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Interaction information
Interaction summary
Short label
PRP24-LSM8
Source database
BioGRID ID
Type
physical association (MI:0915)
Term ID
Name
physical association
Definition
Molecules that are experimentally shown to belong to the same functional or structural complex.
Is-a
1 item(s)
MI:0914
association
Date modified
2011-03-19 23:40:59 JST
Protein information
Short label
PRP24
Gene
PRP24 (Prp24p)
GeneID
Official symbol
PRP24
Description
Prp24p
Other names
1 designation(s)
Splicing factor that reanneals U4 and U6 snRNPs during spliceosome recycling
Ontologies
11 ontology(s)
Functions
5 function(s)
GO:0000166
[IEA] nucleotide binding
Evidence
IEA Term ID
Name
nucleotide binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose moiety.
Is-a
1 item(s)
GO:0005488
binding
GO:0003676
[IEA] nucleic acid binding
Evidence
IEA Term ID
Name
nucleic acid binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with any nucleic acid.
Is-a
1 item(s)
GO:0005488
binding
GO:0003723
[IEA] RNA binding
Evidence
IEA Term ID
Name
RNA binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
Is-a
1 item(s)
GO:0003676
nucleic acid binding
GO:0017069
[IPI] snRNA binding
Evidence
IPI References
1 reference(s)
PubMed
KARADUMAN, Ramazan, et al. , J. Mol. Biol. 2006 Mar;356(5):1248-62
PMID
Title
RNA structure and RNA-protein interactions in purified yeast U6 snRNPs.
Authors
KARADUMAN, Ramazan, et al.
KARADUMAN, Ramazan
FABRIZIO, Patrizia
HARTMUTH, Klaus
URLAUB, Henning
LüHRMANN, Reinhard
Citation
J. Mol. Biol. 2006 Mar;356(5):1248-62
Term ID
Name
snRNA binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
Synonyms
1 synonym(s)
small nuclear RNA binding
Is-a
1 item(s)
GO:0003723
RNA binding
GO:0017070
[IDA] U6 snRNA binding
Evidence
IDA Term ID
Name
U6 snRNA binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with the U6 small nuclear RNA (U6 snRNA).
Is-a
1 item(s)
GO:0017069
snRNA binding
Processes
4 process(s)
GO:0000244
[IDA] assembly of spliceosomal tri-snRNP
Evidence
IDA References
1 reference(s)
PubMed
RAGHUNATHAN, P L, et al. , Science 1998 Feb;279(5352):857-60
PMID
Title
A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles.
Authors
RAGHUNATHAN, P L, et al.
RAGHUNATHAN, P L
GUTHRIE, C
Citation
Science 1998 Feb;279(5352):857-60
Term ID
Name
assembly of spliceosomal tri-snRNP
Namespace
biological_process
Definition
The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
Synonyms
6 synonym(s)
assembly of spliceosomal tri-snRNP U4/U6.U5
assembly of spliceosomal tri-snRNP U4atac/U6atac.U5
snRNP recycling
spliceosomal tri-snRNP assembly
spliceosomal tri-snRNP U4/U6.U5 assembly
spliceosomal tri-snRNP U4atac/U6atac.U5 assembly
Is-a
1 item(s)
GO:0022618
ribonucleoprotein complex assembly
GO:0000245
[IMP] spliceosome assembly
Evidence
IMP References
1 reference(s)
PubMed
LYGEROU, Z, et al. , Mol. Cell. Biol. 1999 Mar;19(3):2008-20
PMID
Title
A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing.
Authors
LYGEROU, Z, et al.
LYGEROU, Z
CHRISTOPHIDES, G
SéRAPHIN, B
Citation
Mol. Cell. Biol. 1999 Mar;19(3):2008-20
Term ID
Name
spliceosome assembly
Namespace
biological_process
Definition
The aggregation, arrangement and bonding together of the spliceosome, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions.
Is-a
1 item(s)
GO:0022618
ribonucleoprotein complex assembly
GO:0006397
[IEA] mRNA processing
Evidence
IEA Term ID
Name
mRNA processing
Namespace
biological_process
Definition
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
Synonyms
1 synonym(s)
Is-a
2 item(s)
GO:0006396
RNA processing
GO:0016071
mRNA metabolic process
GO:0008380
[IEA] RNA splicing
Evidence
IEA Term ID
Name
RNA splicing
Namespace
biological_process
Definition
The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
Synonyms
1 synonym(s)
pre-mRNA splicing factor activity
Is-a
1 item(s)
GO:0006396
RNA processing
Components
2 component(s)
GO:0005634
[IEA] nucleus
Evidence
IEA Term ID
Name
nucleus
Namespace
cellular_component
Definition
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0043231
intracellular membrane-bounded organelle
GO:0005688
[IDA] U6 snRNP
Evidence
IDA References
1 reference(s)
PubMed
STEVENS, S W, et al. , RNA 2001 Nov;7(11):1543-53
PMID
Title
Biochemical and genetic analyses of the U5, U6, and U4/U6 x U5 small nuclear ribonucleoproteins from Saccharomyces cerevisiae.
Authors
STEVENS, S W, et al.
STEVENS, S W
BARTA, I
GE, H Y
MOORE, R E
YOUNG, M K
LEE, T D
ABELSON, J
Citation
RNA 2001 Nov;7(11):1543-53
Term ID
Name
U6 snRNP
Namespace
cellular_component
Definition
A ribonucleoprotein complex that contains small nuclear RNA U6.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0030532
small nuclear ribonucleoprotein complex
Origin
Saccharomyces cerevisiae S288c
NCBI Taxonomy ID
Name
Saccharomyces cerevisiae S288c
Cross references
9 item(s)
RefSeq
Entrez Gene
SGD
UniProt
BioGRID
GenBank Nucleotide
GenBank Protein
GenBank Protein
GenBank Protein
Experimental roles
1 role(s)
Role 1
bait
Term ID
Name
bait
Definition
Molecule experimentally treated to capture its interacting partners.
Is-a
1 item(s)
MI:0495
experimental role
Identification methods
1 identification method(s)
Method 1
predetermined participant
Term ID
Name
predetermined participant
Definition
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
Synonyms
1 synonym(s)
predetermined (PSI-MI-short)
Is-a
1 item(s)
MI:0661
experimental participant identification
RNA information
Short label
LSM8
Gene
LSM8 (Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA)
GeneID
Official symbol
LSM8
Description
Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA
Other names
1 designation(s)
Ontologies
15 ontology(s)
Functions
2 function(s)
GO:0003723
[IDA] RNA binding
Evidence
IDA References
1 reference(s)
PubMed
FERNANDEZ, Cesar F, et al. , Mol. Biol. Cell 2004 Jun;15(6):2842-52
PMID
Title
An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5.
Authors
FERNANDEZ, Cesar F, et al.
FERNANDEZ, Cesar F
PANNONE, Barbara K
CHEN, Xinguo
FUCHS, Gabriele
WOLIN, Sandra L
Citation
Mol. Biol. Cell 2004 Jun;15(6):2842-52
Term ID
Name
RNA binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
Is-a
1 item(s)
GO:0003676
nucleic acid binding
GO:0003723
[IPI] RNA binding
Evidence
IPI References
1 reference(s)
PubMed
SALGADO-GARRIDO, J, et al. , EMBO J. 1999 Jun;18(12):3451-62
PMID
Title
Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin.
Authors
SALGADO-GARRIDO, J, et al.
SALGADO-GARRIDO, J
BRAGADO-NILSSON, E
KANDELS-LEWIS, S
SéRAPHIN, B
Citation
EMBO J. 1999 Jun;18(12):3451-62
Term ID
Name
RNA binding
Namespace
molecular_function
Definition
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
Is-a
1 item(s)
GO:0003676
nucleic acid binding
Processes
5 process(s)
GO:0000398
[IPI] nuclear mRNA splicing, via spliceosome
Evidence
IPI References
1 reference(s)
PubMed
STEVENS, S W, et al. , Proc. Natl. Acad. Sci. U.S.A. 1999 Jun;96(13):7226-31
PMID
Title
Purification of the yeast U4/U6.U5 small nuclear ribonucleoprotein particle and identification of its proteins.
Authors
STEVENS, S W, et al.
Citation
Proc. Natl. Acad. Sci. U.S.A. 1999 Jun;96(13):7226-31
Term ID
Name
nuclear mRNA splicing, via spliceosome
Namespace
biological_process
Definition
The joining together of exons from one or more primary transcripts of nuclear messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology
Synonyms
6 synonym(s)
mRNA splicing
nuclear mRNA splicing via U12-type spliceosome
nuclear mRNA splicing via U2-type spliceosome
pre-mRNA splicing
splicing AT-AC intron
splicing GT-AG intron
Is-a
2 item(s)
GO:0000377
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0006397
mRNA processing
GO:0006364
[IEA] rRNA processing
Evidence
IEA Term ID
Name
rRNA processing
Namespace
biological_process
Definition
Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
Synonyms
1 synonym(s)
35S primary transcript processing
Is-a
2 item(s)
GO:0016072
rRNA metabolic process
GO:0034470
ncRNA processing
GO:0006397
[IEA] mRNA processing
Evidence
IEA Term ID
Name
mRNA processing
Namespace
biological_process
Definition
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
Synonyms
1 synonym(s)
Is-a
2 item(s)
GO:0006396
RNA processing
GO:0016071
mRNA metabolic process
GO:0008033
[IEA] tRNA processing
Evidence
IEA Term ID
Name
tRNA processing
Namespace
biological_process
Definition
The process by which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
Synonyms
1 synonym(s)
Is-a
2 item(s)
GO:0006399
tRNA metabolic process
GO:0034470
ncRNA processing
GO:0018193
[RCA] peptidyl-amino acid modification
Evidence
RCA Term ID
Name
peptidyl-amino acid modification
Namespace
biological_process
Definition
The alteration of an amino acid residue in a peptide.
Is-a
1 item(s)
GO:0006464
protein modification process
Components
8 component(s)
GO:0005634
[IDA] nucleus
Evidence
IDA References
1 reference(s)
PubMed
SHETH, Ujwal, et al. , Science 2003 May;300(5620):805-8
PMID
Title
Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.
Authors
SHETH, Ujwal, et al.
Citation
Science 2003 May;300(5620):805-8
Term ID
Name
nucleus
Namespace
cellular_component
Definition
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0043231
intracellular membrane-bounded organelle
GO:0005634
[IEA] nucleus
Evidence
IEA Term ID
Name
nucleus
Namespace
cellular_component
Definition
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0043231
intracellular membrane-bounded organelle
GO:0005688
[IDA] U6 snRNP
Evidence
IDA References
1 reference(s)
PubMed
SALGADO-GARRIDO, J, et al. , EMBO J. 1999 Jun;18(12):3451-62
PMID
Title
Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin.
Authors
SALGADO-GARRIDO, J, et al.
SALGADO-GARRIDO, J
BRAGADO-NILSSON, E
KANDELS-LEWIS, S
SéRAPHIN, B
Citation
EMBO J. 1999 Jun;18(12):3451-62
Term ID
Name
U6 snRNP
Namespace
cellular_component
Definition
A ribonucleoprotein complex that contains small nuclear RNA U6.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0030532
small nuclear ribonucleoprotein complex
GO:0005688
[TAS] U6 snRNP
Evidence
TAS References
1 reference(s)
PubMed
VIDAL, V P, et al. , RNA 1999 Nov;5(11):1470-81
PMID
Title
Characterization of U6 snRNA-protein interactions.
Authors
VIDAL, V P, et al.
VIDAL, V P
VERDONE, L
MAYES, A E
BEGGS, J D
Citation
RNA 1999 Nov;5(11):1470-81
Term ID
Name
U6 snRNP
Namespace
cellular_component
Definition
A ribonucleoprotein complex that contains small nuclear RNA U6.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0030532
small nuclear ribonucleoprotein complex
GO:0005730
[IDA] nucleolus
Evidence
IDA References
1 reference(s)
PubMed
SPILLER, Michael P, et al. , J. Cell. Sci. 2007 Dec;120(Pt 24):4310-20
PMID
Title
Requirements for nuclear localization of the Lsm2-8p complex and competition between nuclear and cytoplasmic Lsm complexes.
Authors
SPILLER, Michael P, et al.
SPILLER, Michael P
REIJNS, Martin A M
BEGGS, Jean D
Citation
J. Cell. Sci. 2007 Dec;120(Pt 24):4310-20
Term ID
Name
nucleolus
Namespace
cellular_component
Definition
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology
Is-a
2 item(s)
GO:0043232
intracellular non-membrane-bounded organelle
GO:0044428
nuclear part
GO:0005737
[IEA] cytoplasm
Evidence
IEA Term ID
Name
cytoplasm
Namespace
cellular_component
Definition
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
Is-a
1 item(s)
GO:0044424
intracellular part
GO:0030529
[IEA] ribonucleoprotein complex
Evidence
IEA Term ID
Name
ribonucleoprotein complex
Namespace
cellular_component
Definition
A macromolecular complex containing both protein and RNA molecules.
Synonyms
4 synonym(s)
protein-RNA complex
ribonucleoprotein
RNA-protein complex
RNP
Is-a
2 item(s)
GO:0032991
macromolecular complex
GO:0044424
intracellular part
GO:0046540
[IDA] U4/U6 x U5 tri-snRNP complex
Evidence
IDA References
1 reference(s)
PubMed
GOTTSCHALK, A, et al. , EMBO J. 1999 Aug;18(16):4535-48
PMID
Title
Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP.
Authors
GOTTSCHALK, A, et al.
GOTTSCHALK, A
NEUBAUER, G
BANROQUES, J
MANN, M
LüHRMANN, R
FABRIZIO, P
Citation
EMBO J. 1999 Aug;18(16):4535-48
Term ID
Name
U4/U6 x U5 tri-snRNP complex
Namespace
cellular_component
Definition
A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
Synonyms
1 synonym(s)
Is-a
1 item(s)
GO:0030532
small nuclear ribonucleoprotein complex
Origin
Saccharomyces cerevisiae S288c
NCBI Taxonomy ID
Name
Saccharomyces cerevisiae S288c
Cross references
9 item(s)
RefSeq
Entrez Gene
SGD
UniProt
BioGRID
GenBank Nucleotide
GenBank Protein
GenBank Protein
GenBank Protein
Experimental roles
1 role(s)
Role 1
prey
Term ID
Name
prey
Definition
Molecule experimentally identified as being captured by a given bait.
Is-a
1 item(s)
MI:0495
experimental role
Identification methods
1 identification method(s)
Method 1
predetermined participant
Term ID
Name
predetermined participant
Definition
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
Synonyms
1 synonym(s)
predetermined (PSI-MI-short)
Is-a
1 item(s)
MI:0661
experimental participant identification
Experiments (1)
Experiment 1
Karaduman R (2006)
Full name
RNA structure and RNA-protein interactions in purified yeast U6 snRNPs.
Detection method
affinity chromatography technology (MI:0004)
Term ID
Name
affinity chromatography technology
Definition
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
Synonyms
2 synonym(s)
affinity chrom (PSI-MI-short)
Affinity purification (PSI-MI-alternate)
Is-a
2 item(s)
MI:0091
chromatography technology
MI:0400
affinity technology
Host organisms
1 host organism(s)
Origin
unidentified
NCBI Taxonomy ID
Name
unidentified
Synonyms
11 synonym(s).
miscellaneous nucleic acid
none
not shown
not specified
other
sonstige nucleic acid
unidentified organism
unknown
unknown organism
unknwon
unspecified
Reference
KARADUMAN, Ramazan, et al. , J. Mol. Biol. 2006 Mar;356(5):1248-62
PMID
Title
RNA structure and RNA-protein interactions in purified yeast U6 snRNPs.
Authors
KARADUMAN, Ramazan, et al.
KARADUMAN, Ramazan
FABRIZIO, Patrizia
HARTMUTH, Klaus
URLAUB, Henning
LüHRMANN, Reinhard
Citation
J. Mol. Biol. 2006 Mar;356(5):1248-62
References (1)
Reference 1
KARADUMAN, Ramazan, et al. , J. Mol. Biol. 2006 Mar;356(5):1248-62
PMID
Title
RNA structure and RNA-protein interactions in purified yeast U6 snRNPs.
Authors
KARADUMAN, Ramazan, et al.
KARADUMAN, Ramazan
FABRIZIO, Patrizia
HARTMUTH, Klaus
URLAUB, Henning
LüHRMANN, Reinhard
Citation
J. Mol. Biol. 2006 Mar;356(5):1248-62
Attributes (2)
Attributes
2 attribute(s)
comment
Imported from BioGRID, BIOGRID: All Interactions for Build 3.1.74, release 3.1.74, release date 2011-02-25.
BioGRID Evidence Code
Affinity Capture-RNA
206353
MI:0915
855310
GO:0000166
16410014
559292
NP_013995
S000004881
P49960
296147388