Gene Page: SMC3

Summary ?
GeneID9126
SymbolSMC3
SynonymsBAM|BMH|CDLS3|CSPG6|HCAP|SMC3L1
Descriptionstructural maintenance of chromosomes 3
ReferenceMIM:606062|HGNC:HGNC:2468|Ensembl:ENSG00000108055|HPRD:05829|Vega:OTTHUMG00000019042
Gene typeprotein-coding
Map location10q25
Pascal p-value0.049
Sherlock p-value0.411
Fetal beta2.154
eGeneMyers' cis & trans
SupportG2Cdb.humanPSD
G2Cdb.humanPSP

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.6061 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs2083927chr366884108SMC391260.05trans

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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
LINGO10.930.94
DMWD0.890.89
MCOLN10.890.88
FAM160A20.890.89
CACNB30.880.89
EPN10.880.89
GSK3A0.880.89
APBB10.870.89
CLIP30.870.87
DLGAP40.870.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
MT-CO2-0.68-0.63
AF347015.31-0.67-0.62
AF347015.21-0.67-0.67
AF347015.8-0.67-0.63
AL139819.3-0.66-0.67
AF347015.33-0.66-0.60
MT-CYB-0.66-0.61
AF347015.27-0.65-0.63
AF347015.26-0.64-0.59
AP002478.3-0.64-0.65

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0000166nucleotide bindingIEA-
GO:0003777microtubule motor activityNAS11590136 
GO:0005524ATP bindingIEA-
GO:0016887ATPase activityIEA-
GO:0046982protein heterodimerization activityIPI11590136 
GO:0045502dynein bindingIDA11590136 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006281DNA repairIEA-
GO:0007165signal transductionIDA12651860 
GO:0007049cell cycleIEA-
GO:0007062sister chromatid cohesionNAS11590136 
GO:0007067mitosisTAS9506951 
GO:0007126meiosisIDA12498344 
GO:0009294DNA mediated transformationTAS10801778 
GO:0007052mitotic spindle organizationIEP11590136 
GO:0051301cell divisionIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0000800lateral elementIEA-
GO:0000922spindle poleIDA11590136 
GO:0005604basement membraneTAS9015313 
GO:0005634nucleusTAS9506951 
GO:0005694chromosomeIEA-
GO:0005737cytoplasmIDA11590136 
GO:0008278cohesin complexNAS9506951 
GO:0016363nuclear matrixIDA11590136 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CASP4ICE(rel)II | ICEREL-II | ICH-2 | Mih1/TX | TXcaspase 4, apoptosis-related cysteine peptidaseAffinity Capture-MSBioGRID17353931 
CDK4CMM3 | MGC14458 | PSK-J3cyclin-dependent kinase 4Affinity Capture-MSBioGRID17353931 
HDAC2RPD3 | YAF1histone deacetylase 2Co-purificationBioGRID12198550 
KIFAP3FLJ22818 | KAP3 | SMAP | Smg-GDS | dJ190I16.1kinesin-associated protein 3-HPRD,BioGRID9506951 
MAGED1DLXIN-1 | NRAGEmelanoma antigen family D, 1Affinity Capture-MSBioGRID17353931 
MXD1MAD | MAD1 | MGC104659MAX dimerization protein 1Reconstituted Complex
Two-hybrid		BioGRID9528857 
MXD3MAD3 | MGC2383 | bHLHc13MAX dimerization protein 3Reconstituted Complex
Two-hybrid		BioGRID9528857 
MXD4MAD4 | MST149 | MSTP149 | bHLHc12MAX dimerization protein 4Reconstituted Complex
Two-hybrid		BioGRID9528857 
MXI1MAD2 | MGC43220 | MXD2 | MXI | bHLHc11MAX interactor 1Reconstituted Complex
Two-hybrid		BioGRID9528857 
NEK6SID6-1512NIMA (never in mitosis gene a)-related kinase 6Affinity Capture-MSBioGRID17353931 
NUMA1NUMAnuclear mitotic apparatus protein 1Affinity Capture-WesternBioGRID11590136 
REC8HR21spB | MGC950 | REC8L1 | Rec8pREC8 homolog (yeast)Affinity Capture-WesternBioGRID12759374 
SMARCA5ISWI | SNF2H | WCRF135 | hISWI | hSNF2HSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5Co-purificationBioGRID12198550 
SMC1ACDLS2 | DKFZp686L19178 | DXS423E | KIAA0178 | MGC138332 | SB1.8 | SMC1 | SMC1L1 | SMC1alpha | SMCBstructural maintenance of chromosomes 1AAffinity Capture-WesternBioGRID9789013 |11590136 
|11877376 |12759374 
SMC1ACDLS2 | DKFZp686L19178 | DXS423E | KIAA0178 | MGC138332 | SB1.8 | SMC1 | SMC1L1 | SMC1alpha | SMCBstructural maintenance of chromosomes 1A-HPRD9789013 |11076961 
SMC1BFLJ43748 | SMC1BETA | SMC1L2 | bK268H5 | bK268H5.5structural maintenance of chromosomes 1B-HPRD11564881 |12759374 
|15125634 
STAG1DKFZp781D1416 | SA1stromal antigen 1Co-purificationBioGRID11076961 
SYCP3COR1 | MGC71888 | SCP3synaptonemal complex protein 3Affinity Capture-WesternBioGRID12759374 
TUBBM40 | MGC117247 | MGC16435 | OK/SW-cl.56 | TUBB1 | TUBB5tubulin, betaAffinity Capture-WesternBioGRID11590136 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CELL CYCLE 12884All SZGR 2.0 genes in this pathway
KEGG OOCYTE MEIOSIS 11479All SZGR 2.0 genes in this pathway
PID ATM PATHWAY 3425All SZGR 2.0 genes in this pathway
REACTOME MEIOSIS 11681All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE 421253All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE MITOTIC 325185All SZGR 2.0 genes in this pathway
REACTOME MITOTIC M M G1 PHASES 17298All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE 12280All SZGR 2.0 genes in this pathway
REACTOME DNA REPLICATION 192110All SZGR 2.0 genes in this pathway
REACTOME MITOTIC PROMETAPHASE 8751All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC SYNAPSIS 7357All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN 309191All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP 408247All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP 404246All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP 233161All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN 459276All SZGR 2.0 genes in this pathway
GRAHAM CML QUIESCENT VS NORMAL DIVIDING UP 5733All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED UP 633376All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES SKIN DN 2720All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF DN 228137All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL UP 584356All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
PUJANA XPRSS INT NETWORK 168103All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423265All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
PUJANA BRCA CENTERED NETWORK 11772All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP 424268All SZGR 2.0 genes in this pathway
ZHANG RESPONSE TO IKK INHIBITOR AND TNF DN 10364All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPAIR GENES 230137All SZGR 2.0 genes in this pathway
KAUFFMANN DNA REPLICATION GENES 14787All SZGR 2.0 genes in this pathway
OKUMURA INFLAMMATORY RESPONSE LPS 183115All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN 371218All SZGR 2.0 genes in this pathway
MAHAJAN RESPONSE TO IL1A DN 7657All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP 262186All SZGR 2.0 genes in this pathway
BILD CTNNB1 ONCOGENIC SIGNATURE 8252All 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
MITSIADES RESPONSE TO APLIDIN DN 249165All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR DN 185116All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518299All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING 243155All SZGR 2.0 genes in this pathway
LI DCP2 BOUND MRNA 8957All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN 336211All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN 918550All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE 317190All SZGR 2.0 genes in this pathway
BAKKER FOXO3 TARGETS DN 187109All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS DN 882538All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 4533All SZGR 2.0 genes in this pathway