Gene Page: SYNE1

Summary ?
GeneID23345
SymbolSYNE1
Synonyms8B|ARCA1|C6orf98|CPG2|EDMD4|MYNE1|Nesp1|SCAR8|dJ45H2.2
Descriptionspectrin repeat containing, nuclear envelope 1
ReferenceMIM:608441|HGNC:HGNC:17089|Ensembl:ENSG00000131018|HPRD:09762|Vega:OTTHUMG00000015841
Gene typeprotein-coding
Map location6q25
Pascal p-value0.003
Sherlock p-value0.419
TADA p-value0.714
Fetal beta-1.223
SupportG2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
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.
DNM:Guipponi_2014Whole Exome Sequencing analysis49 DNMs were identified by comparing the exome of 53 individuals with sporadic SCZ and of their non-affected parents
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,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.6157 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
SYNE1chr6152545708TGNM_033071
NM_182961		p.7077E>A
p.7148E>A		missense
missense		SchizophreniaDNM:Fromer_2014
SYNE1ATNM_033071p.Q6633Lmissense10.13SchizophreniaDNM:Guipponi_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:0003779actin bindingIDA12408964 
GO:0003779actin bindingIEA-
GO:0005515protein bindingIEA-
GO:0005521lamin bindingIPI11801724 
GO:0005198structural molecule activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0008219cell deathIEA-
GO:0007030Golgi organizationIDA12808039 
GO:0006997nucleus organizationNAS11792814 
GO:0042692muscle cell differentiationIDA11792814 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0045211postsynaptic membraneIDASynap, Neurotransmitter (GO term level: 5)10878022 
GO:0005794Golgi apparatusIDA12808039 
GO:0005856cytoskeletonIEA-
GO:0005634nucleusIEA-
GO:0005635nuclear envelopeIDA11792814 
GO:0005635nuclear envelopeIEA-
GO:0005640nuclear outer membraneIEA-
GO:0005737cytoplasmIEA-
GO:0016021integral to membraneIDA11792814 
GO:0016021integral to membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME MEIOSIS 11681All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE 421253All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE 12280All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC SYNAPSIS 7357All SZGR 2.0 genes in this pathway
WINTER HYPOXIA DN 5230All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP 201125All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN 244147All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA DN 320184All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP 456228All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR UP 164122All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP 1821933All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN 232154All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN 12073All SZGR 2.0 genes in this pathway
LUI THYROID CANCER CLUSTER 2 4231All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP 1037673All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256159All SZGR 2.0 genes in this pathway
KENNY CTNNB1 TARGETS UP 5030All SZGR 2.0 genes in this pathway
NAKAJIMA EOSINOPHIL 3020All SZGR 2.0 genes in this pathway
WANG TARGETS OF MLL CBP FUSION UP 4426All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN 298200All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR DN 10170All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN 271175All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4 196124All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP 293203All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080713All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-15/16/195/424/497362368m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
miR-181644650m8hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-236316371Ahsa-miR-23abrainAUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrainAUCACAUUGCCAGGGAUUACC
miR-29359365m8hsa-miR-29aSZUAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZUAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZUAGCACCAUUUGAAAUCGGU
miR-369-3p7297351Ahsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
miR-374729735m8hsa-miR-374UUAUAAUACAACCUGAUAAGUG
miR-493-5p679685m8hsa-miR-493-5pUUGUACAUGGUAGGCUUUCAUU
miR-5436456521A,m8hsa-miR-543AAACAUUCGCGGUGCACUUCU