Gene Page: SNRPD2
Summary ?
| GeneID | 6633 |
| Symbol | SNRPD2 |
| Synonyms | SMD2|SNRPD1|Sm-D2 |
| Description | small nuclear ribonucleoprotein D2 polypeptide |
| Reference | MIM:601061|HGNC:HGNC:11159|Ensembl:ENSG00000125743|HPRD:03038|Vega:OTTHUMG00000182130 |
| Gene type | protein-coding |
| Map location | 19q13.2 |
| Pascal p-value | 0.179 |
| Sherlock p-value | 0.828 |
| Fetal beta | 0.362 |
| 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:vanEijk_2014 | Genome-wide DNA methylation analysis | This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). | 2 |
| DMG:Wockner_2014 | Genome-wide DNA methylation analysis | This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). | 2 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg08130813 | 19 | 46195655 | QPCTL;SNRPD2 | 1.799E-4 | -0.237 | 0.034 | DMG:Wockner_2014 |
| cg19154438 | 19 | 45825730 | SNRPD2 | 4.192E-4 | -4.336 | DMG:vanEijk_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| snp_a-1856993 | 0 | SNRPD2 | 6633 | 0.18 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 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 | BioGRID | 11713266 |
| DDX20 | DKFZp434H052 | DP103 | GEMIN3 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 | - | HPRD,BioGRID | 10601333 |
| E2F4 | E2F-4 | E2F transcription factor 4, p107/p130-binding | E2F4 interacts with SNRPD2 promoter. | BIND | 15782160 |
| EEF1G | EF1G | GIG35 | eukaryotic translation elongation factor 1 gamma | Two-hybrid | BioGRID | 16169070 |
| EGFR | ERBB | ERBB1 | HER1 | PIG61 | mENA | epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian) | - | HPRD | 12577067 |
| GEMIN5 | DKFZp586M1824 | MGC142174 | gem (nuclear organelle) associated protein 5 | - | HPRD,BioGRID | 11714716 |
| GEMIN6 | FLJ23459 | gem (nuclear organelle) associated protein 6 | Gemin6 interacts with SmD2 | BIND | 11748230 |
| GEMIN6 | FLJ23459 | gem (nuclear organelle) associated protein 6 | Gemin6 interacts with SNRPD2 (SmD2) | BIND | 15939020 |
| GEMIN6 | FLJ23459 | gem (nuclear organelle) associated protein 6 | - | HPRD | 11748230 |
| GEMIN7 | SIP3 | gem (nuclear organelle) associated protein 7 | GEMIN7 interacts with SNRPD2 (SmD2) | BIND | 12065586 |
| KAT5 | ESA1 | HTATIP | HTATIP1 | PLIP | TIP | TIP60 | cPLA2 | K(lysine) acetyltransferase 5 | Two-hybrid | BioGRID | 16169070 |
| LSM10 | MGC15749 | MST074 | MSTP074 | LSM10, U7 small nuclear RNA associated | Affinity Capture-MS | BioGRID | 12975319 |
| LSM11 | FLJ38273 | LSM11, U7 small nuclear RNA associated | - | HPRD | 12975319 |
| LSM6 | YDR378C | LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD,BioGRID | 15231747 |
| 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 |
| SMN1 | BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541 | survival of motor neuron 1, telomeric | Co-fractionation Co-purification | BioGRID | 10942426 |
| SMN2 | BCD541 | C-BCD541 | FLJ76644 | MGC20996 | MGC5208 | SMNC | survival of motor neuron 2, centromeric | - | HPRD | 9323129 |10942426 |
| SNRPD1 | HsT2456 | SMD1 | SNRPD | small nuclear ribonucleoprotein D1 polypeptide 16kDa | Co-crystal Structure Two-hybrid | BioGRID | 9417867 |10025403 |
| SNRPD1 | HsT2456 | SMD1 | SNRPD | small nuclear ribonucleoprotein D1 polypeptide 16kDa | SNRPD2 interacts with SNRPD1. | BIND | 9417867 |
| SNRPE | B-raf | SME | small nuclear ribonucleoprotein polypeptide E | SNRPD2 interacts with SNRPE. | BIND | 9417867 |
| SNRPE | B-raf | SME | small nuclear ribonucleoprotein polypeptide E | Two-hybrid | BioGRID | 9417867 |
| SNRPF | SMF | small nuclear ribonucleoprotein polypeptide F | - | HPRD,BioGRID | 9417867 |11226169 |
| SNRPF | SMF | small nuclear ribonucleoprotein polypeptide F | SNRPD2 interacts with SNRPF. | BIND | 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 |
| 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 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 METABOLISM OF RNA | 330 | 155 | All SZGR 2.0 genes in this pathway |
| RHEIN ALL GLUCOCORTICOID THERAPY DN | 362 | 238 | All SZGR 2.0 genes in this pathway |
| BERENJENO TRANSFORMED BY RHOA UP | 536 | 340 | All SZGR 2.0 genes in this pathway |
| LI AMPLIFIED IN LUNG CANCER | 178 | 108 | 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 |
| NUYTTEN NIPP1 TARGETS UP | 769 | 437 | All SZGR 2.0 genes in this pathway |
| KOYAMA SEMA3B TARGETS UP | 292 | 168 | All SZGR 2.0 genes in this pathway |
| STARK PREFRONTAL CORTEX 22Q11 DELETION DN | 517 | 309 | All SZGR 2.0 genes in this pathway |
| SANA RESPONSE TO IFNG DN | 85 | 56 | All SZGR 2.0 genes in this pathway |
| POMEROY MEDULLOBLASTOMA PROGNOSIS DN | 43 | 28 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE DN | 1237 | 837 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 | 528 | 324 | All SZGR 2.0 genes in this pathway |
| GRADE METASTASIS DN | 45 | 31 | All SZGR 2.0 genes in this pathway |
| GRADE COLON CANCER UP | 871 | 505 | All SZGR 2.0 genes in this pathway |
| WANG TUMOR INVASIVENESS UP | 374 | 247 | All SZGR 2.0 genes in this pathway |
| AGUIRRE PANCREATIC CANCER COPY NUMBER UP | 298 | 174 | All SZGR 2.0 genes in this pathway |
| HSIAO HOUSEKEEPING GENES | 389 | 245 | All SZGR 2.0 genes in this pathway |
| BOYAULT LIVER CANCER SUBCLASS G3 UP | 188 | 121 | All SZGR 2.0 genes in this pathway |
| CHIANG LIVER CANCER SUBCLASS UNANNOTATED DN | 193 | 112 | All SZGR 2.0 genes in this pathway |
| NAKAYAMA FGF2 TARGETS | 29 | 17 | All SZGR 2.0 genes in this pathway |
| KYNG WERNER SYNDROM AND NORMAL AGING DN | 225 | 124 | All SZGR 2.0 genes in this pathway |
| DANG REGULATED BY MYC UP | 72 | 53 | All SZGR 2.0 genes in this pathway |
| YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 13 | 172 | 107 | All SZGR 2.0 genes in this pathway |
| KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP | 756 | 494 | All SZGR 2.0 genes in this pathway |
| KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP | 682 | 440 | All SZGR 2.0 genes in this pathway |