UniProtKB - Q96DI7 (SNR40_HUMAN)
U5 small nuclear ribonucleoprotein 40 kDa protein
SNRNP40
Functioni
GO - Molecular functioni
- RNA binding Source: UniProtKB
GO - Biological processi
- mRNA splicing, via spliceosome Source: Reactome
- RNA processing Source: ProtInc
- RNA splicing Source: ProtInc
- RNA splicing, via transesterification reactions Source: UniProtKB
Keywordsi
Biological process | mRNA processing, mRNA splicing |
Enzyme and pathway databases
PathwayCommonsi | Q96DI7 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
SignaLinki | Q96DI7 |
Names & Taxonomyi
Protein namesi | Recommended name: U5 small nuclear ribonucleoprotein 40 kDa proteinShort 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 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000060688.12 |
HGNCi | HGNC:30857, SNRNP40 |
MIMi | 607797, gene |
neXtProti | NX_Q96DI7 |
Subcellular locationi
Nucleus
- Nucleus 9 Publications
Cytosol
- cytosol Source: HPA
Nucleus
- catalytic step 2 spliceosome Source: UniProtKB
- nuclear speck Source: HPA
- nucleoplasm Source: Reactome
- U2-type catalytic step 2 spliceosome Source: UniProtKB
- U5 snRNP Source: ProtInc
Other locations
- small nucleolar ribonucleoprotein complex Source: UniProtKB
Keywords - Cellular componenti
Nucleus, SpliceosomePathology & Biotechi
Organism-specific databases
DisGeNETi | 9410 |
OpenTargetsi | ENSG00000060688 |
PharmGKBi | PA164726132 |
Miscellaneous databases
Pharosi | Q96DI7, Tbio |
Polymorphism and mutation databases
BioMutai | SNRNP40 |
DMDMi | 67462075 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000051417 | 1 – 357 | U5 small nuclear ribonucleoprotein 40 kDa proteinAdd BLAST | 357 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 18 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 21 | Asymmetric dimethylarginineBy similarity | 1 | |
Cross-linki | 270 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources |
Keywords - PTMi
Isopeptide bond, Methylation, Ubl conjugationProteomic databases
EPDi | Q96DI7 |
jPOSTi | Q96DI7 |
MassIVEi | Q96DI7 |
MaxQBi | Q96DI7 |
PaxDbi | Q96DI7 |
PeptideAtlasi | Q96DI7 |
PRIDEi | Q96DI7 |
ProteomicsDBi | 4882 76291 [Q96DI7-1] |
TopDownProteomicsi | Q96DI7-1 [Q96DI7-1] |
PTM databases
iPTMneti | Q96DI7 |
PhosphoSitePlusi | Q96DI7 |
SwissPalmi | Q96DI7 |
Expressioni
Gene expression databases
Bgeei | ENSG00000060688, Expressed in lung and 213 other tissues |
ExpressionAtlasi | Q96DI7, baseline and differential |
Genevisiblei | Q96DI7, HS |
Organism-specific databases
HPAi | ENSG00000060688, Low tissue specificity |
Interactioni
Subunit structurei
Component of the pre-catalytic and catalytic spliceosome complexes (PubMed:9731529, PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346, PubMed:30315277, PubMed:29360106, PubMed:29301961).
Component of the postcatalytic spliceosome P complex (PubMed:30705154). 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 (PubMed:16723661).
11 PublicationsBinary interactionsi
Hide detailsQ96DI7
With | #Exp. | IntAct |
---|---|---|
DDX23 [Q9BUQ8] | 2 | EBI-538492,EBI-540096 |
EFTUD2 [Q15029] | 2 | EBI-538492,EBI-357897 |
PRPF8 [Q6P2Q9] | 4 | EBI-538492,EBI-538479 |
SNRNP200 [O75643] | 2 | EBI-538492,EBI-1045395 |
Protein-protein interaction databases
BioGRIDi | 114805, 101 interactors |
CORUMi | Q96DI7 |
IntActi | Q96DI7, 58 interactors |
MINTi | Q96DI7 |
STRINGi | 9606.ENSP00000263694 |
Miscellaneous databases
RNActi | Q96DI7, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q96DI7 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Repeati | 64 – 103 | WD 1Add BLAST | 40 | |
Repeati | 107 – 146 | WD 2Add BLAST | 40 | |
Repeati | 149 – 189 | WD 3Add BLAST | 41 | |
Repeati | 191 – 230 | WD 4Add BLAST | 40 | |
Repeati | 233 – 272 | WD 5Add BLAST | 40 | |
Repeati | 283 – 322 | WD 6Add BLAST | 40 | |
Repeati | 325 – 357 | WD 7Add BLAST | 33 |
Keywords - Domaini
Repeat, WD repeatPhylogenomic databases
eggNOGi | KOG0265, Eukaryota |
GeneTreei | ENSGT00940000155058 |
HOGENOMi | CLU_000288_57_2_1 |
InParanoidi | Q96DI7 |
OMAi | NTCYPAR |
OrthoDBi | 606683at2759 |
PhylomeDBi | Q96DI7 |
TreeFami | TF300039 |
Family and domain databases
Gene3Di | 2.130.10.10, 1 hit |
InterProi | View 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 |
Pfami | View protein in Pfam PF00400, WD40, 7 hits |
PRINTSi | PR00320, GPROTEINBRPT |
SMARTi | View protein in SMART SM00320, WD40, 7 hits |
SUPFAMi | SSF50978, SSF50978, 1 hit |
PROSITEi | View protein in PROSITE PS00678, WD_REPEATS_1, 5 hits PS50082, WD_REPEATS_2, 7 hits PS50294, WD_REPEATS_REGION, 1 hit |
s (2+)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketQ9NSS8 | Q9NSS8_HUMAN | U5 small nuclear ribonucleoprotein ... | SNRNP40 DKFZp434D199, WDR57, hCG_20041 | 127 | Annotation score: |
Sequence cautioni
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 3 | E → D in AAC69625 (PubMed:9774689).Curated | 1 | |
Sequence conflicti | 162 – 163 | RG → KS in AAC69625 (PubMed:9774689).Curated | 2 | |
Sequence conflicti | 187 | I → V in AAC64084 (PubMed:9731529).Curated | 1 | |
Sequence conflicti | 343 | I → L (PubMed:9731529).Curated | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_056395 | 343 – 357 | ISASS…MGEIQ → ETGFHRIGQGGHELLTSSNP PASASQSAGITGVSHCAQLQ TVFMWVSMSVSPLLISGESK SNAPFSS in isoform 2. 1 PublicationAdd BLAST | 15 |
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. |
CCDSi | CCDS340.1 [Q96DI7-1] |
RefSeqi | NP_004805.2, NM_004814.2 [Q96DI7-1] |
Genome annotation databases
Ensembli | ENST00000263694; ENSP00000263694; ENSG00000060688 [Q96DI7-1] |
GeneIDi | 9410 |
KEGGi | hsa:9410 |
UCSCi | uc001bso.4, human [Q96DI7-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar 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. |
CCDSi | CCDS340.1 [Q96DI7-1] |
RefSeqi | NP_004805.2, NM_004814.2 [Q96DI7-1] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3JCR | electron microscopy | 7.00 | D | 1-357 | [»] | |
5MQF | electron microscopy | 5.90 | F | 1-357 | [»] | |
5O9Z | electron microscopy | 4.50 | D | 1-357 | [»] | |
5XJC | electron microscopy | 3.60 | E | 1-357 | [»] | |
5YZG | electron microscopy | 4.10 | E | 1-357 | [»] | |
5Z56 | electron microscopy | 5.10 | E | 1-357 | [»] | |
5Z57 | electron microscopy | 6.50 | E | 1-357 | [»] | |
5Z58 | electron microscopy | 4.90 | E | 1-357 | [»] | |
6AH0 | electron microscopy | 5.70 | E | 1-357 | [»] | |
6AHD | electron microscopy | 3.80 | E | 1-357 | [»] | |
6FF7 | electron microscopy | 4.50 | F | 1-357 | [»] | |
6ICZ | electron microscopy | 3.00 | E | 1-357 | [»] | |
6ID0 | electron microscopy | 2.90 | E | 1-357 | [»] | |
6ID1 | electron microscopy | 2.86 | E | 1-357 | [»] | |
6QDV | electron microscopy | 3.30 | N | 51-357 | [»] | |
6QW6 | electron microscopy | 2.92 | 5O | 1-357 | [»] | |
6QX9 | electron microscopy | 3.28 | 5O | 1-357 | [»] | |
SMRi | Q96DI7 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 114805, 101 interactors |
CORUMi | Q96DI7 |
IntActi | Q96DI7, 58 interactors |
MINTi | Q96DI7 |
STRINGi | 9606.ENSP00000263694 |
PTM databases
iPTMneti | Q96DI7 |
PhosphoSitePlusi | Q96DI7 |
SwissPalmi | Q96DI7 |
Polymorphism and mutation databases
BioMutai | SNRNP40 |
DMDMi | 67462075 |
Proteomic databases
EPDi | Q96DI7 |
jPOSTi | Q96DI7 |
MassIVEi | Q96DI7 |
MaxQBi | Q96DI7 |
PaxDbi | Q96DI7 |
PeptideAtlasi | Q96DI7 |
PRIDEi | Q96DI7 |
ProteomicsDBi | 4882 76291 [Q96DI7-1] |
TopDownProteomicsi | Q96DI7-1 [Q96DI7-1] |
Protocols and materials databases
Antibodypediai | 16742, 123 antibodies |
DNASUi | 9410 |
Genome annotation databases
Ensembli | ENST00000263694; ENSP00000263694; ENSG00000060688 [Q96DI7-1] |
GeneIDi | 9410 |
KEGGi | hsa:9410 |
UCSCi | uc001bso.4, human [Q96DI7-1] |
Organism-specific databases
CTDi | 9410 |
DisGeNETi | 9410 |
EuPathDBi | HostDB:ENSG00000060688.12 |
GeneCardsi | SNRNP40 |
HGNCi | HGNC:30857, SNRNP40 |
HPAi | ENSG00000060688, Low tissue specificity |
MIMi | 607797, gene |
neXtProti | NX_Q96DI7 |
OpenTargetsi | ENSG00000060688 |
PharmGKBi | PA164726132 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG0265, Eukaryota |
GeneTreei | ENSGT00940000155058 |
HOGENOMi | CLU_000288_57_2_1 |
InParanoidi | Q96DI7 |
OMAi | NTCYPAR |
OrthoDBi | 606683at2759 |
PhylomeDBi | Q96DI7 |
TreeFami | TF300039 |
Enzyme and pathway databases
PathwayCommonsi | Q96DI7 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway R-HSA-72165, mRNA Splicing - Minor Pathway |
SignaLinki | Q96DI7 |
Miscellaneous databases
BioGRID-ORCSi | 9410, 574 hits in 859 CRISPR screens |
ChiTaRSi | SNRNP40, human |
GeneWikii | WDR57 |
GenomeRNAii | 9410 |
Pharosi | Q96DI7, Tbio |
PROi | PR:Q96DI7 |
RNActi | Q96DI7, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000060688, Expressed in lung and 213 other tissues |
ExpressionAtlasi | Q96DI7, baseline and differential |
Genevisiblei | Q96DI7, HS |
Family and domain databases
Gene3Di | 2.130.10.10, 1 hit |
InterProi | View 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 |
Pfami | View protein in Pfam PF00400, WD40, 7 hits |
PRINTSi | PR00320, GPROTEINBRPT |
SMARTi | View protein in SMART SM00320, WD40, 7 hits |
SUPFAMi | SSF50978, SSF50978, 1 hit |
PROSITEi | View protein in PROSITE PS00678, WD_REPEATS_1, 5 hits PS50082, WD_REPEATS_2, 7 hits PS50294, WD_REPEATS_REGION, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | SNR40_HUMAN | |
Accessioni | Q96DI7Primary (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: | December 2, 2020 | |
This is version 185 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | 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. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - Human chromosome 1
Human chromosome 1: entries, gene names and cross-references to MIM