Summary ?
GeneID6640
SymbolSNTA1
SynonymsLQT12|SNT1|TACIP1|dJ1187J4.5
Descriptionsyntrophin alpha 1
ReferenceMIM:601017|HGNC:HGNC:11167|Ensembl:ENSG00000101400|HPRD:03009|Vega:OTTHUMG00000032259
Gene typeprotein-coding
Map location20q11.2
Pascal p-value0.421
Sherlock p-value0.057
Fetal beta-1.849
DMG1 (# studies)
eGeneMeta
SupportG2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
CompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:vanEijk_2014Genome-wide DNA methylation analysisThis dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). 1
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 2 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.0279 

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
SNTA1chr2031997942TCNM_003098
NM_003098
.
.
silent
splice-donor-ex2ag
SchizophreniaDNM:Fromer_2014

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg150564122032262523SNTA10.0016.267DMG:vanEijk_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 bindingIEA-
GO:0005509calcium ion bindingIEA-
GO:0005516calmodulin bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007528neuromuscular junction developmentIEASynap (GO term level: 10)-
GO:0006936muscle contractionTAS8576247 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0005856cytoskeletonIEA-
GO:0005737cytoplasmIEA-
GO:0042383sarcolemmaIEA-
GO:0030054cell junctionIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CALM1CALML2 | CAMI | DD132 | PHKDcalmodulin 1 (phosphorylase kinase, delta)-HPRD9512352 
DGKZDAGK5 | DAGK6 | DGK-ZETA | hDGKzetadiacylglycerol kinase, zeta 104kDa-HPRD,BioGRID11352924 
DMDBMD | CMD3B | DXS142 | DXS164 | DXS206 | DXS230 | DXS239 | DXS268 | DXS269 | DXS270 | DXS272dystrophin-HPRD,BioGRID7890602 
DTNAD18S892E | DRP3 | DTN | FLJ96209 | LVNC1dystrobrevin, alpha-HPRD12206805 
DTNAD18S892E | DRP3 | DTN | FLJ96209 | LVNC1dystrobrevin, alpha-HPRD11069112 |12206805|12206805 
DTNBMGC17163 | MGC57126dystrobrevin, betaAffinity Capture-WesternBioGRID10545507 
GLSAAD20 | DKFZp686O15119 | FLJ10358 | GLS1 | KIAA0838glutaminase-HPRD,BioGRID11163757 
GRB2ASH | EGFRBP-GRB2 | Grb3-3 | MST084 | MSTP084growth factor receptor-bound protein 2-HPRD,BioGRID11278583 |11551227 
KCNJ12FLJ14167 | IRK2 | KCNJN1 | Kir2.2 | Kir2.2v | hIRK | hIRK1 | hkir2.2x | kcnj12xpotassium inwardly-rectifying channel, subfamily J, member 12-HPRD,BioGRID15024025 
KCNJ4HIR | HIRK2 | HRK1 | IRK3 | Kir2.3 | MGC142066 | MGC142068potassium inwardly-rectifying channel, subfamily J, member 4Affinity Capture-WesternBioGRID15024025 
MAPK12ERK3 | ERK6 | P38GAMMA | PRKM12 | SAPK-3 | SAPK3mitogen-activated protein kinase 12Affinity Capture-Western
Biochemical Activity
Two-hybrid
BioGRID10212242 
NOS1IHPS1 | NOS | nNOSnitric oxide synthase 1 (neuronal)-HPRD11747091 
NOS1IHPS1 | NOS | nNOSnitric oxide synthase 1 (neuronal)Reconstituted ComplexBioGRID9412493 
SCN1AFEB3 | GEFSP2 | HBSCI | NAC1 | Nav1.1 | SCN1 | SMEIsodium channel, voltage-gated, type I, alpha subunitAffinity Capture-Western
Protein-peptide
BioGRID9412493 
SCN5ACDCD2 | CMD1E | CMPD2 | HB1 | HB2 | HBBD | HH1 | ICCD | IVF | LQT3 | Nav1.5 | PFHB1 | SSS1sodium channel, voltage-gated, type V, alpha subunitAffinity Capture-Western
Protein-peptide
BioGRID9412493 
UTRNDMDL | DRP | DRP1 | FLJ23678utrophin-HPRD,BioGRID8576247 
XRCC6CTC75 | CTCBF | G22P1 | KU70 | ML8 | TLAAX-ray repair complementing defective repair in Chinese hamster cells 6Two-hybridBioGRID16169070 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
PID P38 GAMMA DELTA PATHWAY 119All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP 368234All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP 184125All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN 232154All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 3 UP 329196All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS F UP 185119All SZGR 2.0 genes in this pathway
LUI THYROID CANCER PAX8 PPARG DN 4529All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR UP 487286All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI UP 412249All SZGR 2.0 genes in this pathway
YAGI AML FAB MARKERS 191131All SZGR 2.0 genes in this pathway
MOREAUX B LYMPHOCYTE MATURATION BY TACI UP 9258All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM UP 8458All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE UP 9564All SZGR 2.0 genes in this pathway
JIANG HYPOXIA NORMAL 311205All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP 317208All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP 756494All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA CLASSICAL 162122All SZGR 2.0 genes in this pathway
GREGORY SYNTHETIC LETHAL WITH IMATINIB 14583All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS UP 217131All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS GROUP1 13676All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770480All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-124/506234240m8hsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC
miR-135268274m8hsa-miR-135aUAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135bUAUGGCUUUUCAUUCCUAUGUG
miR-185488494m8hsa-miR-185brainUGGAGAGAAAGGCAGUUC
miR-34b6773m8hsa-miR-34bUAGGCAGUGUCAUUAGCUGAUUG