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O43172

- PRP4_HUMAN

UniProt

O43172 - PRP4_HUMAN

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Protein

U4/U6 small nuclear ribonucleoprotein Prp4

Gene

PRPF4

Organism
Homo sapiens (Human)
Status
Reviewed - 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.

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA splicing, via spliceosome Source: BHF-UCL
  3. RNA processing Source: ProtInc
  4. RNA splicing Source: Reactome
  5. RNA splicing, via transesterification reactions Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiREACT_467. 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
ProteomesiUP000005640: Chromosome 9

Organism-specific databases

HGNCiHGNC:17349. PRPF4.

Subcellular locationi

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

GO - Cellular componenti

  1. Cajal body Source: BHF-UCL
  2. nucleoplasm Source: Reactome
  3. nucleus Source: HPA
  4. spliceosomal complex Source: UniProtKB
  5. U4/U6 snRNP Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

Orphaneti791. Retinitis pigmentosa.
PharmGKBiPA38448.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 522522U4/U6 small nuclear ribonucleoprotein Prp4PRO_0000051149Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei27 – 271N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiO43172.
PaxDbiO43172.
PRIDEiO43172.

PTM databases

PhosphoSiteiO43172.

Expressioni

Gene expression databases

BgeeiO43172.
CleanExiHS_PRPF4.
ExpressionAtlasiO43172. baseline and differential.
GenevestigatoriO43172.

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, NHP2L1, EFTUD2, SART1 and USP39.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
GPKOWQ929172EBI-718395,EBI-746309
PPIHO434472EBI-718395,EBI-1055615

Protein-protein interaction databases

BioGridi114576. 72 interactions.
IntActiO43172. 35 interactions.
MINTiMINT-270624.
STRINGi9606.ENSP00000363313.

Structurei

Secondary structure

1
522
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi108 – 1147
Beta strandi119 – 1213
Helixi126 – 13611

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MZWX-ray2.00B107-137[»]
ProteinModelPortaliO43172.
SMRiO43172. Positions 107-137, 239-519.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43172.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati229 – 26840WD 1Add
BLAST
Repeati271 – 31848WD 2Add
BLAST
Repeati321 – 36040WD 3Add
BLAST
Repeati363 – 40240WD 4Add
BLAST
Repeati405 – 44440WD 5Add
BLAST
Repeati447 – 48741WD 6Add
BLAST
Repeati490 – 52132WD 7Add
BLAST

Sequence similaritiesi

Contains 7 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiCOG2319.
GeneTreeiENSGT00760000118869.
HOGENOMiHOG000157615.
HOVERGENiHBG030892.
InParanoidiO43172.
KOiK12662.
OMAiHPSRQAY.
OrthoDBiEOG7P5T0Z.
PhylomeDBiO43172.
TreeFamiTF314922.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. 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]
PANTHERiPTHR19846. PTHR19846. 1 hit.
PfamiPF08799. PRP4. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti78 – 10326HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261. (PubMed:9328476)CuratedAdd
BLAST
Sequence conflicti78 – 781H → R in AAC51925. (PubMed:9404889)Curated
Sequence conflicti86 – 861V → L in AAB87640. (PubMed:9257651)Curated
Sequence conflicti134 – 1341R → K in AAB87640. (PubMed:9257651)Curated
Sequence conflicti141 – 1411G → D in AAB87640. (PubMed:9257651)Curated
Sequence conflicti176 – 1761Missing in AAC02261. (PubMed:9328476)Curated
Sequence conflicti275 – 2828NVGAIVFH → KKEQLHSI in AAC02261. (PubMed:9328476)Curated
Sequence conflicti405 – 4051G → D in AAB87640. (PubMed:9257651)Curated
Sequence conflicti447 – 4471A → P in AAB87640. (PubMed:9257651)Curated
Sequence conflicti510 – 5101C → Y in AAB87640. (PubMed:9257651)Curated
Sequence conflicti521 – 5211A → L in AAB87640. (PubMed:9257651)Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei10 – 101Missing in isoform 2. 2 PublicationsVSP_006785

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
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.3. human. [O43172-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS59142.1. [O43172-2 ]
CCDS6791.1. [O43172-1 ]
RefSeqi NP_001231855.1. NM_001244926.1. [O43172-2 ]
NP_004688.2. NM_004697.4. [O43172-1 ]
UniGenei Hs.744014.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1MZW X-ray 2.00 B 107-137 [» ]
ProteinModelPortali O43172.
SMRi O43172. Positions 107-137, 239-519.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 114576. 72 interactions.
IntActi O43172. 35 interactions.
MINTi MINT-270624.
STRINGi 9606.ENSP00000363313.

Chemistry

BindingDBi O43172.
ChEMBLi CHEMBL1163119.

PTM databases

PhosphoSitei O43172.

Proteomic databases

MaxQBi O43172.
PaxDbi O43172.
PRIDEi O43172.

Protocols and materials databases

DNASUi 9128.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000374198 ; ENSP00000363313 ; ENSG00000136875 . [O43172-1 ]
ENST00000374199 ; ENSP00000363315 ; ENSG00000136875 . [O43172-2 ]
GeneIDi 9128.
KEGGi hsa:9128.
UCSCi uc004bgx.3. human. [O43172-1 ]

Organism-specific databases

CTDi 9128.
GeneCardsi GC09P116037.
HGNCi HGNC:17349. PRPF4.
HPAi HPA021794.
HPA022248.
MIMi 607795. gene.
neXtProti NX_O43172.
Orphaneti 791. Retinitis pigmentosa.
PharmGKBi PA38448.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG2319.
GeneTreei ENSGT00760000118869.
HOGENOMi HOG000157615.
HOVERGENi HBG030892.
InParanoidi O43172.
KOi K12662.
OMAi HPSRQAY.
OrthoDBi EOG7P5T0Z.
PhylomeDBi O43172.
TreeFami TF314922.

Enzyme and pathway databases

Reactomei REACT_467. mRNA Splicing - Major Pathway.
SignaLinki O43172.

Miscellaneous databases

EvolutionaryTracei O43172.
GeneWikii PRPF4.
GenomeRNAii 9128.
NextBioi 34217.
PROi O43172.
SOURCEi Search...

Gene expression databases

Bgeei O43172.
CleanExi HS_PRPF4.
ExpressionAtlasi O43172. baseline and differential.
Genevestigatori O43172.

Family and domain databases

Gene3Di 2.130.10.10. 1 hit.
InterProi IPR020472. 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 ]
PANTHERi PTHR19846. PTHR19846. 1 hit.
Pfami PF08799. PRP4. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view ]
PRINTSi PR00320. GPROTEINBRPT.
SMARTi SM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view ]
SUPFAMi SSF50978. SSF50978. 1 hit.
PROSITEi PS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. 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.

Entry informationi

Entry nameiPRP4_HUMAN
AccessioniPrimary (citable) accession number: O43172
Secondary accession number(s): O43445
, O43864, Q5T1M8, Q96DG2, Q96IK4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 2, 2002
Last sequence update: May 2, 2002
Last modified: October 29, 2014
This is version 147 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 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3