Gene Page:SNRPD3

Summary?
GeneID 6634
Symbol SNRPD3
Synonyms SMD3|Sm-D3
Description small nuclear ribonucleoprotein D3 polypeptide
Reference MIM:601062|HGNC:HGNC:11160|HPRD:03039|
Gene type protein-coding
Map location 22q11.23
Pascal p-value 0.108
Sherlock p-value 0.974
Fetal beta 0.671
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Nishioka_2013 Genome-wide DNA methylation analysis The 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_I Genome scan meta-analysis Psr: 0.031

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg21703572 22 24951237 SNRPD3 -0.024 0.39 DMG:Nishioka_2013

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs10182691 chr2 34122007 SNRPD3 6634 0.05 trans
rs7595584 chr2 175652187 SNRPD3 6634 0.1 trans
rs17146240 chr5 119522933 SNRPD3 6634 0 trans
rs17146261 chr5 119534252 SNRPD3 6634 0 trans
rs6032295 chr20 44178138 SNRPD3 6634 0.04 trans
rs5952167 chrX 115529371 SNRPD3 6634 0.07 trans

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
Gene Pearson's Correlation Spearman's Correlation
DNAH7 0.82 0.73
LRRC6 0.80 0.74
TSGA10 0.79 0.58
WDR66 0.79 0.67
UBXN10 0.78 0.69
CASC1 0.77 0.61
AC079354.2 0.77 0.56
CCDC39 0.76 0.65
AK7 0.76 0.62
NPHP1 0.75 0.58
Top 10 negatively co-expressed genes
Gene Pearson'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 function GO term Evidence Neuro keywords PubMed ID
GO:0005515 protein binding 新闻学会 11714716|11748230|12065586
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0000387 spliceosomal snRNP biogenesis EXP 15130578
GO:0008380 RNA splicing TAS 1701240
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005829 cytosol EXP 10531003
GO:0005634 nucleus IEA -
GO:0005654 nucleoplasm EXP 10531003
GO:0005681 spliceosome TAS 7527560
GO:0005730 nucleolus IDA 18029348
GO:0005737 cytoplasm IDA 18029348
GO:0030532 small nuclear ribonucleoprotein complex TAS 1701240

Section IV. Protein-protein interaction annotation

Interactors Aliases B Official full name B Experimental Source PubMed ID
CLNS1A CLCI | CLNS1B | ICln chloride channel, nucleotide-sensitive, 1A Affinity Capture-Western
Reconstituted Complex		 BioGRID 11713266
DDX20 DKFZp434H052 | DP103 | GEMIN3 DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 - HPRD,BioGRID 10601333
GEMIN5 DKFZp586M1824 | MGC142174 gem (nuclear organelle) associated protein 5 - HPRD,BioGRID 11714716
GEMIN6 FLJ23459 gem (nuclear organelle) associated protein 6 Gemin6 interacts with SNRPD3 (SmD3) BIND 15939020
GEMIN6 FLJ23459 gem (nuclear organelle) associated protein 6 Gemin6 interacts with SmD3. BIND 11748230
GEMIN7 SIP3 gem (nuclear organelle) associated protein 7 GEMIN7 interacts with SNRPD3 (SmD3) BIND 12065586
LSM10 MGC15749 | MST074 | MSTP074 LSM10, U7 small nuclear RNA associated Affinity Capture-MS BioGRID 12975319
LSM3 SMX4 | USS2 | YLR438C LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) - HPRD,BioGRID 15231747
LSM7 YNL147W LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) - HPRD,BioGRID 15231747
PRMT5 HRMT1L5 | IBP72 | JBP1 | SKB1 | SKB1Hs protein arginine methyltransferase 5 - HPRD,BioGRID 11713266
RNU11 U11 RNA, U11 small nuclear Affinity Capture-MS BioGRID 15146077
RNU12 U12 RNA, U12 small nuclear Affinity Capture-MS BioGRID 15146077
SF3A2 PRP11 | PRPF11 | SAP62 | SF3a66 splicing factor 3a, subunit 2, 66kDa Affinity Capture-MS BioGRID 12234937
SFRS12 DKFZp564B176 | MGC133045 | SRrp508 | SRrp86 splicing factor, arginine/serine-rich 12 - HPRD 14559993
SMN1 BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541 survival of motor neuron 1, telomeric Reconstituted Complex BioGRID 10851237
SMN2 BCD541 | C-BCD541 | FLJ76644 | MGC20996 | MGC5208| SMNC survival of motor neuron 2, centromeric - HPRD 9323129
SNRPB COD | SNRPB1 | SmB/SmB' | snRNP-B small nuclear ribonucleoprotein polypeptides B and B1 - HPRD,BioGRID 10025403
SNRPE B-raf | SME 小型核核糖核蛋白多肽E Two-hybrid BioGRID 9417867
SNRPE B-raf | SME 小型核核糖核蛋白多肽E SNRPD3 interacts with SNRPE. BIND 9417867
SNRPG MGC117317 | SMG small nuclear ribonucleoprotein polypeptide G Two-hybrid BioGRID 9417867
SNRPG MGC117317 | SMG small nuclear ribonucleoprotein polypeptide G SNRPD3 interacts with SNRPG. BIND 9417867
SNRPN DKFZp686C0927 | DKFZp686M12165 | DKFZp761I1912 | DKFZp762N022 | FLJ33569 | FLJ36996 | FLJ39265 | HCERN3 | MGC29886 | PWCR | RT-LI | SM-D | SMN | SNRNP-N | SNURF-SNRPN small nuclear ribonucleoprotein polypeptide N SNRPD3 interacts with SNRPN. BIND 9417867
SNRPN DKFZp686C0927 | DKFZp686M12165 | DKFZp761I1912 | DKFZp762N022 | FLJ33569 | FLJ36996 | FLJ39265 | HCERN3 | MGC29886 | PWCR | RT-LI | SM-D | SMN | SNRNP-N | SNURF-SNRPN small nuclear ribonucleoprotein polypeptide N Two-hybrid BioGRID 9417867
STXBP3 MUNC18-3 | MUNC18C | PSP | UNC-18C syntaxin binding protein 3 - HPRD 12065586
WDR77 HKMT1069 | MEP50 | MGC2722 | Nbla10071 | RP11-552M11.3 | p44 WD repeat domain 77 - HPRD,BioGRID 11756452


Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG SPLICEOSOME 128 72 All SZGR 2.0 genes in this pathway
KEGG SYSTEMIC LUPUS ERYTHEMATOSUS 140 100 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF NON CODING RNA 49 29 All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 140 77 All SZGR 2.0 genes in this pathway
REACTOME SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 11 5 All SZGR 2.0 genes in this pathway
REACTOME RNA POL II TRANSCRIPTION 105 54 All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING 161 86 All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING 111 58 All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING MINOR PATHWAY 45 19 All SZGR 2.0 genes in this pathway
REACTOME PROCESSING OF CAPPED INTRONLESS PRE MRNA 23 10 All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION 210 127 All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF RNA 330 155 All SZGR 2.0 genes in this pathway
REACTOME CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 44 22 All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS DN 431 263 All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP 1382 904 All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN 362 238 All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557 331 All SZGR 2.0 genes in this pathway
OUELLET OVARIAN CANCER INVASIVE VS LMP UP 117 85 All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP 536 340 All SZGR 2.0 genes in this pathway
MATTIOLI MGUS VS PCL 116 62 All SZGR 2.0 genes in this pathway
JAERVINEN AMPLIFIED IN LARYNGEAL CANCER 40 24 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779 480 All SZGR 2.0 genes in this pathway
FERREIRA EWINGS SARCOMA UNSTABLE VS STABLE UP 167 92 All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN 514 330 All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 12HR UP 116 79 All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS 734 436 All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775 494 All SZGR 2.0 genes in this pathway
MANALO HYPOXIA DN 289 166 All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN 309 206 All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546 351 All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP 555 346 All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA SUBGROUPS 30 20 All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C4 20 14 All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN 123 76 All SZGR 2.0 genes in this pathway
CLAUS PGR POSITIVE MENINGIOMA UP 10 7 All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING 246 152 All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP 871 505 All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL UP 51 32 All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER DN 238 145 All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP 72 53 All SZGR 2.0 genes in this pathway
DANG MYC TARGETS UP 143 100 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 14 143 86 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B 549 316 All SZGR 2.0 genes in this pathway
BILANGES SERUM SENSITIVE VIA TSC2 39 25 All SZGR 2.0 genes in this pathway
KIM TIAL1 TARGETS 32 22 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882 506 All SZGR 2.0 genes in this pathway
ABRAMSON INTERACT WITH AIRE 45 33 All SZGR 2.0 genes in this pathway