0272. Eukaryota.
ENOG410XNP8. LUCA.
GeneTreeiENSGT00810000125363.
HOGENOMiHOG000157615.
HOVERGENiHBG030892.
InParanoidiO43172.
KOiK12662.
OMAiCWDVRKV.
OrthoDBiEOG091G0HXT.
PhylomeDBiO43172.
TreeFamiTF314922.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000136875-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SignaLinkiO43172.

Miscellaneous databases

EvolutionaryTraceiO43172.
GeneWikiiPRPF4.
GenomeRNAii9128.
PROiO43172.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000136875.
CleanExiHS_PRPF4.
ExpressionAtlasiO43172. baseline and differential.
GenevisibleiO43172. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR027106. Prp4.
IPR014906. PRP4-like.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PANTHERiPTHR19846. PTHR19846. 1 hit.
PfamiPF08799. PRP4. 1 hit.
PF00400. WD40. 6 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF158230. SSF158230. 1 hit.
SSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRP4_HUMAN
AccessioniPrimary (citable) accession number: O43172
Secondary accession number(s): O43445
, O43864, Q5T1M8, Q96DG2, Q96IK4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: May 2, 2002
Last modified: November 30, 2016
This is version 170 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.