PIPs: Human Protein-Protein Interaction Prediction

Evidence of Interaction Between LSM6 and SNRPD3

The interaction score between LSM6 and SNRPD3 is 1.58E5.

This page provides the details about the evidence that was used to calculate the interaction Score between the two proteins

The Scores that are listed with each module are based on the interaction score where that module provides the only source of evidence. The final Score is the integration of all the sources of evidence.

Feature

Evidence

Score (?)

Gene Expression

Pearson's Correlation between LSM6 and SNRPD3 = 0.83

The original expression data was collated from the NCBI GEO database. For further information about this dataset please refer to the NCBI GEO dataset GDS596.

0.027

Orthology

Organism	LSM6 Orthologue		SNRPD3 Orthologue		Experiment
Organism	Accession	Inparalog Score	Accession	Inparalog Score	Experiment
bakers yeast	YDR378C	1	YLR147C	1	Other AffinityCaptureMS Get References From PubMed
worm	Q95XN6	1	Q17348	1
fly	Q9W2P5	1	O44437	1

The Inparalog Score is calculated by InParanoid

The experiment type Other refers to techniques other than Y2H, MS, Immunoprecipitation, SurfacePlasmonResonance, XrayDiffraction, Xlinking, CompetitionBinding, Immunofluorescence, GelRetardationAssay, AffinityChromatography, InVitroBinding, InVitro, InVivo, FarWestern, pullDown, AffinityCaptureMS, EpistaticMiniArrayProfile, AffinityCaptureWestern, BiochemicalActivity, CoCrystalStructure, FRET, ReconstitutedComplex, CoLocalization, CoPurification or CoFractionation.

0.593

Domains

Domains present in LSM6 and SNRPD3:

Domains in LSM6

Domains in SNRPD3

IPR001163	Small nuclear ribonucleoprotein (Sm protein)
IPR010920	Small nuclear-like ribonucleoprotein
IPR006649	snRNP domain

IPR001163	Small nuclear ribonucleoprotein (Sm protein)
IPR010920	Small nuclear-like ribonucleoprotein
IPR006649	snRNP domain

The Chi square scores for co-occurrence of domains that are present in LSM6 and SNRPD3 are listed below.

Domain 1		Domain 2		Chi Square
IPR001163	Small nuclear ribonucleoprotein (Sm protein)	IPR006649	snRNP domain	1325.87
IPR001163	Small nuclear ribonucleoprotein (Sm protein)	IPR001163	Small nuclear ribonucleoprotein (Sm protein)	1297.61
IPR006649	snRNP domain	IPR006649	snRNP domain	1206.57
IPR010920	Small nuclear-like ribonucleoprotein	IPR006649	snRNP domain	1168.89
IPR001163	Small nuclear ribonucleoprotein (Sm protein)	IPR010920	Small nuclear-like ribonucleoprotein	1143.95
IPR010920	Small nuclear-like ribonucleoprotein	IPR010920	Small nuclear-like ribonucleoprotein	355.236

The background colour of the table refers to:

Blue Domain is only present in LSM6
Yellow Domain is only present in SNRPD3
Green Domain is present in both LSM6 and SNRPD3

0.265

Post-translational Modifications

Protein: LSM6

PTM	Residue	Reference

Protein: SNRPD3

PTM	Residue	Reference
Methylation	110	PubMed, HPRD
Methylation	112	PubMed, HPRD
Methylation	114	PubMed, HPRD
Methylation	118	PubMed, HPRD

Localisation

Protein: LSM6

Localisation	Reference
Nucleus	HPRD
Cytoplasm	HPRD

Protein: SNRPD3

Localisation	Reference
Nucleus	HPRD
Nucleolus	HPRD

Transitive Score

The common interactors between LSM6 and SNRPD3 that are considered by the Transitive module are listed below.

The Scores listed are the values used by the transitive module to calculate the final interaction Score between LSM6 andSNRPD3. The values listed are therefore not the final Score value for the listed interactions.

With a Score value ≥0.025 , LSM6 has 213 interactors and SNRPD3 has 1151 interactors of which there are 200 common interactors.

Common Interactor	Name of Common Interactor	Score for LSM6-Interactor (?)	Score for SNRPD3-Interactor (?)
LSM5	LSM5: U6 snRNA-associated Sm-like protein LSm5	1.64E3	3.41E3
LSM3	LSM3, MDS017: U6 snRNA-associated Sm-like protein LSm3	323.00	12.80
LSM4	LSM4: U6 snRNA-associated Sm-like protein LSm4	323.00	323.00
LSM7	LSM7: U6 snRNA-associated Sm-like protein LSm7	323.00	205.00
LSM2	LSM2, C6orf28, G7b: U6 snRNA-associated Sm-like protein LSm2	323.00	1.59E3
SNRPD2	SNRPD2, SNRPD1: Small nuclear ribonucleoprotein Sm D2	323.00	2.07E3
LSM1	LSM1, CASM: U6 snRNA-associated Sm-like protein LSm1	158.00	1.22
KIAA0788	ASCC3L1, HELIC2, KIAA0788: U5 small nuclear ribonucleoprotein 200 kDa helicase	32.60	431.00
PRPF4	PRPF4, PRP4: U4/U6 small nuclear ribonucleoprotein Prp4	32.60	69.60
PRP19	PRPF19, NMP200, PRP19, SNEV: Pre-mRNA-processing factor 19	25.60	25.60
SART1	SART1: U4/U6.U5 tri-snRNP-associated protein 1	3.05	5.94
SNRPB	SNRPB, COD, SNRPB1: Small nuclear ribonucleoprotein-associated proteins B and B'	2.91	2.91
SNRPE	SNRPE: Small nuclear ribonucleoprotein E	2.91	8.73
LSM8	LSM8: U6 snRNA-associated Sm-like protein LSm8	2.60	10.30
PRPF8	PRPF8, PRPC8: Pre-mRNA-processing-splicing factor 8	1.84	3.05
PRPF3	PRPF3, HPRP3, PRP3: U4/U6 small nuclear ribonucleoprotein Prp3	1.84	1.84
PRPF31	PRPF31, PRP31: U4/U6 small nuclear ribonucleoprotein Prp31	1.82	1.82
SF3B3	N/A	1.82	3.89
TXNL4A	TXNL4A, DIM1, TXNL4: Thioredoxin-like protein 4A	1.82	1.82
SNRPG	SNRPG, PBSCG: Small nuclear ribonucleoprotein G	1.22	2.07E3
SNRPD1	SNRPD1: Small nuclear ribonucleoprotein Sm D1	1.22	3.41E3
SNRPF	SNRPF, PBSCF: Small nuclear ribonucleoprotein F	1.22	691.00
PRPF6	PRPF6, C20orf14: Pre-mRNA-processing factor 6	1.10	1.10
DCP1A	DCP1A, SMIF: mRNA-decapping enzyme 1A	0.494	0.032
DHX15	DHX15, DBP1, DDX15: Putative pre-mRNA-splicing factor ATP-dependent RNA helicase	0.293	0.881
GTF3C2	GTF3C2, KIAA0011: General transcription factor 3C polypeptide 2	0.293	0.137
BAT1	N/A	0.263	0.263
LSM10	LSM10: U7 snRNA-associated Sm-like protein LSm10	0.237	0.237
LSM11	LSM11: U7 snRNA-associated Sm-like protein LSm11	0.237	0.237
SNRPN	HCERN3, SNRPN, SMN: Small nuclear ribonucleoprotein-associated protein N	0.141	0.141
CHD4	CHD4: Chromodomain-helicase-DNA-binding protein 4	0.137	1.81
DDX50	DDX50: ATP-dependent RNA helicase DDX50	0.137	0.293
WDR41	N/A	0.137	0.137
GNB2L1	Lung cancer oncogene 7	0.137	1.81
DDX21	DDX21: Nucleolar RNA helicase 2	0.137	1.81
FBXW2	FBXW2, FBW2, FWD2: F-box/WD repeat-containing protein 2	0.137	0.137
DDX46	DDX46, KIAA0801: Probable ATP-dependent RNA helicase DDX46	0.137	1.81
DDX27	DDX27, RHLP, HSPC259, PP3241: Probable ATP-dependent RNA helicase DDX27	0.123	0.123
DHX16	DHX16, DBP2, DDX16, KIAA0577: Putative pre-mRNA-splicing factor ATP-dependent RN	0.123	0.763
CSTF1	CSTF1: Cleavage stimulation factor 50 kDa subunit	0.123	0.763
IEF-SSP-9502	PWP1: Periodic tryptophan protein 1 homolog	0.123	1.62
TSSC1	TSSC1: Protein TSSC1	0.123	0.123
DDX47	E4-DBP: DEAD box protein	0.123	0.263
DDX19A	DDX19A, DDX19L: ATP-dependent RNA helicase DDX19A	0.123	0.123
CNOT7	CNOT7, CAF1: CCR4-NOT transcription complex subunit 7	0.123	0.263
WDR39	CIAO1, WDR39: Protein CIAO1	0.123	0.074
PPP2R2A	PPP2R2A: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alp	0.123	0.123
DDX18	DDX18: ATP-dependent RNA helicase DDX18	0.123	0.263
CGI-48	UTP18, WDR50, CDABP0061, CGI-48: U3 small nucleolar RNA-associated protein 18 ho	0.123	0.763
CDC40	CDC40, EHB3, PRP17, PRPF17: Pre-mRNA-processing factor 17	0.123	0.123
EIF4A1	EIF4A1, DDX2A, EIF4A: Eukaryotic initiation factor 4A-I	0.123	0.263
RBBP4	RBBP4, RBAP48: Histone-binding protein RBBP4	0.123	1.62
WDR68	WDR68, HAN11: WD repeat-containing protein 68	0.123	0.123
NUP43	N/A	0.123	0.263
DDX39	DDX39: ATP-dependent RNA helicase DDX39	0.123	0.123
BOP1	BOP1, KIAA0124: Ribosome biogenesis protein BOP1	0.123	0.123
DDX49	DDX49: Probable ATP-dependent RNA helicase DDX49	0.123	0.123
CORO1A	CORO1A, CORO1: Coronin-1A	0.123	0.074
DDX23	DDX23: Probable ATP-dependent RNA helicase DDX23	0.123	0.263
WDR3	WDR3: WD repeat-containing protein 3	0.123	0.123
NULL	N/A	0.119	0.119
NULL	N/A	0.119	0.119
SEC13L1	SEC13, D3S1231E, SEC13L1, SEC13R: Protein SEC13 homolog	0.083	0.137
SMARCA4	SMARCA4, BRG1, SNF2B, SNF2L4: Probable global transcription activator SNF2L4	0.083	0.515
DDB2	DDB2: DNA damage-binding protein 2	0.083	0.083
SMARCAL1	SMARCAL1, HARP: SWI/SNF-related matrix-associated actin-dependent regulator of c	0.083	0.137
WDR8	WDR8: WD repeat-containing protein 8	0.083	0.083
DDX48	EIF4A3, DDX48, KIAA0111: Eukaryotic initiation factor 4A-III	0.074	0.123
EIF3S2	EIF3S2, TRIP1: Eukaryotic translation initiation factor 3 subunit 2	0.074	0.763
DDX28	DDX28, MDDX28: Probable ATP-dependent RNA helicase DDX28	0.074	0.060
CNOT8	CNOT8, CALIF, POP2: CCR4-NOT transcription complex subunit 8	0.074	0.074
ARPC1B	ARC41, ARPC1B: Actin-related protein 2/3 complex subunit 1B	0.074	0.372
DDX17	DDX17: Probable ATP-dependent RNA helicase DDX17	0.074	0.074
SMARCA5	SMARCA5, SNF2H, WCRF135: SWI/SNF-related matrix-associated actin-dependent regul	0.074	1.62
RECQL	RECQL, RECQL1: ATP-dependent DNA helicase Q1	0.074	0.123
CORO7	CORO7: Coronin-7	0.074	0.074
DDX41	DDX41, ABS: Probable ATP-dependent RNA helicase DDX41	0.074	0.763
DDX5	DDX5, G17P1, HELR, HLR1: Probable ATP-dependent RNA helicase DDX5	0.074	0.461
LRBA	LRBA, BGL, CDC4L, LBA: Lipopolysaccharide-responsive and beige-like anchor prote	0.074	0.074
FLJ10439	WDR74, NSA1: WD repeat-containing protein 74	0.074	0.074
SND1	SND1, TDRD11: Staphylococcal nuclease domain-containing protein 1	0.074	0.763
WDR77	WDR77, HKMT1069, hCG_39991: Androgen receptor cofactor p44	0.074	0.123
IFIH1	IFIH1, MDA5, RH116: Interferon-induced helicase C domain-containing protein 1	0.074	0.074
POLD1	POLD1, POLD: DNA polymerase delta catalytic subunit	0.074	0.123
WDR57	WDR57, PRP8BP, SFP38: WD repeat-containing protein 57	0.074	0.074
DDX54	DDX54: ATP-dependent RNA helicase DDX54	0.074	0.074
HELLS	HELLS, PASG, Nbla10143, SMARCA6: Lymphoid-specific helicase	0.074	0.060
DDX3X	DDX3X, DBX, DDX3: ATP-dependent RNA helicase DDX3X	0.074	0.763
DDX10	DDX10: Probable ATP-dependent RNA helicase DDX10	0.074	0.074
TAF5	TAF5, TAF2D: Transcription initiation factor TFIID subunit 5	0.074	0.123
DHX38	DHX38, DDX38, KIAA0224, PRP16: Pre-mRNA-splicing factor ATP-dependent RNA helica	0.074	0.074
STRAP	STRAP, MAWD, UNRIP: Serine-threonine kinase receptor-associated protein	0.074	0.123
EML3	EML3: Echinoderm microtubule-associated protein-like 3	0.074	0.060
BLM	BLM, RECQ2, RECQL3: Bloom syndrome protein	0.074	0.461
RBBP7	RBBP7, RBAP46: Histone-binding protein RBBP7	0.074	0.123
NUP37	NUP37: Nucleoporin Nup37	0.074	0.263
XPMC2H	REXO4, PMC2, XPMC2H: RNA exonuclease 4	0.074	0.074
POLE	POLE, POLE1: DNA polymerase epsilon catalytic subunit A	0.074	0.074
DICER1	DICER1, DICER, HERNA, KIAA0928: Endoribonuclease Dicer	0.074	0.275
BTAF1	BTAF1, TAF172: TATA-binding protein-associated factor 172	0.074	0.763
LOC119358	similar to small nuclear ribonucleoprotein D2	0.071	0.071
WDR1	N/A	0.067	0.515
PHF20	PHF20, C20orf104, GLEA2, HCA58, NZF, TZP: PHD finger protein 20	0.065	0.065
RNU3IP2	RRP9, RNU3IP2, U355K: U3 small nucleolar RNA-interacting protein 2	0.060	0.074
POLA	POLA1, POLA: DNA polymerase alpha catalytic subunit	0.060	0.060
GNB1	GNB1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	0.060	0.372
SKIV2L	SKIV2L, XXbac-BCX116I9.5-001, XXbac-BPG116M5.1-001: Superkiller viralicidic acti	0.060	0.372
KIAA0052	SKIV2L2, KIAA0052: Superkiller viralicidic activity 2-like 2	0.060	0.060
GNB2	GNB2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-2	0.060	0.275
PIK3R4	PIK3R4: Phosphoinositide 3-kinase regulatory subunit 4	0.060	0.060
DDX3Y	DDX3Y, DBY: ATP-dependent RNA helicase DDX3Y	0.060	0.275
AAMP	AAMP: Angio-associated migratory cell protein	0.060	0.060
SEC31L1	N/A	0.060	0.461
GRWD1	GRWD1, GRWD, WDR28: Glutamate-rich WD repeat-containing protein 1	0.060	0.060
Nle	NLE1, HUSSY-07: Notchless protein homolog 1	0.060	0.275
NBEAL2	N/A	0.060	0.044
CDC20	CDC20: Cell division cycle protein 20 homolog	0.060	0.461
PWP2H	PWP2, PWP2H: Periodic tryptophan protein 2 homolog	0.060	0.074
LGP2	DHX58, D11LGP2E, LGP2: Probable ATP-dependent RNA helicase DHX58	0.060	0.060
JMJD2C	JMJD2C, GASC1, JHDM3C, KIAA0780: JmjC domain-containing histone demethylation pr	0.060	0.074
PAK1IP1	PAK1IP1, PIP1, WDR84: p21-activated protein kinase-interacting protein 1	0.060	0.461
COPA	COPA: Coatomer subunit alpha	0.060	0.461
RAE1	RAE1, MRNP41: mRNA export factor	0.060	0.060
CHAF1B	CHAF1B, CAF1A, CAF1P60, MPHOSPH7, MPP7: Chromatin assembly factor 1 subunit B	0.060	0.372
ASCC3	ASCC3, HELIC1: Activating signal cointegrator 1 complex subunit 3	0.060	0.123
DDX1	DDX1: ATP-dependent RNA helicase DDX1	0.060	0.123
DHX35	C20orf15, DHX35, DDX35: Probable ATP-dependent RNA helicase DHX35	0.060	0.074
WDR67	WDR67: WD repeat-containing protein 67	0.060	0.060
WDR12	WDR12: WD repeat-containing protein 12	0.060	0.074
COPB2	COPB2: Coatomer subunit beta'	0.060	0.461
RAD54L	RAD54L, RAD54A: DNA repair and recombination protein RAD54-like	0.060	0.074
WDR18	N/A	0.060	0.074
WIPI2	WIPI2, CGI-50: WD repeat domain phosphoinositide-interacting protein 2	0.060	0.060
RNASEH1	RNASEH1, RNH1: Ribonuclease H1	0.055	0.055
ISG20	ISG20, HEM45: Interferon-stimulated gene 20 kDa protein	0.050	0.067
GNB1L	GNB1L, GY2, FKSG1, KIAA1645, WDR14: Guanine nucleotide-binding protein subunit b	0.050	0.050
RAD54B	RAD54B: DNA repair and recombination protein RAD54B	0.050	0.050
NUTF2	NUTF2, NTF2: Nuclear transport factor 2	0.047	0.059
HIRA	HIRA, DGCR1, HIR, TUPLE1: Protein HIRA	0.044	0.372
DDX24	DDX24: ATP-dependent RNA helicase DDX24	0.044	0.275
TTF2	TTF2: Transcription termination factor 2	0.044	0.044
WDR37	N/A	0.044	0.044
WDR42A	N/A	0.044	0.044
WDR48	WDR48, KIAA1449: WD repeat-containing protein 48	0.044	0.044
SETDB1	SETDB1, KIAA0067: Histone-lysine N-methyltransferase SETDB1	0.044	0.036
THRAP5	MED16, DRIP92, THRAP5: Mediator of RNA polymerase II transcription subunit 16	0.044	0.044
WDR45L	N/A	0.044	0.036
ERCC3	ERCC3, XPB, XPBC: TFIIH basal transcription factor complex helicase XPB subunit	0.044	0.275
TLE4	TLE4: TLE4 protein	0.044	0.028
PARN	PARN, DAN: Poly(A)-specific ribonuclease PARN	0.044	0.044
AAAS	AAAS, ADRACALA, GL003: Aladin	0.044	0.060
DDX56	DDX56, DDX21, NOH61: Probable ATP-dependent RNA helicase DDX56	0.044	0.044
CORO1C	CORO1C, CRNN4: Coronin-1C	0.044	0.372
WRN	WRN, RECQ3, RECQL2: Werner syndrome ATP-dependent helicase	0.044	0.461
WDR26	WDR26, CDW2, PRO0852, MIP2: WD repeat-containing protein 26	0.044	0.060
DDX58	DDX58: Probable ATP-dependent RNA helicase DDX58	0.044	0.044
WDR13	WDR13: WD repeat-containing protein 13	0.041	0.041
REV3L	REV3L, POLZ, REV3: DNA polymerase zeta catalytic subunit	0.041	0.041
NUP214	N/A	0.041	0.191
SMARCA3	HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1: Helicase-like transcription factor	0.036	0.372
WDHD1	WDHD1, AND1: WD repeat and HMG-box DNA-binding protein 1	0.036	0.275
BRIP1	BRIP1, BACH1, FANCJ: Fanconi anemia group J protein	0.036	0.171
DDX52	DDX52, ROK1, HUSSY-19: Probable ATP-dependent RNA helicase DDX52	0.036	0.036
RECQL4	RECQL4, RECQ4: ATP-dependent DNA helicase Q4	0.036	0.060
EML4	EML4, C2orf2, EMAPL4: Echinoderm microtubule-associated protein-like 4	0.036	0.225
CORO1B	CORO1B: Coronin-1B	0.036	0.028
REXO2	REXO2, SFN, CGI-114, SMFN: Oligoribonuclease, mitochondrial precursor	0.036	0.372
PEX7	PEX7, PTS2R: Peroxisomal targeting signal 2 receptor	0.036	0.028
EIF4A2	EIF4A2, DDX2B, EIF4F: Eukaryotic initiation factor 4A-II	0.036	0.036
LBR	LBR: Lamin-B receptor	0.0331	0.0331
BRWD2	BRWD2, WDR11, WDR15: Bromodomain and WD repeat-containing protein 2	0.0331	0.027
POLG	POLG, MDP1, POLG1, POLGA: DNA polymerase subunit gamma-1	0.0331	0.055
SH3BP3		0.0308	0.152
ARPC1A	ARPC1A, SOP2L: Actin-related protein 2/3 complex subunit 1A	0.028	0.044
DGUOK	N/A	0.027	0.027
HNRPD	N/A	0.027	0.082
TLE3	TLE3, KIAA1547: Transducin-like enhancer protein 3	0.027	0.165
DDX53	DDX53, CAGE: Probable ATP-dependent RNA helicase DDX53	0.027	0.027
NEDD1	N/A	0.027	0.027
WDR54	N/A	0.027	0.165
REXO1L1	REXO1L1, GOR: Exonuclease GOR	0.027	0.027
RFWD2	RFWD2, COP1, RNF200: E3 ubiquitin-protein ligase RFWD2	0.027	0.027
FLJ12671	ISG20L2, HSD38, HSD-38: Interferon-stimulated 20 kDa exonuclease-like 2	0.027	0.027
TDRD4	TDRD4: Tudor domain-containing protein 4	0.027	0.027
WDR17	N/A	0.027	0.027
WSB1	WSB1, SWIP1: WD repeat and SOCS box-containing protein 1	0.027	0.027
PHF1	N/A	0.027	0.027
KIF21A	N/A	0.027	0.027
FBXW8	FBXW8, FBW6, FBW8, FBX29, FBXO29, FBXW6: F-box/WD repeat-containing protein 8	0.027	0.027
BRWD1	N/A	0.027	0.027
TAF5L	TAF5L, PAF65B: TAF5-like RNA polymerase II p300/CBP-associated factor-associated	0.027	0.027
ERCC8	ERCC8, CKN1, CSA: DNA excision repair protein ERCC-8	0.027	0.027
WDR53	N/A	0.027	0.027
WDR34	N/A	0.027	0.027
TLE6	TLE6: Transducin-like enhancer protein 6	0.027	0.027
TREX1	TREX1: Three prime repair exonuclease 1	0.027	0.027
WDR72	N/A	0.027	0.027
SMARCAD1	SMARCAD1, KIAA1122: SWI/SNF-related matrix-associated actin-dependent regulator	0.027	0.165
EXOSC8	EXOSC8, OIP2, RRP43: Exosome complex exonuclease RRP43	0.027	0.057
SNRPB	N/A	0.0258	0.0258

0.572

Total Score

1.58E5