Gene Page: SMC1A

Summary ?
GeneID8243
SymbolSMC1A
SynonymsCDLS2|DXS423E|SB1.8|SMC1|SMC1L1|SMC1alpha|SMCB
Descriptionstructural maintenance of chromosomes 1A
ReferenceMIM:300040|HGNC:HGNC:11111|Ensembl:ENSG00000072501|HPRD:02077|Vega:OTTHUMG00000021614
Gene typeprotein-coding
Map locationXp11.22-p11.21
Fetal beta0.588
eGeneMyers' cis & trans

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

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17028363chr241913161SMC1A82430.2trans
rs16829545chr2151977407SMC1A82432.03E-28trans
rs16841750chr2158288461SMC1A82430.07trans
rs3845734chr2171125572SMC1A82430.04trans
rs7584986chr2184111432SMC1A82431.767E-6trans
rs6741060chr2217169088SMC1A82430.06trans
rs9810143chr35060209SMC1A82430.09trans
rs6797307chr38601563SMC1A82430.13trans
snp_a-18157710SMC1A82430.01trans
rs2183142chr4159232695SMC1A82431.239E-4trans
rs170776chr4173276735SMC1A82430.06trans
rs1396222chr4173279496SMC1A82430.06trans
rs335993chr4173321789SMC1A82430.11trans
rs335980chr4173329784SMC1A82430.03trans
rs335982chr4173330945SMC1A82430.13trans
rs337984chr4173411662SMC1A82430.1trans
rs17762315chr576807576SMC1A82430.01trans
rs10474151chr584286402SMC1A82430.02trans
snp_a-42186000SMC1A82430trans
rs133604960SMC1A82430.07trans
rs12196880chr624313746SMC1A82430.19trans
rs10806988chr624341768SMC1A82430.05trans
rs9461864chr633481468SMC1A82430.04trans
rs16890367chr638078448SMC1A82430.11trans
rs7787830chr798797019SMC1A82439.247E-4trans
rs6996695chr877540580SMC1A82430.03trans
rs9406868chr925223372SMC1A82430.2trans
rs11139334chr984209393SMC1A82430trans
snp_a-21085300SMC1A82430.11trans
rs11061703chr121436977SMC1A82430.19trans
rs7337967chr1353519044SMC1A82430.04trans
rs9989228chr1437809252SMC1A82430.06trans
rs16955618chr1529937543SMC1A82433.788E-24trans
rs2077735chr1558479024SMC1A82430.07trans
rs9941296chr162759498SMC1A82430.02trans
rs16945437chr1711797650SMC1A82430.03trans
rs11873184chr181584081SMC1A82430.01trans
rs12458173chr1831430166SMC1A82430.07trans
rs11882889chr1919887684SMC1A82430.19trans
rs7274477chr201676942SMC1A82430.02trans
rs1041786chr2122617710SMC1A82435.099E-4trans
rs16986332chrX10958354SMC1A82430.09trans
rs16990575chrX32691327SMC1A82430.2trans
rs16993189chrX144666166SMC1A82430.09trans

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 IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ATMAT1 | ATA | ATC | ATD | ATDC | ATE | DKFZp781A0353 | MGC74674 | TEL1 | TELO1ataxia telangiectasia mutatedAffinity Capture-Western
Reconstituted Complex		BioGRID11877376 
BLMBS | MGC126616 | MGC131618 | MGC131620 | RECQ2 | RECQL2 | RECQL3Bloom syndrome-HPRD11877377 
BRCA1BRCAI | BRCC1 | IRIS | PSCP | RNF53breast cancer 1, early onset-HPRD11877377 
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 
CHTF18C16orf41 | C321D2.2 | C321D2.3 | C321D2.4 | CHL12 | Ctf18 | RUVBLCTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)Affinity Capture-WesternBioGRID12930902 
MDC1DKFZp781A0122 | KIAA0170 | MGC166888 | NFBD1mediator of DNA damage checkpoint 1-HPRD12607005 
MSH2COCA1 | FCC1 | HNPCC | HNPCC1 | LCFS2mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)-HPRD14657349 
MSH6GTBP | HNPCC5 | HSAPmutS homolog 6 (E. coli)Reconstituted ComplexBioGRID14657349 
NDC80HEC | HEC1 | KNTC2 | TID3 | hsNDC80NDC80 homolog, kinetochore complex component (S. cerevisiae)-HPRD,BioGRID9295362 
NUMA1NUMAnuclear mitotic apparatus protein 1-HPRD,BioGRID11590136 
RAD21FLJ25655 | FLJ40596 | HR21 | HRAD21 | KIAA0078 | MCD1 | NXP1 | SCC1 | hHR21RAD21 homolog (S. pombe)Affinity 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 
SMC3BAM | BMH | CDLS3 | CSPG6 | HCAP | SMC3L1structural maintenance of chromosomes 3Affinity Capture-WesternBioGRID9789013 |11590136 
|11877376 |12759374 
SMC3BAM | BMH | CDLS3 | CSPG6 | HCAP | SMC3L1structural maintenance of chromosomes 3-HPRD9789013 |11076961 
STAG1DKFZp781D1416 | SA1stromal antigen 1Co-purificationBioGRID11076961 
STYXL1DUSP24 | MK-STYXserine/threonine/tyrosine interacting-like 1Affinity Capture-MSBioGRID17353931 
SYCP3COR1 | MGC71888 | SCP3synaptonemal complex protein 3Affinity Capture-WesternBioGRID12759374 


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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 14077All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE MITOTIC 325185All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING 16186All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING 11158All 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
SENGUPTA NASOPHARYNGEAL CARCINOMA UP 294178All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA UP 305185All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL DN 244153All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
BIDUS METASTASIS UP 214134All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
CHOW RASSF1 TARGETS UP 2717All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN 485334All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN 12267All SZGR 2.0 genes in this pathway
MATTIOLI MGUS VS PCL 11662All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN 514319All SZGR 2.0 genes in this pathway
PUJANA BREAST CANCER LIT INT NETWORK 10173All 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 NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX 795478All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428306All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS UP 424268All SZGR 2.0 genes in this pathway
MORI EMU MYC LYMPHOMA BY ONSET TIME UP 11069All 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
TARTE PLASMA CELL VS PLASMABLAST DN 309206All SZGR 2.0 genes in this pathway
CROMER METASTASIS UP 7946All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND DN 225163All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP 198132All 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
BLUM RESPONSE TO SALIRASIB DN 342220All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP 374247All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN 366257All SZGR 2.0 genes in this pathway
BOYAULT LIVER CANCER SUBCLASS G3 UP 188121All SZGR 2.0 genes in this pathway
YAGI AML WITH T 9 11 TRANSLOCATION 13087All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS 289187All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN 553343All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 4533All SZGR 2.0 genes in this pathway