Gene Page:SYNE1

Summary?
GeneID 23345
Symbol SYNE1
Synonyms 8B|ARCA1|C6orf98|CPG2|EDMD4|MYNE1|Nesp1|SCAR8|dJ45H2.2
Description spectrin repeat containing, nuclear envelope 1
Reference MIM:608441|HGNC:HGNC:17089|Ensembl:ENSG00000131018|HPRD:09762|Vega:OTTHUMG00000015841
Gene type protein-coding
Map location 6q25
Pascal p-value 0.003
Sherlock p-value 0.419
TADA p-value 0.714
Fetal beta -1.223
Support G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWAScat Genome-wide Association Studies This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb Genome-wide Association Studies GWASdb records for schizophrenia
CV:PGCnp Genome-wide Association Study GWAS
DNM:Fromer_2014 Whole Exome Sequencing analysis This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
DNM:Guipponi_2014 Whole Exome Sequencing analysis 49 DNMs were identified by comparing the exome of 53 individuals with sporadic SCZ and of their non-affected parents
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias Click to show details
GO_Annotation Mapping neuro-related keywords to Gene Ontology annotations Hits with neuro-related keywords: 1
Network Shortest path distance of core genes in the Human protein-protein interaction network Contribution to shortest path in PPI network: 0.6157

Section I. Genetics and epigenetics annotation

@DNM table

Gene Chromosome Position Ref Alt Transcript AA change Mutation type Sift CG46 Trait Study
SYNE1 chr6 152545708 T G NM_033071
NM_182961		 p.7077E>A
p.7148E>A		 missense
missense		 Schizophrenia DNM:Fromer_2014
SYNE1 A T NM_033071 p.Q6633L missense 1 0.13 Schizophrenia DNM: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 function GO term Evidence Neuro keywords PubMed ID
GO:0003779 actin binding IDA 12408964
GO:0003779 actin binding IEA -
GO:0005515 protein binding IEA -
GO:0005521 lamin binding 新闻学会 11801724
GO:0005198 structural molecule activity IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0008219 cell death IEA -
GO:0007030 Golgi organization IDA 12808039
GO:0006997 nucleus organization NAS 11792814
GO:0042692 muscle cell differentiation IDA 11792814
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0045211 postsynaptic membrane IDA Synap, Neurotransmitter (GO term level: 5) 10878022
GO:0005794 Golgi apparatus IDA 12808039
GO:0005856 cytoskeleton IEA -
GO:0005634 nucleus IEA -
GO:0005635 nuclear envelope IDA 11792814
GO:0005635 nuclear envelope IEA -
GO:0005640 nuclear outer membrane IEA -
GO:0005737 cytoplasm IEA -
GO:0016021 integral to membrane IDA 11792814
GO:0016021 integral to membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
REACTOME MEIOSIS 116 81 All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE 421 253 All SZGR 2.0 genes in this pathway
REACTOME CHROMOSOME MAINTENANCE 122 80 All SZGR 2.0 genes in this pathway
REACTOME MEIOTIC SYNAPSIS 73 57 All SZGR 2.0 genes in this pathway
WINTER HYPOXIA DN 52 30 All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567 375 All SZGR 2.0 genes in this pathway
HOLLMANN APOPTOSIS VIA CD40 UP 201 125 All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE DN 244 147 All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA DN 320 184 All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP 456 228 All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536 332 All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR UP 164 122 All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP 1821 933 All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN 232 154 All SZGR 2.0 genes in this pathway
DN CHEBOTAEV GR目标 120 73 All SZGR 2.0 genes in this pathway
LUI THYROID CANCER CLUSTER 2 42 31 All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP 1037 673 All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118 744 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256 159 All SZGR 2.0 genes in this pathway
KENNY CTNNB1 TARGETS UP 50 30 All SZGR 2.0 genes in this pathway
NAKAJIMA EOSINOPHIL 30 20 All SZGR 2.0 genes in this pathway
WANG TARGETS OF MLL CBP FUSION UP 44 26 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN 298 200 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR DN 101 70 All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN DN 271 175 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476 285 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510 309 All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A4 196 124 All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP 293 203 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 1972 1213 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080 713 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-15/16/195/424/497 362 368 m8 hsa-miR-15abrain UAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brain UAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrain UAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZ UAGCAGCACAGAAAUAUUGGC
hsa-miR-424 CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497 CAGCAGCACACUGUGGUUUGU
miR-181 644 650 m8 hsa-miR-181abrain AACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZ AACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrain AACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrain AACAUUCAUUGUUGUCGGUGGGUU
miR-23 631 637 1A hsa-miR-23abrain AUCACAUUGCCAGGGAUUUCC
hsa-miR-23bbrain AUCACAUUGCCAGGGAUUACC
miR-29 359 365 m8 hsa-miR-29aSZ UAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZ UAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZ UAGCACCAUUUGAAAUCGGU
miR-369-3p 729 735 1A hsa-miR-369-3p AAUAAUACAUGGUUGAUCUUU
miR-374 729 735 m8 hsa-miR-374 UUAUAAUACAACCUGAUAAGUG
miR-493-5p 679 685 m8 hsa-miR-493-5p UUGUACAUGGUAGGCUUUCAUU
miR-543 645 652 1A,m8 hsa-miR-543 AAACAUUCGCGGUGCACUUCU