Gene Page: LSM3

Summary ?
GeneID27258
SymbolLSM3
SynonymsSMX4|USS2|YLR438C
DescriptionLSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
ReferenceMIM:607283|HGNC:HGNC:17874|HPRD:06283|
Gene typeprotein-coding
Map location3p25.1
Pascal p-value0.843
Sherlock p-value0.661
Fetal beta0.153
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GSMA_IGenome scan meta-analysisPsr: 0.006 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.3063 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
LSM3chr314239557AGNM_014463p.84M>VmissenseSchizophreniaDNM:Fromer_2014


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003723RNA bindingIEA-
GO:0005515protein bindingIPI15231747 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006397mRNA processingTAS10369684 
GO:0008380RNA splicingIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusTAS10369684 
GO:0005681spliceosomeIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
EEF1A1CCS-3 | CCS3 | EEF-1 | EEF1A | EF-Tu | EF1A | FLJ25721 | GRAF-1EF | HNGC:16303 | LENG7 | MGC102687 | MGC131894 | MGC16224 | PTI1 | eEF1A-1eukaryotic translation elongation factor 1 alpha 1Two-hybridBioGRID16169070 
GDF9-growth differentiation factor 9Two-hybridBioGRID16169070 
LSM1CASM | YJL124CLSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
LSM10MGC15749 | MST074 | MSTP074LSM10, U7 small nuclear RNA associatedTwo-hybridBioGRID15231747 |16189514 
LSM2C6orf28 | G7b | YBL026W | snRNPLSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 |15231747 
LSM2C6orf28 | G7b | YBL026W | snRNPLSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae)Two-hybridBioGRID14667819 |15231747 
|16169070 |16189514 
LSM4YER112WLSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID11920408 
LSM5FLJ12710 | YER146WLSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
LSM6YDR378CLSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
LSM7YNL147WLSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID11920408 |15231747 
LSM8YJR022WLSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD11920408 
SMN1BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541survival of motor neuron 1, telomeric-HPRD10851237 
SNRPD3SMD3small nuclear ribonucleoprotein D3 polypeptide 18kDa-HPRD,BioGRID15231747 
SNRPEB-raf | SMEsmall nuclear ribonucleoprotein polypeptide E-HPRD,BioGRID15231747 
UTP14AKIAA0266 | NY-CO-16 | SDCCAG16 | dJ537K23.3UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)Two-hybridBioGRID16169070 
XPCXP3 | XPCCxeroderma pigmentosum, complementation group C-HPRD,BioGRID15231747 
XRN2-5'-3' exoribonuclease 2-HPRD,BioGRID15231747 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG RNA DEGRADATION 5937All SZGR 2.0 genes in this pathway
KEGG SPLICEOSOME 12872All SZGR 2.0 genes in this pathway
REACTOME MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 1510All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF MRNA 284128All SZGR 2.0 genes in this pathway
REACTOME DEADENYLATION DEPENDENT MRNA DECAY 4829All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330155All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA DN 526357All SZGR 2.0 genes in this pathway
LAIHO COLORECTAL CANCER SERRATED UP 11271All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557331All SZGR 2.0 genes in this pathway
CHOW RASSF1 TARGETS UP 2717All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF DN 228137All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP 536340All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN 800473All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS 988594All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BASSO B LYMPHOCYTE NETWORK 14396All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP 203135All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS 13891All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 4 4832All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP 428266All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229713All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED 728415All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
MUELLER PLURINET 299189All SZGR 2.0 genes in this pathway
CHANG CORE SERUM RESPONSE UP 212128All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238145All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP 442263All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 13 172107All SZGR 2.0 genes in this pathway
JIANG HYPOXIA VIA VHL 3424All SZGR 2.0 genes in this pathway
LI DCP2 BOUND MRNA 8957All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN 180116All SZGR 2.0 genes in this pathway
HOLLEMAN VINCRISTINE RESISTANCE B ALL DN 1510All SZGR 2.0 genes in this pathway