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Protein

U5 small nuclear ribonucleoprotein 40 kDa protein

Gene

SNRNP40

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs.1 Publication

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • gene expression Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • RNA processing Source: ProtInc
  • RNA splicing Source: Reactome
  • RNA splicing, via transesterification reactions Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.
SignaLinkiQ96DI7.

Names & Taxonomyi

Protein namesi
Recommended name:
U5 small nuclear ribonucleoprotein 40 kDa protein
Short name:
U5 snRNP 40 kDa protein
Short name:
U5-40K
Alternative name(s):
38 kDa-splicing factor
Prp8-binding protein
Short name:
hPRP8BP
U5 snRNP-specific 40 kDa protein
WD repeat-containing protein 57
Gene namesi
Name:SNRNP40
Synonyms:PRP8BP, SFP38, WDR57
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:30857. SNRNP40.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytoplasm Source: HPA
  • nucleoplasm Source: HPA
  • small nucleolar ribonucleoprotein complex Source: UniProtKB
  • U5 snRNP Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164726132.

Polymorphism and mutation databases

BioMutaiSNRNP40.
DMDMi67462075.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 357357U5 small nuclear ribonucleoprotein 40 kDa proteinPRO_0000051417Add
BLAST

Proteomic databases

MaxQBiQ96DI7.
PaxDbiQ96DI7.
PeptideAtlasiQ96DI7.
PRIDEiQ96DI7.

PTM databases

PhosphoSiteiQ96DI7.

Expressioni

Gene expression databases

BgeeiQ96DI7.
CleanExiHS_SNRNP40.
ExpressionAtlasiQ96DI7. baseline and differential.
GenevisibleiQ96DI7. HS.

Organism-specific databases

HPAiHPA026527.
HPA027345.

Interactioni

Subunit structurei

Identified in the spliceosome C complex. Part of the U5 snRNP complex. Interacts with PRPF8. 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 USP39.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PRPF8Q6P2Q93EBI-538492,EBI-538479

Protein-protein interaction databases

BioGridi114805. 61 interactions.
IntActiQ96DI7. 21 interactions.
MINTiMINT-1410013.
STRINGi9606.ENSP00000263694.

Structurei

3D structure databases

ProteinModelPortaliQ96DI7.
SMRiQ96DI7. Positions 40-353.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati64 – 10340WD 1Add
BLAST
Repeati107 – 14640WD 2Add
BLAST
Repeati149 – 18941WD 3Add
BLAST
Repeati191 – 23040WD 4Add
BLAST
Repeati233 – 27240WD 5Add
BLAST
Repeati283 – 32240WD 6Add
BLAST
Repeati325 – 35733WD 7Add
BLAST

Sequence similaritiesi

Contains 7 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiCOG2319.
GeneTreeiENSGT00760000118869.
HOGENOMiHOG000091644.
HOVERGENiHBG105197.
InParanoidiQ96DI7.
KOiK12857.
OMAiEEVINTM.
OrthoDBiEOG7992QT.
PhylomeDBiQ96DI7.
TreeFamiTF300039.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 7 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 5 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 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: Q96DI7-1) [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
MIEQQKRKGP ELPLVPVKRQ RHELLLGAGS GPGAGQQQAT PGALLQAGPP
60 70 80 90 100
RCSSLQAPIM LLSGHEGEVY CCKFHPNGST LASAGFDRLI LLWNVYGDCD
110 120 130 140 150
NYATLKGHSG AVMELHYNTD GSMLFSASTD KTVAVWDSET GERVKRLKGH
160 170 180 190 200
TSFVNSCYPA RRGPQLVCTG SDDGTVKLWD IRKKAAIQTF QNTYQVLAVT
210 220 230 240 250
FNDTSDQIIS GGIDNDIKVW DLRQNKLTYT MRGHADSVTG LSLSSEGSYL
260 270 280 290 300
LSNAMDNTVR VWDVRPFAPK ERCVKIFQGN VHNFEKNLLR CSWSPDGSKI
310 320 330 340 350
AAGSADRFVY VWDTTSRRIL YKLPGHAGSI NEVAFHPDEP IIISASSDKR

LYMGEIQ
Length:357
Mass (Da):39,311
Last modified:December 1, 2001 - v1
Checksum:iDE8CADEB098E560C
GO
Isoform 2 (identifier: Q96DI7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     343-357: ISASSDKRLYMGEIQ → ETGFHRIGQG...ESKSNAPFSS

Note: No experimental confirmation available.
Show »
Length:409
Mass (Da):44,516
Checksum:i06BC77CD284995FF
GO

Sequence cautioni

The sequence AAC64084.1 differs from that shown. Reason: Frameshift at position 319. An insertion/deletion of a short nucleotide stretch in its cDNA resulting in a frameshift.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti3 – 31E → D in AAC69625 (PubMed:9774689).Curated
Sequence conflicti162 – 1632RG → KS in AAC69625 (PubMed:9774689).Curated
Sequence conflicti187 – 1871I → V in AAC64084 (PubMed:9731529).Curated
Sequence conflicti343 – 3431I → L (PubMed:9731529).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei343 – 35715ISASS…MGEIQ → ETGFHRIGQGGHELLTSSNP PASASQSAGITGVSHCAQLQ TVFMWVSMSVSPLLISGESK SNAPFSS in isoform 2. 1 PublicationVSP_056395Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF090988 mRNA. Translation: AAC69625.1.
AK298823 mRNA. Translation: BAG60953.1.
AL451070, AC114495 Genomic DNA. Translation: CAH71848.1.
BC001494 mRNA. Translation: AAH01494.1.
AF083383 mRNA. Translation: AAC64084.1. Sequence problems.
CCDSiCCDS340.1. [Q96DI7-1]
RefSeqiNP_004805.2. NM_004814.2. [Q96DI7-1]
UniGeneiHs.33962.

Genome annotation databases

EnsembliENST00000263694; ENSP00000263694; ENSG00000060688. [Q96DI7-1]
GeneIDi9410.
KEGGihsa:9410.
UCSCiuc001bso.3. human. [Q96DI7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF090988 mRNA. Translation: AAC69625.1.
AK298823 mRNA. Translation: BAG60953.1.
AL451070, AC114495 Genomic DNA. Translation: CAH71848.1.
BC001494 mRNA. Translation: AAH01494.1.
AF083383 mRNA. Translation: AAC64084.1. Sequence problems.
CCDSiCCDS340.1. [Q96DI7-1]
RefSeqiNP_004805.2. NM_004814.2. [Q96DI7-1]
UniGeneiHs.33962.

3D structure databases

ProteinModelPortaliQ96DI7.
SMRiQ96DI7. Positions 40-353.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114805. 61 interactions.
IntActiQ96DI7. 21 interactions.
MINTiMINT-1410013.
STRINGi9606.ENSP00000263694.

PTM databases

PhosphoSiteiQ96DI7.

Polymorphism and mutation databases

BioMutaiSNRNP40.
DMDMi67462075.

Proteomic databases

MaxQBiQ96DI7.
PaxDbiQ96DI7.
PeptideAtlasiQ96DI7.
PRIDEiQ96DI7.

Protocols and materials databases

DNASUi9410.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263694; ENSP00000263694; ENSG00000060688. [Q96DI7-1]
GeneIDi9410.
KEGGihsa:9410.
UCSCiuc001bso.3. human. [Q96DI7-1]

Organism-specific databases

CTDi9410.
GeneCardsiGC01M031732.
HGNCiHGNC:30857. SNRNP40.
HPAiHPA026527.
HPA027345.
MIMi607797. gene.
neXtProtiNX_Q96DI7.
PharmGKBiPA164726132.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG2319.
GeneTreeiENSGT00760000118869.
HOGENOMiHOG000091644.
HOVERGENiHBG105197.
InParanoidiQ96DI7.
KOiK12857.
OMAiEEVINTM.
OrthoDBiEOG7992QT.
PhylomeDBiQ96DI7.
TreeFamiTF300039.

Enzyme and pathway databases

ReactomeiREACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.
SignaLinkiQ96DI7.

Miscellaneous databases

ChiTaRSiSNRNP40. human.
GeneWikiiWDR57.
GenomeRNAii9410.
NextBioi35252.
PROiQ96DI7.
SOURCEiSearch...

Gene expression databases

BgeeiQ96DI7.
CleanExiHS_SNRNP40.
ExpressionAtlasiQ96DI7. baseline and differential.
GenevisibleiQ96DI7. HS.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamiPF00400. WD40. 7 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS00678. WD_REPEATS_1. 5 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein."
    Achsel T., Ahrens K., Brahms H., Teigelkamp S., Luehrmann R.
    Mol. Cell. Biol. 18:6756-6766(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, IDENTIFICATION IN U5 SNRP COMPLEX, INTERACTION WITH PRPF8.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  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.
    , 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. "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] (ISOFORM 1).
    Tissue: Placenta.
  5. "Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex."
    Neubauer G., King A., Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A.I., Mann M.
    Nat. Genet. 20:46-50(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-357 (ISOFORM 1), IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, IDENTIFICATION IN SPLICEOSOMAL COMPLEX.
  6. "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
    Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
    RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOME C COMPLEX.
  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. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiSNR40_HUMAN
AccessioniPrimary (citable) accession number: Q96DI7
Secondary accession number(s): B4DQJ1, O75938, O95320
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: December 1, 2001
Last modified: June 24, 2015
This is version 136 of the entry and version 1 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: 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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.