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Q96DI7

- SNR40_HUMAN

UniProt

Q96DI7 - SNR40_HUMAN

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Protein

U5 small nuclear ribonucleoprotein 40 kDa protein

Gene

SNRNP40

Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  1. gene expression Source: Reactome
  2. mRNA splicing, via spliceosome Source: UniProtKB
  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_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: Chromosome 1

Organism-specific databases

HGNCiHGNC:30857. SNRNP40.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. catalytic step 2 spliceosome Source: UniProtKB
  2. cytoplasm Source: HPA
  3. nucleoplasm Source: Reactome
  4. nucleus Source: HPA
  5. small nucleolar ribonucleoprotein complex Source: UniProtKB
  6. U5 snRNP Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA164726132.

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.
GenevestigatoriQ96DI7.

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. 58 interactions.
IntActiQ96DI7. 21 interactions.
MINTiMINT-1410013.
STRINGi9606.ENSP00000263694.

Structurei

3D structure databases

ProteinModelPortaliQ96DI7.
SMRiQ96DI7. Positions 9-349.
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.
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. Align

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]

Polymorphism databases

DMDMi67462075.

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.
CCDSi CCDS340.1. [Q96DI7-1 ]
RefSeqi NP_004805.2. NM_004814.2. [Q96DI7-1 ]
UniGenei Hs.33962.

3D structure databases

ProteinModelPortali Q96DI7.
SMRi Q96DI7. Positions 9-349.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 114805. 58 interactions.
IntActi Q96DI7. 21 interactions.
MINTi MINT-1410013.
STRINGi 9606.ENSP00000263694.

PTM databases

PhosphoSitei Q96DI7.

Polymorphism databases

DMDMi 67462075.

Proteomic databases

MaxQBi Q96DI7.
PaxDbi Q96DI7.
PeptideAtlasi Q96DI7.
PRIDEi Q96DI7.

Protocols and materials databases

DNASUi 9410.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000263694 ; ENSP00000263694 ; ENSG00000060688 . [Q96DI7-1 ]
GeneIDi 9410.
KEGGi hsa:9410.
UCSCi uc001bso.3. human. [Q96DI7-1 ]

Organism-specific databases

CTDi 9410.
GeneCardsi GC01M031732.
HGNCi HGNC:30857. SNRNP40.
HPAi HPA026527.
HPA027345.
MIMi 607797. gene.
neXtProti NX_Q96DI7.
PharmGKBi PA164726132.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG2319.
GeneTreei ENSGT00760000118869.
HOGENOMi HOG000091644.
HOVERGENi HBG105197.
InParanoidi Q96DI7.
KOi K12857.
OrthoDBi EOG7992QT.
PhylomeDBi Q96DI7.
TreeFami TF300039.

Enzyme and pathway databases

Reactomei REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.
SignaLinki Q96DI7.

Miscellaneous databases

ChiTaRSi SNRNP40. human.
GeneWikii WDR57.
GenomeRNAii 9410.
NextBioi 35252.
PROi Q96DI7.
SOURCEi Search...

Gene expression databases

Bgeei Q96DI7.
CleanExi HS_SNRNP40.
ExpressionAtlasi Q96DI7. baseline and differential.
Genevestigatori Q96DI7.

Family and domain databases

Gene3Di 2.130.10.10. 1 hit.
InterProi IPR020472. 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 ]
Pfami PF00400. WD40. 7 hits.
[Graphical view ]
PRINTSi PR00320. GPROTEINBRPT.
SMARTi SM00320. WD40. 7 hits.
[Graphical view ]
SUPFAMi SSF50978. SSF50978. 1 hit.
PROSITEi PS00678. WD_REPEATS_1. 5 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: November 26, 2014
This is version 130 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