Gene Page: SNRPD3

Summary ?
GeneID6634
SymbolSNRPD3
SynonymsSMD3|Sm-D3
Descriptionsmall nuclear ribonucleoprotein D3 polypeptide
ReferenceMIM:601062|HGNC:HGNC:11160|HPRD:03039|
Gene typeprotein-coding
Map location22q11.23
Pascal p-value0.108
Sherlock p-value0.974
Fetal beta0.671
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Nishioka_2013Genome-wide DNA methylation analysisThe authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 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
cg217035722224951237SNRPD3-0.0240.39DMG:Nishioka_2013

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10182691chr234122007SNRPD366340.05trans
rs7595584chr2175652187SNRPD366340.1trans
rs17146240chr5119522933SNRPD366340trans
rs17146261chr5119534252SNRPD366340trans
rs6032295chr2044178138SNRPD366340.04trans
rs5952167chrX115529371SNRPD366340.07trans

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
DNAH70.820.73
LRRC60.800.74
TSGA100.790.58
WDR660.790.67
UBXN100.780.69
CASC10.770.61
AC079354.20.770.56
CCDC390.760.65
AK70.760.62
NPHP10.750.58
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.34-0.17
AF347015.2-0.31-0.17
MT-CO2-0.30-0.18
AF347015.18-0.30-0.13
AF347015.8-0.29-0.15
AC098691.2-0.29-0.25
AF347015.31-0.28-0.18
MT-CYB-0.27-0.14
AF347015.15-0.26-0.13
AF347015.33-0.26-0.13

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005515protein bindingIPI11714716 |11748230 |12065586 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0000387spliceosomal snRNP biogenesisEXP15130578 
GO:0008380RNA splicingTAS1701240 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005829cytosolEXP10531003 
GO:0005634nucleusIEA-
GO:0005654nucleoplasmEXP10531003 
GO:0005681spliceosomeTAS7527560 
GO:0005730nucleolusIDA18029348 
GO:0005737cytoplasmIDA18029348 
GO:0030532small nuclear ribonucleoprotein complexTAS1701240 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CLNS1ACLCI | CLNS1B | IClnchloride channel, nucleotide-sensitive, 1AAffinity Capture-Western
Reconstituted Complex		BioGRID11713266 
DDX20DKFZp434H052 | DP103 | GEMIN3DEAD (Asp-Glu-Ala-Asp) box polypeptide 20-HPRD,BioGRID10601333 
GEMIN5DKFZp586M1824 | MGC142174gem (nuclear organelle) associated protein 5-HPRD,BioGRID11714716 
GEMIN6FLJ23459gem (nuclear organelle) associated protein 6Gemin6 interacts with SNRPD3 (SmD3)BIND15939020 
GEMIN6FLJ23459gem (nuclear organelle) associated protein 6Gemin6 interacts with SmD3.BIND11748230 
GEMIN7SIP3gem (nuclear organelle) associated protein 7GEMIN7 interacts with SNRPD3 (SmD3)BIND12065586 
LSM10MGC15749 | MST074 | MSTP074LSM10, U7 small nuclear RNA associatedAffinity Capture-MSBioGRID12975319 
LSM3SMX4 | USS2 | YLR438CLSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID15231747 
LSM7YNL147WLSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)-HPRD,BioGRID15231747 
PRMT5HRMT1L5 | IBP72 | JBP1 | SKB1 | SKB1Hsprotein arginine methyltransferase 5-HPRD,BioGRID11713266 
RNU11U11RNA, U11 small nuclearAffinity Capture-MSBioGRID15146077 
RNU12U12RNA, U12 small nuclearAffinity Capture-MSBioGRID15146077 
SF3A2PRP11 | PRPF11 | SAP62 | SF3a66splicing factor 3a, subunit 2, 66kDaAffinity Capture-MSBioGRID12234937 
SFRS12DKFZp564B176 | MGC133045 | SRrp508 | SRrp86splicing factor, arginine/serine-rich 12-HPRD14559993 
SMN1BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541survival of motor neuron 1, telomericReconstituted ComplexBioGRID10851237 
SMN2BCD541 | C-BCD541 | FLJ76644 | MGC20996 | MGC5208 | SMNCsurvival of motor neuron 2, centromeric-HPRD9323129 
SNRPBCOD | SNRPB1 | SmB/SmB' | snRNP-Bsmall nuclear ribonucleoprotein polypeptides B and B1-HPRD,BioGRID10025403 
SNRPEB-raf | SMEsmall nuclear ribonucleoprotein polypeptide ETwo-hybridBioGRID9417867 
SNRPEB-raf | SMEsmall nuclear ribonucleoprotein polypeptide ESNRPD3 interacts with SNRPE.BIND9417867 
SNRPGMGC117317 | SMGsmall nuclear ribonucleoprotein polypeptide GTwo-hybridBioGRID9417867 
SNRPGMGC117317 | SMGsmall nuclear ribonucleoprotein polypeptide GSNRPD3 interacts with SNRPG.BIND9417867 
SNRPNDKFZp686C0927 | DKFZp686M12165 | DKFZp761I1912 | DKFZp762N022 | FLJ33569 | FLJ36996 | FLJ39265 | HCERN3 | MGC29886 | PWCR | RT-LI | SM-D | SMN | SNRNP-N | SNURF-SNRPNsmall nuclear ribonucleoprotein polypeptide NSNRPD3 interacts with SNRPN.BIND9417867 
SNRPNDKFZp686C0927 | DKFZp686M12165 | DKFZp761I1912 | DKFZp762N022 | FLJ33569 | FLJ36996 | FLJ39265 | HCERN3 | MGC29886 | PWCR | RT-LI | SM-D | SMN | SNRNP-N | SNURF-SNRPNsmall nuclear ribonucleoprotein polypeptide NTwo-hybridBioGRID9417867 
STXBP3MUNC18-3 | MUNC18C | PSP | UNC-18Csyntaxin binding protein 3-HPRD12065586 
WDR77HKMT1069 | MEP50 | MGC2722 | Nbla10071 | RP11-552M11.3 | p44WD repeat domain 77-HPRD,BioGRID11756452 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG SPLICEOSOME 12872All SZGR 2.0 genes in this pathway
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS 140100All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF NON CODING RNA 4929All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 14077All SZGR 2.0 genes in this pathway
REACTOME SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 115All SZGR 2.0 genes in this pathway
REACTOME RNA POL II TRANSCRIPTION 10554All 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 MRNA SPLICING MINOR PATHWAY 4519All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRONLESS PRE MRNA 2310All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION 210127All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330155All SZGR 2.0 genes in this pathway
REACTOME CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 4422All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS DN 431263All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382904All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362238All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557331All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP 11785All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP 536340All SZGR 2.0 genes in this pathway
MATTIOLI MGUS VS PCL 11662All SZGR 2.0 genes in this pathway
JAERVINEN AMPLIFIED IN LARYNGEAL CANCER 4024All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE UP 16792All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514330All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR UP 11679All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734436All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289166All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309206All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP 555346All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA SUBGROUPS 3020All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C4 2014All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN 12376All SZGR 2.0 genes in this pathway
CLAUS PGR POSITIVE MENINGIOMA UP 107All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING 246152All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871505All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL UP 5132All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238145All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP 7253All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP 143100All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 14 14386All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549316All SZGR 2.0 genes in this pathway
BILANGES SERUM SENSITIVE VIA TSC2 3925All SZGR 2.0 genes in this pathway
KIM TIAL1 TARGETS 3222All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882506All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 4533All SZGR 2.0 genes in this pathway