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Protein

U4/U6 small nuclear ribonucleoprotein Prp3

Gene

PRPF3

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

Functioni

Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex).1 Publication2 Publications

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • 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

Keywordsi

Biological processmRNA 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:HPRP31 Publication, PRP3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000117360.12
HGNCiHGNC:17348 PRPF3
MIMi607301 gene
neXtProtiNX_O43395

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 18 (RP18)3 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)DescriptionActionsGraphical viewLength
Natural variantiVAR_046735493P → S in RP18. 1 PublicationCorresponds to variant dbSNP:rs121434242EnsemblClinVar.1
Natural variantiVAR_016877494T → 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 PublicationsCorresponds to variant dbSNP:rs121434241EnsemblClinVar.1

Keywords - Diseasei

Disease mutation, Retinitis pigmentosa

Organism-specific databases

DisGeNETi9129
GeneReviewsiPRPF3
MalaCardsiPRPF3
MIMi601414 phenotype
OpenTargetsiENSG00000117360
Orphaneti791 Retinitis pigmentosa
PharmGKBiPA134892509

Polymorphism and mutation databases

BioMutaiPRPF3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000970441 – 683U4/U6 small nuclear ribonucleoprotein Prp3Add BLAST683

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki139Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei164PhosphoserineCombined sources1
Modified residuei167PhosphothreonineCombined sources1
Cross-linki244Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki252Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei619PhosphoserineCombined sources1

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

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO43395
MaxQBiO43395
PaxDbiO43395
PeptideAtlasiO43395
PRIDEiO43395
ProteomicsDBi48921

PTM databases

iPTMnetiO43395
PhosphoSitePlusiO43395

Miscellaneous databases

PMAP-CutDBiO43395

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 Expressed in 227 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_PRPF3
GenevisibleiO43395 HS

Organism-specific databases

HPAiHPA027226
HPA067116

Interactioni

Subunit structurei

Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:9328476, PubMed:9404889, PubMed:28781166, PubMed:26912367, PubMed:17932117). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:16723661, PubMed:26912367). Interacts directly with PRPF4 (PubMed:9328476, PubMed:9404889, PubMed:17932117). Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA (PubMed:9404889). Interacts with SART3; the interaction is direct and recruits the deubiquitinase USP4 to PRPF3 (PubMed:15314151, PubMed:20595234). 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 (PubMed:20595234).8 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114577, 136 interactors
CORUMiO43395
DIPiDIP-34508N
IntActiO43395, 62 interactors
MINTiO43395
STRINGi9606.ENSP00000315379

Structurei

Secondary structure

1683
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO43395
SMRiO43395
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43395

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 87PWIPROSITE-ProRule annotationAdd BLAST87

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni416 – 550Mediates interaction with SART31 PublicationAdd BLAST135

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi579 – 584Poly-Val6

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR010541 DUF1115
IPR013881 Pre-mRNA_splic_Prp3
IPR027104 Prp3
IPR002483 PWI_dom
IPR036483 PWI_dom_sf
PANTHERiPTHR14212 PTHR14212, 1 hit
PfamiView protein in Pfam
PF06544 DUF1115, 1 hit
PF08572 PRP3, 1 hit
PF01480 PWI, 1 hit
SMARTiView protein in SMART
SM00311 PWI, 1 hit
SUPFAMiSSF101233 SSF101233, 1 hit
PROSITEiView protein in PROSITE
PS51025 PWI, 1 hit

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)DescriptionActionsGraphical viewLength
Sequence conflicti142I → T in AAC09069 (PubMed:9328476).Curated1
Sequence conflicti273 – 274EL → SV in AAC09069 (PubMed:9328476).Curated2

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05128612K → N. Corresponds to variant dbSNP:rs12736964Ensembl.1
Natural variantiVAR_046735493P → S in RP18. 1 PublicationCorresponds to variant dbSNP:rs121434242EnsemblClinVar.1
Natural variantiVAR_016877494T → 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 PublicationsCorresponds to variant dbSNP:rs121434241EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0562651 – 135Missing in isoform 2. 1 PublicationAdd BLAST135
Alternative sequenceiVSP_056266402 – 416TEENP…FGITN → GKSQERRLFWNHKSC in isoform 2. 1 PublicationAdd BLAST15
Alternative sequenceiVSP_056267417 – 683Missing in isoform 2. 1 PublicationAdd BLAST267

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 No translation available.
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

Similar proteinsi

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 No translation available.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X4QNMR-A1-79[»]
3JCRelectron microscopy7.00K1-683[»]
5O9Zelectron microscopy4.50E1-683[»]
ProteinModelPortaliO43395
SMRiO43395
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114577, 136 interactors
CORUMiO43395
DIPiDIP-34508N
IntActiO43395, 62 interactors
MINTiO43395
STRINGi9606.ENSP00000315379

PTM databases

iPTMnetiO43395
PhosphoSitePlusiO43395

Polymorphism and mutation databases

BioMutaiPRPF3

Proteomic databases

EPDiO43395
MaxQBiO43395
PaxDbiO43395
PeptideAtlasiO43395
PRIDEiO43395
ProteomicsDBi48921

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
DisGeNETi9129
EuPathDBiHostDB:ENSG00000117360.12
GeneCardsiPRPF3
GeneReviewsiPRPF3
HGNCiHGNC:17348 PRPF3
HPAiHPA027226
HPA067116
MalaCardsiPRPF3
MIMi601414 phenotype
607301 gene
neXtProtiNX_O43395
OpenTargetsiENSG00000117360
Orphaneti791 Retinitis pigmentosa
PharmGKBiPA134892509
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
SIGNORiO43395

Miscellaneous databases

ChiTaRSiPRPF3 human
EvolutionaryTraceiO43395
GeneWikiiPRPF3
GenomeRNAii9129
PMAP-CutDBiO43395
PROiPR:O43395
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000117360 Expressed in 227 organ(s), highest expression level in left lobe of thyroid gland
CleanExiHS_PRPF3
GenevisibleiO43395 HS

Family and domain databases

InterProiView protein in InterPro
IPR010541 DUF1115
IPR013881 Pre-mRNA_splic_Prp3
IPR027104 Prp3
IPR002483 PWI_dom
IPR036483 PWI_dom_sf
PANTHERiPTHR14212 PTHR14212, 1 hit
PfamiView protein in Pfam
PF06544 DUF1115, 1 hit
PF08572 PRP3, 1 hit
PF01480 PWI, 1 hit
SMARTiView protein in SMART
SM00311 PWI, 1 hit
SUPFAMiSSF101233 SSF101233, 1 hit
PROSITEiView protein in PROSITE
PS51025 PWI, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPRPF3_HUMAN
AccessioniPrimary (citable) accession number: O43395
Secondary accession number(s): B4DSY9, O43446, Q5VT54
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: September 26, 2003
Last modified: November 7, 2018
This is version 182 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

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
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