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Protein

U5 small nuclear ribonucleoprotein 40 kDa protein

Gene

SNRNP40

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor 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
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000060688.12
HGNCiHGNC:30857 SNRNP40
MIMi607797 gene
neXtProtiNX_Q96DI7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi9410
OpenTargetsiENSG00000060688
PharmGKBiPA164726132

Polymorphism and mutation databases

BioMutaiSNRNP40
DMDMi67462075

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000514171 – 357U5 small nuclear ribonucleoprotein 40 kDa proteinAdd BLAST357

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki18Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei21Asymmetric dimethylarginineBy similarity1
Cross-linki270Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

EPDiQ96DI7
MaxQBiQ96DI7
PaxDbiQ96DI7
PeptideAtlasiQ96DI7
PRIDEiQ96DI7
ProteomicsDBi76291
TopDownProteomicsiQ96DI7-1 [Q96DI7-1]

PTM databases

iPTMnetiQ96DI7
PhosphoSitePlusiQ96DI7
SwissPalmiQ96DI7

Expressioni

Gene expression databases

BgeeiENSG00000060688 Expressed in 202 organ(s), highest expression level in lung
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, SNU13, EFTUD2, SART1 and USP39.4 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi114805, 80 interactors
CORUMiQ96DI7
IntActiQ96DI7, 30 interactors
MINTiQ96DI7
STRINGi9606.ENSP00000263694

Structurei

3D structure databases

ProteinModelPortaliQ96DI7
SMRiQ96DI7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati64 – 103WD 1Add BLAST40
Repeati107 – 146WD 2Add BLAST40
Repeati149 – 189WD 3Add BLAST41
Repeati191 – 230WD 4Add BLAST40
Repeati233 – 272WD 5Add BLAST40
Repeati283 – 322WD 6Add BLAST40
Repeati325 – 357WD 7Add BLAST33

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0265 Eukaryota
ENOG410XSEW LUCA
GeneTreeiENSGT00810000125363
HOGENOMiHOG000091644
HOVERGENiHBG105197
InParanoidiQ96DI7
KOiK12857
OMAiGDCENYG
OrthoDBiEOG091G0DR4
PhylomeDBiQ96DI7
TreeFamiTF300039

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PfamiView protein in Pfam
PF00400 WD40, 7 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00320 WD40, 7 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS00678 WD_REPEATS_1, 5 hits
PS50082 WD_REPEATS_2, 7 hits
PS50294 WD_REPEATS_REGION, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 1 potential isoform that is computationally mapped.iShow all

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q9NSS8Q9NSS8_HUMAN
U5 small nuclear ribonucleoprotein ...
SNRNP40 DKFZp434D199, WDR57, hCG_20041
127Annotation score:

Sequence cautioni

The sequence AAC64084 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)DescriptionActionsGraphical viewLength
Sequence conflicti3E → D in AAC69625 (PubMed:9774689).Curated1
Sequence conflicti162 – 163RG → KS in AAC69625 (PubMed:9774689).Curated2
Sequence conflicti187I → V in AAC64084 (PubMed:9731529).Curated1
Sequence conflicti343I → L (PubMed:9731529).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_056395343 – 357ISASS…MGEIQ → ETGFHRIGQGGHELLTSSNP PASASQSAGITGVSHCAQLQ TVFMWVSMSVSPLLISGESK SNAPFSS in isoform 2. 1 PublicationAdd BLAST15

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF090988 mRNA Translation: AAC69625.1
AK298823 mRNA Translation: BAG60953.1
AC114495 Genomic DNA No translation available.
AL451070 Genomic DNA No translation available.
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.4 human [Q96DI7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF090988 mRNA Translation: AAC69625.1
AK298823 mRNA Translation: BAG60953.1
AC114495 Genomic DNA No translation available.
AL451070 Genomic DNA No translation available.
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.00D1-357[»]
5MQFelectron microscopy5.90F1-357[»]
5O9Zelectron microscopy4.50D1-357[»]
5XJCelectron microscopy3.60E1-357[»]
ProteinModelPortaliQ96DI7
SMRiQ96DI7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114805, 80 interactors
CORUMiQ96DI7
IntActiQ96DI7, 30 interactors
MINTiQ96DI7
STRINGi9606.ENSP00000263694

PTM databases

iPTMnetiQ96DI7
PhosphoSitePlusiQ96DI7
SwissPalmiQ96DI7

Polymorphism and mutation databases

BioMutaiSNRNP40
DMDMi67462075

Proteomic databases

EPDiQ96DI7
MaxQBiQ96DI7
PaxDbiQ96DI7
PeptideAtlasiQ96DI7
PRIDEiQ96DI7
ProteomicsDBi76291
TopDownProteomicsiQ96DI7-1 [Q96DI7-1]

Protocols and materials databases

DNASUi9410
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000263694; ENSP00000263694; ENSG00000060688 [Q96DI7-1]
GeneIDi9410
KEGGihsa:9410
UCSCiuc001bso.4 human [Q96DI7-1]

Organism-specific databases

CTDi9410
DisGeNETi9410
EuPathDBiHostDB:ENSG00000060688.12
GeneCardsiSNRNP40
HGNCiHGNC:30857 SNRNP40
HPAiHPA026527
HPA027345
MIMi607797 gene
neXtProtiNX_Q96DI7
OpenTargetsiENSG00000060688
PharmGKBiPA164726132
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0265 Eukaryota
ENOG410XSEW LUCA
GeneTreeiENSGT00810000125363
HOGENOMiHOG000091644
HOVERGENiHBG105197
InParanoidiQ96DI7
KOiK12857
OMAiGDCENYG
OrthoDBiEOG091G0DR4
PhylomeDBiQ96DI7
TreeFamiTF300039

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
SignaLinkiQ96DI7

Miscellaneous databases

ChiTaRSiSNRNP40 human
GeneWikiiWDR57
GenomeRNAii9410
PROiPR:Q96DI7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000060688 Expressed in 202 organ(s), highest expression level in lung
CleanExiHS_SNRNP40
ExpressionAtlasiQ96DI7 baseline and differential
GenevisibleiQ96DI7 HS

Family and domain databases

Gene3Di2.130.10.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
PfamiView protein in Pfam
PF00400 WD40, 7 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00320 WD40, 7 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS00678 WD_REPEATS_1, 5 hits
PS50082 WD_REPEATS_2, 7 hits
PS50294 WD_REPEATS_REGION, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSNR40_HUMAN
AccessioniPrimary (citable) accession number: Q96DI7
Secondary accession number(s): B4DQJ1, O75938, O95320
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: December 1, 2001
Last modified: September 12, 2018
This is version 167 of the entry and version 1 of the sequence. See 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, Reference proteome
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Main funding by: National Institutes of Health

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