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O43395 (PRPF3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 136. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:PRPF3
Synonyms:HPRP3, PRP3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length683 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Subunit structure

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, NHP2L1, EFTUD2, SART1 and USP39. Ref.1 Ref.2 Ref.7

Subcellular location

Nucleus speckle. Note: Colocalizes with spliceosomal snRNPs.

Tissue specificity

Highly expressed in retina, liver, kidney and blood. Detected at lower levels in heart and brain. Ref.16

Involvement in disease

Retinitis pigmentosa 18 (RP18) [MIM:601414]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.16 Ref.17 Ref.18

Sequence similarities

Contains 1 PWI domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 683683U4/U6 small nuclear ribonucleoprotein Prp3
PRO_0000097044

Regions

Domain1 – 8787PWI
Compositional bias579 – 5846Poly-Val

Amino acid modifications

Modified residue1641Phosphoserine Ref.8 Ref.12
Modified residue1671Phosphothreonine Ref.8 Ref.12
Modified residue6191Phosphoserine Ref.6 Ref.9 Ref.11 Ref.12 Ref.14

Natural variations

Natural variant121K → N.
Corresponds to variant rs12736964 [ dbSNP | Ensembl ].
VAR_051286
Natural variant4931P → S in RP18. Ref.16
VAR_046735
Natural variant4941T → 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. Ref.16 Ref.17 Ref.18
VAR_016877

Experimental info

Sequence conflict1421I → T in AAC09069. Ref.1
Sequence conflict273 – 2742EL → SV in AAC09069. Ref.1

Secondary structure

........... 683
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O43395 [UniParc].

Last modified September 26, 2003. Version 2.
Checksum: 4AA6AA4C99110284

FASTA68377,529
        10         20         30         40         50         60 
MALSKRELDE LKPWIEKTVK RVLGFSEPTV VTAALNCVGK GMDKKKAADH LKPFLDDSTL 

        70         80         90        100        110        120 
RFVDKLFEAV EEGRSSRHSK SSSDRSRKRE LKEVFGDDSE ISKESSGVKK RRIPRFEEVE 

       130        140        150        160        170        180 
EEPEVIPGPP SESPGMLTKL QIKQMMEAAT RQIEERKKQL SFISPPTPQP KTPSSSQPER 

       190        200        210        220        230        240 
LPIGNTIQPS QAATFMNDAI EKARKAAELQ ARIQAQLALK PGLIGNANMV GLANLHAMGI 

       250        260        270        280        290        300 
APPKVELKDQ TKPTPLILDE QGRTVDATGK EIELTHRMPT LKANIRAVKR EQFKQQLKEK 

       310        320        330        340        350        360 
PSEDMESNTF FDPRVSIAPS QRQRRTFKFH DKGKFEKIAQ RLRTKAQLEK LQAEISQAAR 

       370        380        390        400        410        420 
KTGIHTSTRL ALIAPKKELK EGDIPEIEWW DSYIIPNGFD LTEENPKRED YFGITNLVEH 

       430        440        450        460        470        480 
PAQLNPPVDN DTPVTLGVYL TKKEQKKLRR QTRREAQKEL QEKVRLGLMP PPEPKVRISN 

       490        500        510        520        530        540 
LMRVLGTEAV QDPTKVEAHV RAQMAKRQKA HEEANAARKL TAEQRKVKKI KKLKEDISQG 

       550        560        570        580        590        600 
VHISVYRVRN LSNPAKKFKI EANAGQLYLT GVVVLHKDVN VVVVEGGPKA QKKFKRLMLH 

       610        620        630        640        650        660 
RIKWDEQTSN TKGDDDEESD EEAVKKTNKC VLVWEGTAKD RSFGEMKFKQ CPTENMAREH 

       670        680 
FKKHGAEHYW DLALSESVLE STD 

« Hide

References

« Hide 'large scale' references
[1]"Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome."
Wang A., Forman-Kay J., Luo Y., Luo M., Chow Y.-H., Plumb J., Friesen J.D., Tsui L.-C., Heng H.H.Q., Woolford J.L. Jr., Hu J.
Hum. Mol. Genet. 6:2117-2126(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH PRPF4 AND U4/U5/U6 SNRNPS.
[2]"A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs."
Horowitz D.S., Kobayashi R., Krainer A.R.
RNA 3:1374-1387(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 93-101; 253-267; 351-361; 409-428 AND 560-576, INTERACTION WITH PPIH; PRPF4 AND U4/U6 SNRNPS.
Tissue: Neuroepithelium.
[3]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Eye and Skin.
[6]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-619, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[8]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-164 AND THR-167, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography."
Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D., Zou H., Gu J.
Proteomics 8:1346-1361(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-619, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Liver.
[10]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-619, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[12]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-164; THR-167 AND SER-619, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[13]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-619, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Solution structure of PWI domain in U4/U6 small nuclear ribonucleoprotein PRP3(HPRP3)."
RIKEN structural genomics initiative (RSGI)
Submitted (NOV-2005) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 1-79.
[16]"Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa."
Chakarova C.F., Hims M.M., Bolz H., Abu-Safieh L., Patel R.J., Papaioannou M.G., Inglehearn C.F., Keen T.J., Willis C., Moore A.T., Rosenberg T., Webster A.R., Bird A.C., Gal A., Hunt D., Vithana E.N., Bhattacharya S.S.
Hum. Mol. Genet. 11:87-92(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANTS RP18 SER-493 AND MET-494, TISSUE SPECIFICITY.
[17]"Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa."
Martinez-Gimeno M., Gamundi M.J., Hernan I., Maseras M., Milla E., Ayuso C., Garcia-Sandoval B., Beneyto M., Vilela C., Baiget M., Antinolo G., Carballo M.
Invest. Ophthalmol. Vis. Sci. 44:2171-2177(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT RP18 MET-494.
[18]"Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex."
Gonzalez-Santos J.M., Cao H., Duan R.C., Hu J.
Hum. Mol. Genet. 17:225-239(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION OF VARIANT RP18 MET-494.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF001947 mRNA. Translation: AAC09069.1.
AF016370 mRNA. Translation: AAC51926.1.
AL611942 Genomic DNA. Translation: CAH70312.1.
CH471121 Genomic DNA. Translation: EAW53556.1.
BC000184 mRNA. Translation: AAH00184.1.
BC001954 mRNA. Translation: AAH01954.1.
CCDSCCDS951.1.
PIRT50839.
T50840.
RefSeqNP_004689.1. NM_004698.2.
UniGeneHs.11776.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1X4QNMR-A1-79[»]
ProteinModelPortalO43395.
SMRO43395. Positions 1-73.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114577. 72 interactions.
DIPDIP-34508N.
IntActO43395. 29 interactions.
MINTMINT-1445186.
STRING9606.ENSP00000315379.

PTM databases

PhosphoSiteO43395.

Proteomic databases

MaxQBO43395.
PaxDbO43395.
PRIDEO43395.

Protocols and materials databases

DNASU9129.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000324862; ENSP00000315379; ENSG00000117360.
ENST00000578639; ENSP00000463536; ENSG00000265228.
GeneID9129.
KEGGhsa:9129.
UCSCuc001eum.4. human.

Organism-specific databases

CTD9129.
GeneCardsGC01P150293.
GeneReviewsPRPF3.
HGNCHGNC:17348. PRPF3.
HPAHPA027226.
MIM601414. phenotype.
607301. gene.
neXtProtNX_O43395.
Orphanet791. Retinitis pigmentosa.
PharmGKBPA134892509.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG268901.
HOGENOMHOG000205412.
HOVERGENHBG053699.
InParanoidO43395.
KOK12843.
OMAPWVERTV.
PhylomeDBO43395.
TreeFamTF313082.

Gene expression databases

ArrayExpressO43395.
BgeeO43395.
CleanExHS_PRPF3.
GenevestigatorO43395.

Family and domain databases

Gene3D1.20.1390.10. 1 hit.
InterProIPR010541. DUF1115.
IPR013881. Pre-mRNA_splic_Prp3.
IPR027104. Prp3.
IPR002483. PWI_dom.
[Graphical view]
PANTHERPTHR14212. PTHR14212. 1 hit.
PfamPF06544. DUF1115. 1 hit.
PF08572. PRP3. 1 hit.
PF01480. PWI. 1 hit.
[Graphical view]
SMARTSM00311. PWI. 1 hit.
[Graphical view]
SUPFAMSSF101233. SSF101233. 1 hit.
PROSITEPS51025. PWI. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO43395.
GeneWikiPRPF3.
GenomeRNAi9129.
NextBio34221.
PMAP-CutDBO43395.
PROO43395.
SOURCESearch...

Entry information

Entry namePRPF3_HUMAN
AccessionPrimary (citable) accession number: O43395
Secondary accession number(s): O43446, Q5VT54
Entry history
Integrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: September 26, 2003
Last modified: July 9, 2014
This is version 136 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM