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Protein

U4/U6 small nuclear ribonucleoprotein Prp4

Gene

PRPF4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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: UniProtKB
  • RNA processing Source: ProtInc
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000136875.12
HGNCiHGNC:17349 PRPF4
MIMi607795 gene
neXtProtiNX_O43172

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 dbSNP:rs41296057Ensembl.1
Natural variantiVAR_071872315P → L in RP70. 1 PublicationCorresponds to variant dbSNP:rs587777599EnsemblClinVar.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
ProteomicsDBi48788
48789 [O43172-2]

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

Show more details

Protein-protein interaction databases

BioGridi114576, 147 interactors
CORUMiO43172
IntActiO43172, 80 interactors
MINTiO43172
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[»]
5O9Zelectron microscopy4.50F1-522[»]
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

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0272 Eukaryota
ENOG410XNP8 LUCA
GeneTreeiENSGT00900000140925
HOGENOMiHOG000157615
HOVERGENiHBG030892
InParanoidiO43172
KOiK12662
OMAiDSSWRLW
OrthoDBiEOG091G0HXT
PhylomeDBiO43172
TreeFamiTF314922

Family and domain databases

Gene3Di1.10.720.150, 1 hit
2.130.10.10, 2 hits
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR027106 Prp4
IPR014906 PRP4-like
IPR036285 PRP4-like_sf
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PANTHERiPTHR19846 PTHR19846, 1 hit
PfamiView protein in Pfam
PF08799 PRP4, 1 hit
PF00400 WD40, 6 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00500 SFM, 1 hit
SM00320 WD40, 7 hits
SUPFAMiSSF158230 SSF158230, 1 hit
SSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS00678 WD_REPEATS_1, 2 hits
PS50082 WD_REPEATS_2, 6 hits
PS50294 WD_REPEATS_REGION, 1 hit

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 dbSNP:rs41296057Ensembl.1
Natural variantiVAR_071872315P → L in RP70. 1 PublicationCorresponds to variant dbSNP:rs587777599EnsemblClinVar.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 No translation available.
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

Similar proteinsi

Entry informationi

Entry nameiPRP4_HUMAN
AccessioniPrimary (citable) accession number: O43172
Secondary accession number(s): O43445
, O43864, Q5T1M8, Q96DG2, Q96IK4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: May 2, 2002
Last modified: June 20, 2018
This is version 184 of the entry and version 2 of the sequence. See 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

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