Q96DI7 (SNR40_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	SNRNP40
Synonyms:	PRP8BP, SFP38, WDR57

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	357 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1
Subunit structure	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. Ref.1 Ref.4 Ref.5 Ref.6
Subcellular location	Nucleus Ref.4.
Sequence similarities	Contains 7 WD repeats.
Sequence caution	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.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Repeat WD repeat
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	mRNA splicing, via spliceosome Inferred by curator Ref.5. Source: UniProtKB
Cellular_component	U5 snRNP Traceable author statement Ref.1. Source: ProtInc catalytic step 2 spliceosome Inferred from direct assay Ref.5. Source: UniProtKB cytoplasm Inferred from direct assay. Source: HPA nucleoplasm Traceable author statement. Source: Reactome small nucleolar ribonucleoprotein complex Non-traceable author statement Ref.1. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
PRPF8	Q6P2Q9	3	EBI-538492,EBI-538479

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 357	357	U5 small nuclear ribonucleoprotein 40 kDa protein		PRO_0000051417
Regions
	Repeat	64 – 103	40	WD 1
	Repeat	107 – 146	40	WD 2
	Repeat	149 – 189	41	WD 3
	Repeat	191 – 230	40	WD 4
	Repeat	233 – 272	40	WD 5
	Repeat	283 – 322	40	WD 6
	Repeat	325 – 357	33	WD 7
Experimental info
	Sequence conflict	3	1	E → D in AAC69625. Ref.1
	Sequence conflict	162 – 163	2	RG → KS in AAC69625. Ref.1
	Sequence conflict	187	1	I → V in AAC64084. Ref.4
	Sequence conflict	343	1	I → L Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Q96DI7 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: DE8CADEB098E560C	FASTA	357	39,311
	10 20 30 40 50 60 MIEQQKRKGP ELPLVPVKRQ RHELLLGAGS GPGAGQQQAT PGALLQAGPP RCSSLQAPIM 70 80 90 100 110 120 LLSGHEGEVY CCKFHPNGST LASAGFDRLI LLWNVYGDCD NYATLKGHSG AVMELHYNTD 130 140 150 160 170 180 GSMLFSASTD KTVAVWDSET GERVKRLKGH TSFVNSCYPA RRGPQLVCTG SDDGTVKLWD 190 200 210 220 230 240 IRKKAAIQTF QNTYQVLAVT FNDTSDQIIS GGIDNDIKVW DLRQNKLTYT MRGHADSVTG 250 260 270 280 290 300 LSLSSEGSYL LSNAMDNTVR VWDVRPFAPK ERCVKIFQGN VHNFEKNLLR CSWSPDGSKI 310 320 330 340 350 AAGSADRFVY VWDTTSRRIL YKLPGHAGSI NEVAFHPDEP IIISASSDKR LYMGEIQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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], FUNCTION, IDENTIFICATION IN U5 SNRP COMPLEX, INTERACTION WITH PRPF8.
[2]	"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].
[3]	"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: Placenta.
[4]	"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, IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, IDENTIFICATION IN SPLICEOSOME COMPLEX.
[5]	"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.
[6]	"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.
[7]	"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].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF090988 mRNA. Translation: AAC69625.1. AL451070, AC114495 Genomic DNA. Translation: CAH71848.1. BC001494 mRNA. Translation: AAH01494.1. AF083383 mRNA. Translation: AAC64084.1. Sequence problems.
IPI	IPI00940685.
RefSeq	NP_004805.2. NM_004814.2.
UniGene	Hs.33962.
3D structure databases
ProteinModelPortal	Q96DI7.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q96DI7. 16 interactions.
MINT	MINT-1410013.
STRING	9606.ENSP00000263694.
PTM databases
PhosphoSite	Q96DI7.
Polymorphism databases
DMDM	67462075.
Proteomic databases
PaxDb	Q96DI7.
PeptideAtlas	Q96DI7.
PRIDE	Q96DI7.
Protocols and materials databases
DNASU	9410.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000263694; ENSP00000263694; ENSG00000060688.
GeneID	9410.
KEGG	hsa:9410.
UCSC	uc001bso.3. human.
Organism-specific databases
CTD	9410.
GeneCards	GC01M031732.
HGNC	HGNC:30857. SNRNP40.
HPA	HPA026527. HPA027345.
MIM	607797. gene.
neXtProt	NX_Q96DI7.
PharmGKB	PA164726132.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG2319.
HOGENOM	HOG000091644.
HOVERGEN	HBG105197.
InParanoid	Q96DI7.
KO	K12857.
OrthoDB	EOG4JM7Q0.
PhylomeDB	Q96DI7.
Enzyme and pathway databases
Reactome	REACT_1675. mRNA Processing. REACT_71. Gene Expression.
Gene expression databases
ArrayExpress	Q96DI7.
Bgee	Q96DI7.
CleanEx	HS_SNRNP40.
Genevestigator	Q96DI7.
GermOnline	ENSG00000060688. Homo sapiens.
Family and domain databases
Gene3D	2.130.10.10. 1 hit.
InterPro	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]
Pfam	PF00400. WD40. 7 hits. [Graphical view]
PRINTS	PR00320. GPROTEINBRPT.
SMART	SM00320. WD40. 7 hits. [Graphical view]
SUPFAM	SSF50978. WD40_like. 1 hit.
PROSITE	PS00678. WD_REPEATS_1. 5 hits. PS50082. WD_REPEATS_2. 7 hits. PS50294. WD_REPEATS_REGION. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	SNRNP40. human.
GenomeRNAi	9410.
NextBio	35252.
SOURCE	Search...

Entry information

Entry name

SNR40_HUMAN

Accession

Primary (citable) accession number: Q96DI7
Secondary accession number(s): O75938, O95320

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 114 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.