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Protein

U4/U6 small nuclear ribonucleoprotein Prp3

Gene

PRPF3

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 Publication2 Publications

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA processing Source: ProtInc
  • mRNA splicing, via spliceosome Source: UniProtKB
  • RNA splicing Source: ProtInc
  • RNA splicing, via transesterification reactions Source: UniProtKB
  • spliceosomal tri-snRNP complex assembly Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SIGNORiO43395.

Names & Taxonomyi

Protein namesi
Recommended name:
U4/U6 small nuclear ribonucleoprotein Prp3
Alternative name(s):
Pre-mRNA-splicing factor 3
Short name:
hPrp3
U4/U6 snRNP 90 kDa protein
Gene namesi
Name:PRPF3
Synonyms:HPRP3, PRP3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:17348. PRPF3.

Subcellular locationi

GO - Cellular componenti

  • Cajal body Source: BHF-UCL
  • cytoplasm Source: HPA
  • nuclear speck Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • protein complex Source: Ensembl
  • spliceosomal complex 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 18 (RP18)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:601414
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti493 – 4931P → S in RP18. 1 Publication
Corresponds to variant rs121434242 [ dbSNP | Ensembl ].
VAR_046735
Natural varianti494 – 4941T → M in RP18; reduces phosphorylation; impairs binding to PRPF4; impairs self-association; affects interaction with the U4/U5/U6 tri-snRNP complex; does not affect global pre-mRNA splicing. 3 Publications
Corresponds to variant rs121434241 [ dbSNP | Ensembl ].
VAR_016877

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

MalaCardsiPRPF3.
MIMi601414. phenotype.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA134892509.

Polymorphism and mutation databases

BioMutaiPRPF3.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 683683U4/U6 small nuclear ribonucleoprotein Prp3PRO_0000097044Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei164 – 1641PhosphoserineCombined sources
Modified residuei167 – 1671PhosphothreonineCombined sources
Modified residuei619 – 6191PhosphoserineCombined sources

Post-translational modificationi

Ubiquitinated. Undergoes 'Lys-63'-linked polyubiquitination by PRPF19 and deubiquitination by USP4. 'Lys-63'-linked ubiquitination increases the affinity for PRPF8 and may regulate the assembly of the U4/U6-U5 tri-snRNP complex.1 Publication

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO43395.
MaxQBiO43395.
PaxDbiO43395.
PeptideAtlasiO43395.
PRIDEiO43395.

PTM databases

iPTMnetiO43395.
PhosphoSiteiO43395.

Miscellaneous databases

PMAP-CutDBO43395.

Expressioni

Tissue specificityi

Highly expressed in retina, liver, kidney and blood. Detected at lower levels in heart and brain.1 Publication

Gene expression databases

BgeeiENSG00000117360.
CleanExiHS_PRPF3.
GenevisibleiO43395. HS.

Organism-specific databases

HPAiHPA027226.
HPA067116.

Interactioni

Subunit structurei

Interacts directly with PRPF4. 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, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39. Interacts with SART3; the interaction is direct and recruits the deubiquitinase USP4 to PRPF3. Interacts with PRPF19. Interacts ('Lys-63'-linked polyubiquitinated) with PRPF8 (via the MPN (JAB/Mov34) domain); may stabilize the U4/U6-U5 tri-snRNP complex.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-744322,EBI-744322
DVL3Q929972EBI-744322,EBI-739789
FAM9BQ8IZU03EBI-744322,EBI-10175124
MFAP1P550812EBI-744322,EBI-1048159
NKAPQ8N5F72EBI-744322,EBI-721539
SF3B2Q134352EBI-744322,EBI-749111
SLU7O953912EBI-744322,EBI-750559
SMNDC1O759402EBI-744322,EBI-1052641
TRIM39Q9HCM94EBI-744322,EBI-739510
U2AF2P263682EBI-744322,EBI-742339

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi114577. 120 interactions.
DIPiDIP-34508N.
IntActiO43395. 36 interactions.
MINTiMINT-1445186.
STRINGi9606.ENSP00000315379.

Structurei

Secondary structure

1
683
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi5 – 2319Combined sources
Helixi28 – 3912Combined sources
Helixi44 – 518Combined sources
Turni52 – 554Combined sources
Helixi56 – 583Combined sources
Helixi60 – 7314Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X4QNMR-A1-79[»]
3JCRelectron microscopy7.00K1-683[»]
ProteinModelPortaliO43395.
SMRiO43395. Positions 1-73, 542-670.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43395.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 8787PWIPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni416 – 550135Mediates interaction with SART31 PublicationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi579 – 5846Poly-Val

Sequence similaritiesi

Contains 1 PWI domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2769. Eukaryota.
ENOG410XQV0. LUCA.
GeneTreeiENSGT00390000011497.
HOGENOMiHOG000205412.
HOVERGENiHBG053699.
InParanoidiO43395.
KOiK12843.
OMAiPWVERTV.
OrthoDBiEOG091G05VO.
PhylomeDBiO43395.
TreeFamiTF313082.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
InterProiIPR010541. DUF1115.
IPR013881. Pre-mRNA_splic_Prp3.
IPR027104. Prp3.
IPR002483. PWI_dom.
[Graphical view]
PANTHERiPTHR14212. PTHR14212. 1 hit.
PfamiPF06544. DUF1115. 1 hit.
PF08572. PRP3. 1 hit.
PF01480. PWI. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
PROSITEiPS51025. PWI. 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: O43395-1) [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
MALSKRELDE LKPWIEKTVK RVLGFSEPTV VTAALNCVGK GMDKKKAADH
60 70 80 90 100
LKPFLDDSTL RFVDKLFEAV EEGRSSRHSK SSSDRSRKRE LKEVFGDDSE
110 120 130 140 150
ISKESSGVKK RRIPRFEEVE EEPEVIPGPP SESPGMLTKL QIKQMMEAAT
160 170 180 190 200
RQIEERKKQL SFISPPTPQP KTPSSSQPER LPIGNTIQPS QAATFMNDAI
210 220 230 240 250
EKARKAAELQ ARIQAQLALK PGLIGNANMV GLANLHAMGI APPKVELKDQ
260 270 280 290 300
TKPTPLILDE QGRTVDATGK EIELTHRMPT LKANIRAVKR EQFKQQLKEK
310 320 330 340 350
PSEDMESNTF FDPRVSIAPS QRQRRTFKFH DKGKFEKIAQ RLRTKAQLEK
360 370 380 390 400
LQAEISQAAR KTGIHTSTRL ALIAPKKELK EGDIPEIEWW DSYIIPNGFD
410 420 430 440 450
LTEENPKRED YFGITNLVEH PAQLNPPVDN DTPVTLGVYL TKKEQKKLRR
460 470 480 490 500
QTRREAQKEL QEKVRLGLMP PPEPKVRISN LMRVLGTEAV QDPTKVEAHV
510 520 530 540 550
RAQMAKRQKA HEEANAARKL TAEQRKVKKI KKLKEDISQG VHISVYRVRN
560 570 580 590 600
LSNPAKKFKI EANAGQLYLT GVVVLHKDVN VVVVEGGPKA QKKFKRLMLH
610 620 630 640 650
RIKWDEQTSN TKGDDDEESD EEAVKKTNKC VLVWEGTAKD RSFGEMKFKQ
660 670 680
CPTENMAREH FKKHGAEHYW DLALSESVLE STD
Length:683
Mass (Da):77,529
Last modified:September 26, 2003 - v2
Checksum:i4AA6AA4C99110284
GO
Isoform 2 (identifier: O43395-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-135: Missing.
     402-416: TEENPKREDYFGITN → GKSQERRLFWNHKSC
     417-683: Missing.

Note: No experimental confirmation available.
Show »
Length:281
Mass (Da):31,889
Checksum:i35DEDDAF71195A31
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti142 – 1421I → T in AAC09069 (PubMed:9328476).Curated
Sequence conflicti273 – 2742EL → SV in AAC09069 (PubMed:9328476).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti12 – 121K → N.
Corresponds to variant rs12736964 [ dbSNP | Ensembl ].
VAR_051286
Natural varianti493 – 4931P → S in RP18. 1 Publication
Corresponds to variant rs121434242 [ dbSNP | Ensembl ].
VAR_046735
Natural varianti494 – 4941T → M in RP18; reduces phosphorylation; impairs binding to PRPF4; impairs self-association; affects interaction with the U4/U5/U6 tri-snRNP complex; does not affect global pre-mRNA splicing. 3 Publications
Corresponds to variant rs121434241 [ dbSNP | Ensembl ].
VAR_016877

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 135135Missing in isoform 2. 1 PublicationVSP_056265Add
BLAST
Alternative sequencei402 – 41615TEENP…FGITN → GKSQERRLFWNHKSC in isoform 2. 1 PublicationVSP_056266Add
BLAST
Alternative sequencei417 – 683267Missing in isoform 2. 1 PublicationVSP_056267Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001947 mRNA. Translation: AAC09069.1.
AF016370 mRNA. Translation: AAC51926.1.
AK299980 mRNA. Translation: BAG61801.1.
AL611942 Genomic DNA. Translation: CAH70312.1.
CH471121 Genomic DNA. Translation: EAW53556.1.
BC000184 mRNA. Translation: AAH00184.1.
BC001954 mRNA. Translation: AAH01954.1.
CCDSiCCDS951.1. [O43395-1]
PIRiT50839.
T50840.
RefSeqiNP_004689.1. NM_004698.2. [O43395-1]
UniGeneiHs.11776.

Genome annotation databases

EnsembliENST00000324862; ENSP00000315379; ENSG00000117360. [O43395-1]
GeneIDi9129.
KEGGihsa:9129.
UCSCiuc001eum.5. human. [O43395-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001947 mRNA. Translation: AAC09069.1.
AF016370 mRNA. Translation: AAC51926.1.
AK299980 mRNA. Translation: BAG61801.1.
AL611942 Genomic DNA. Translation: CAH70312.1.
CH471121 Genomic DNA. Translation: EAW53556.1.
BC000184 mRNA. Translation: AAH00184.1.
BC001954 mRNA. Translation: AAH01954.1.
CCDSiCCDS951.1. [O43395-1]
PIRiT50839.
T50840.
RefSeqiNP_004689.1. NM_004698.2. [O43395-1]
UniGeneiHs.11776.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X4QNMR-A1-79[»]
3JCRelectron microscopy7.00K1-683[»]
ProteinModelPortaliO43395.
SMRiO43395. Positions 1-73, 542-670.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114577. 120 interactions.
DIPiDIP-34508N.
IntActiO43395. 36 interactions.
MINTiMINT-1445186.
STRINGi9606.ENSP00000315379.

PTM databases

iPTMnetiO43395.
PhosphoSiteiO43395.

Polymorphism and mutation databases

BioMutaiPRPF3.

Proteomic databases

EPDiO43395.
MaxQBiO43395.
PaxDbiO43395.
PeptideAtlasiO43395.
PRIDEiO43395.

Protocols and materials databases

DNASUi9129.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000324862; ENSP00000315379; ENSG00000117360. [O43395-1]
GeneIDi9129.
KEGGihsa:9129.
UCSCiuc001eum.5. human. [O43395-1]

Organism-specific databases

CTDi9129.
GeneCardsiPRPF3.
GeneReviewsiPRPF3.
HGNCiHGNC:17348. PRPF3.
HPAiHPA027226.
HPA067116.
MalaCardsiPRPF3.
MIMi601414. phenotype.
607301. gene.
neXtProtiNX_O43395.
Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA134892509.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2769. Eukaryota.
ENOG410XQV0. LUCA.
GeneTreeiENSGT00390000011497.
HOGENOMiHOG000205412.
HOVERGENiHBG053699.
InParanoidiO43395.
KOiK12843.
OMAiPWVERTV.
OrthoDBiEOG091G05VO.
PhylomeDBiO43395.
TreeFamiTF313082.

Enzyme and pathway databases

ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
SIGNORiO43395.

Miscellaneous databases

ChiTaRSiPRPF3. human.
EvolutionaryTraceiO43395.
GeneWikiiPRPF3.
GenomeRNAii9129.
PMAP-CutDBO43395.
PROiO43395.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000117360.
CleanExiHS_PRPF3.
GenevisibleiO43395. HS.

Family and domain databases

Gene3Di1.20.1390.10. 1 hit.
InterProiIPR010541. DUF1115.
IPR013881. Pre-mRNA_splic_Prp3.
IPR027104. Prp3.
IPR002483. PWI_dom.
[Graphical view]
PANTHERiPTHR14212. PTHR14212. 1 hit.
PfamiPF06544. DUF1115. 1 hit.
PF08572. PRP3. 1 hit.
PF01480. PWI. 1 hit.
[Graphical view]
SMARTiSM00311. PWI. 1 hit.
[Graphical view]
SUPFAMiSSF101233. SSF101233. 1 hit.
PROSITEiPS51025. PWI. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRPF3_HUMAN
AccessioniPrimary (citable) accession number: O43395
Secondary accession number(s): B4DSY9, O43446, Q5VT54
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: September 26, 2003
Last modified: September 7, 2016
This is version 159 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 1
    Human chromosome 1: 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.