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O43172 (PRP4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 144. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:PRPF4
Synonyms:PRP4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length522 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 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, NHP2L1, EFTUD2, SART1 and USP39. Ref.2 Ref.3 Ref.7 Ref.8

Subcellular location

Nucleus speckle By similarity. Note: Colocalizes with spliceosomal snRNPs By similarity.

Sequence similarities

Contains 7 WD repeats.

Binary interactions

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O43172-1)

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.
Isoform 2 (identifier: O43172-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 522522U4/U6 small nuclear ribonucleoprotein Prp4
PRO_0000051149

Regions

Repeat229 – 26840WD 1
Repeat271 – 31848WD 2
Repeat321 – 36040WD 3
Repeat363 – 40240WD 4
Repeat405 – 44440WD 5
Repeat447 – 48741WD 6
Repeat490 – 52132WD 7

Amino acid modifications

Modified residue271N6-acetyllysine Ref.9

Natural variations

Alternative sequence101Missing in isoform 2.
VSP_006785

Experimental info

Sequence conflict78 – 10326HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261. Ref.3
Sequence conflict781H → R in AAC51925. Ref.2
Sequence conflict861V → L in AAB87640. Ref.1
Sequence conflict1341R → K in AAB87640. Ref.1
Sequence conflict1411G → D in AAB87640. Ref.1
Sequence conflict1761Missing in AAC02261. Ref.3
Sequence conflict275 – 2828NVGAIVFH → KKEQLHSI in AAC02261. Ref.3
Sequence conflict4051G → D in AAB87640. Ref.1
Sequence conflict4471A → P in AAB87640. Ref.1
Sequence conflict5101C → Y in AAB87640. Ref.1
Sequence conflict5211A → L in AAB87640. Ref.1

Secondary structure

....... 522
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 2, 2002. Version 2.
Checksum: 08975A26D0B21857

FASTA52258,449
        10         20         30         40         50         60 
MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI LGKDGLKAGI 

        70         80         90        100        110        120 
EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN VSTDDSEVKA CLRALGEPIT 

       130        140        150        160        170        180 
LFGEGPAERR ERLRNILSVV GTDALKKTKK DDEKSKKSKE EYQQTWYHEG PNSLKVARLW 

       190        200        210        220        230        240 
IANYSLPRAM KRLEEARLHK EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS 

       250        260        270        280        290        300 
PNSKMLATAC WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA 

       310        320        330        340        350        360 
ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW DLEAQEEILH 

       370        380        390        400        410        420 
QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI MFLEGHLKEI YGINFSPNGY 

       430        440        450        460        470        480 
HIATGSGDNT CKVWDLRQRR CVYTIPAHQN LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP 

       490        500        510        520 
GWSPLKTLAG HEGKVMGLDI SSDGQLIATC SYDRTFKLWM AE 

« Hide

Isoform 2 [UniParc].

Checksum: B4EF92D9E12C9188
Show »

FASTA52158,321

References

« Hide 'large scale' references
[1]"The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p."
Lauber J., Plessel G., Prehn S., Will C.L., Fabrizio P., Groning K., Lane W.S., Luehrmann R.
RNA 3:926-941(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2).
[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] (ISOFORM 1), PROTEIN SEQUENCE OF 28-38; 58-85; 95-106; 193-200 AND 457-472, INTERACTION WITH U4/U5/U6 SNRNPS.
[3]"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] (ISOFORM 2), INTERACTION WITH PRPF3 AND U4/U5/U6 SNRNPS.
[4]"DNA sequence and analysis of human chromosome 9."
Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. expand/collapse author list , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]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 (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] (ISOFORMS 1 AND 2).
Tissue: Colon and Ovary.
[7]"A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor."
Horowitz D.S., Krainer A.R.
Genes Dev. 11:139-151(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH PRPF18.
[8]"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.
[9]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"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].
[11]"Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide."
Reidt U., Wahl M.C., Fasshauer D., Horowitz D.S., Luehrmann R., Ficner R.
J. Mol. Biol. 331:45-56(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 107-137 IN COMPLEX WITH PPIH.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS59142.1. [O43172-2]
CCDS6791.1. [O43172-1]
RefSeqNP_001231855.1. NM_001244926.1. [O43172-2]
NP_004688.2. NM_004697.4. [O43172-1]
UniGeneHs.744014.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1MZWX-ray2.00B107-137[»]
ProteinModelPortalO43172.
SMRO43172. Positions 107-137, 239-519.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114576. 67 interactions.
IntActO43172. 35 interactions.
MINTMINT-270624.
STRING9606.ENSP00000363313.

Chemistry

BindingDBO43172.
ChEMBLCHEMBL1163119.

PTM databases

PhosphoSiteO43172.

Proteomic databases

MaxQBO43172.
PaxDbO43172.
PRIDEO43172.

Protocols and materials databases

DNASU9128.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000374198; ENSP00000363313; ENSG00000136875. [O43172-1]
ENST00000374199; ENSP00000363315; ENSG00000136875. [O43172-2]
GeneID9128.
KEGGhsa:9128.
UCSCuc004bgx.3. human. [O43172-1]

Organism-specific databases

CTD9128.
GeneCardsGC09P116037.
HGNCHGNC:17349. PRPF4.
HPAHPA021794.
HPA022248.
MIM607795. gene.
neXtProtNX_O43172.
PharmGKBPA38448.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG2319.
HOGENOMHOG000157615.
HOVERGENHBG030892.
InParanoidO43172.
KOK12662.
OMAHPSRQAY.
OrthoDBEOG7P5T0Z.
PhylomeDBO43172.
TreeFamTF314922.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.
SignaLinkO43172.

Gene expression databases

ArrayExpressO43172.
BgeeO43172.
CleanExHS_PRPF4.
GenevestigatorO43172.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR020472. G-protein_beta_WD-40_rep.
IPR027106. Prp4.
IPR014906. PRP4-like.
IPR003648. SFM.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PANTHERPTHR19846. PTHR19846. 1 hit.
PfamPF08799. PRP4. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]
PRINTSPR00320. GPROTEINBRPT.
SMARTSM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMSSF50978. SSF50978. 1 hit.
PROSITEPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO43172.
GeneWikiPRPF4.
GenomeRNAi9128.
NextBio34217.
PROO43172.
SOURCESearch...

Entry information

Entry namePRP4_HUMAN
AccessionPrimary (citable) accession number: O43172
Secondary accession number(s): O43445 expand/collapse secondary AC list , O43864, Q5T1M8, Q96DG2, Q96IK4
Entry history
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: May 2, 2002
Last modified: July 9, 2014
This is version 144 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 chromosome 9

Human chromosome 9: entries, gene names and cross-references to MIM