Gene Page: SF3A1

Summary ?
GeneID10291
SymbolSF3A1
SynonymsPRP21|PRPF21|SAP114|SF3A120
Descriptionsplicing factor 3a subunit 1
ReferenceMIM:605595|HGNC:HGNC:10765|Ensembl:ENSG00000099995|HPRD:06903|Vega:OTTHUMG00000151005
Gene typeprotein-coding
Map location22q12.2
Pascal p-value0.002
Sherlock p-value0.032
Fetal beta-0.096
DMG1 (# studies)
eGeneMyers' cis & trans
Meta

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
GSMA_IGenome scan meta-analysisPsr: 0.031 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg114755102230752584SF3A12.14E-8-0.0087.26E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs12408656chr1162946658SF3A1102910.18trans

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
TCEAL70.780.85
CALM20.760.84
UBE2B0.740.75
GLRX20.740.77
NKIRAS10.730.81
MOCS20.720.76
COMMD80.720.79
KRT222P0.720.73
NDUFAF40.710.80
FBXO90.710.76
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
HIF3A-0.47-0.54
AC020763.2-0.45-0.49
CDC42EP4-0.44-0.50
SEMA4B-0.43-0.47
FAM59B-0.43-0.48
RP4-697K14.1-0.43-0.53
SMTN-0.43-0.51
EPHA2-0.42-0.50
MTSS1L-0.39-0.44
NFKB2-0.39-0.45

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003723RNA bindingIDA10882114 
GO:0003723RNA bindingIEA-
GO:0005515protein bindingIPI10976766 |17353931 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000389nuclear mRNA 3'-splice site recognitionTAS15647371 
GO:0000398nuclear mRNA splicing, via spliceosomeEXP12226669 
GO:0000398nuclear mRNA splicing, via spliceosomeIDA10882114 
GO:0006396RNA processingIEA-
GO:0008380RNA splicingIEA-
GO:0006464protein modification processIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005634nucleusIEA-
GO:0005684U2-dependent spliceosomeIDA10882114 
GO:0005730nucleolusIDA18029348 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SPLICEOSOME 12872All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 14077All 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
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS DN 186114All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER DN 406230All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP 1142669All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN 584395All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 UP 209139All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS 957597All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN 187122All SZGR 2.0 genes in this pathway
LIN APC TARGETS 7755All SZGR 2.0 genes in this pathway
DER IFN GAMMA RESPONSE UP 7145All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP 11371All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238145All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605377All SZGR 2.0 genes in this pathway
THILLAINADESAN ZNF217 TARGETS UP 4422All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN 180116All SZGR 2.0 genes in this pathway