Gene Page: SMN1
Summary ?
| GeneID | 6606 |
| Symbol | SMN1 |
| Synonyms | BCD541|GEMIN1|SMA|SMA1|SMA2|SMA3|SMA4|SMA@|SMN|SMNT|T-BCD541|TDRD16A |
| Description | survival of motor neuron 1, telomeric |
| Reference | MIM:600354|HGNC:HGNC:11117|Ensembl:ENSG00000172062|HPRD:02646|Vega:OTTHUMG00000099361 |
| Gene type | protein-coding |
| Map location | 5q13.2 |
| Sherlock p-value | 0.004 |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| Network | Shortest path distance of core genes in the Human protein-protein interaction network | Contribution to shortest path in PPI network: 0.1944 |
Section I. Genetics and epigenetics annotation
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| TCF12 | 0.87 | 0.88 |
| NARG2 | 0.86 | 0.84 |
| HAUS6 | 0.85 | 0.88 |
| EPB41L5 | 0.84 | 0.81 |
| TULP3 | 0.84 | 0.76 |
| CDO1 | 0.84 | 0.77 |
| TMEM194A | 0.84 | 0.84 |
| DHX40 | 0.83 | 0.85 |
| C6orf167 | 0.83 | 0.82 |
| PRKD3 | 0.83 | 0.79 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MT-CO2 | -0.54 | -0.74 |
| AF347015.31 | -0.53 | -0.71 |
| FXYD1 | -0.53 | -0.71 |
| IFI27 | -0.51 | -0.70 |
| C5orf53 | -0.51 | -0.63 |
| CXCL14 | -0.51 | -0.72 |
| AF347015.33 | -0.51 | -0.67 |
| AF347015.27 | -0.50 | -0.67 |
| MYL3 | -0.50 | -0.70 |
| AF347015.21 | -0.50 | -0.74 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003676 | nucleic acid binding | IEA | - |
Section IV. Protein-protein interaction annotation
| Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
|---|---|---|---|---|---|
| BAT3 | BAG-6 | BAG6 | D6S52E | G3 | HLA-B associated transcript 3 | Two-hybrid | BioGRID | 16169070 |
| BCL2 | Bcl-2 | B-cell CLL/lymphoma 2 | - | HPRD,BioGRID | 9389483 |
| C1orf103 | FLJ11269 | RIF1 | RP11-96K19.1 | chromosome 1 open reading frame 103 | Two-hybrid | BioGRID | 16169070 |
| COIL | CLN80 | p80-coilin | coilin | - | HPRD,BioGRID | 11641277 |12361597 |
| COPS6 | CSN6 | MOV34-34KD | COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis) | Two-hybrid | BioGRID | 16169070 |
| DDX20 | DKFZp434H052 | DP103 | GEMIN3 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 | - | HPRD,BioGRID | 10601333 |
| DHX9 | DDX9 | LKP | NDHII | RHA | DEAH (Asp-Glu-Ala-His) box polypeptide 9 | - | HPRD,BioGRID | 11149922 |
| FBL | FIB | FLRN | RNU3IP1 | fibrillarin | Affinity Capture-Western Co-localization Reconstituted Complex | BioGRID | 11509230 |
| FUBP1 | FBP | FUBP | far upstream element (FUSE) binding protein 1 | - | HPRD,BioGRID | 10734235 |
| GAR1 | NOLA1 | GAR1 ribonucleoprotein homolog (yeast) | - | HPRD,BioGRID | 11509230 |
| GDF9 | - | growth differentiation factor 9 | Two-hybrid | BioGRID | 16169070 |
| GEMIN4 | DKFZp434B131 | DKFZp434D174 | HC56 | HCAP1 | HHRF-1 | p97 | gem (nuclear organelle) associated protein 4 | Affinity Capture-Western Co-fractionation Co-purification | BioGRID | 10942426 |12668731 |
| GEMIN5 | DKFZp586M1824 | MGC142174 | gem (nuclear organelle) associated protein 5 | - | HPRD,BioGRID | 11714716 |
| GEMIN6 | FLJ23459 | gem (nuclear organelle) associated protein 6 | Affinity Capture-Western | BioGRID | 11748230 |
| GEMIN7 | SIP3 | gem (nuclear organelle) associated protein 7 | - | HPRD,BioGRID | 12065586 |
| HNRNPR | FLJ25714 | HNRPR | hnRNP-R | heterogeneous nuclear ribonucleoprotein R | - | HPRD,BioGRID | 11574476 |11773003 |
| KPNB1 | IMB1 | IPOB | Impnb | MGC2155 | MGC2156 | MGC2157 | NTF97 | karyopherin (importin) beta 1 | - | HPRD,BioGRID | 12095920 |
| LENG8 | KIAA1932 | MGC40108 | pp13842 | leukocyte receptor cluster (LRC) member 8 | Two-hybrid | BioGRID | 16189514 |
| LGALS1 | DKFZp686E23103 | GAL1 | GBP | lectin, galactoside-binding, soluble, 1 | Affinity Capture-Western | BioGRID | 11522829 |
| LSM1 | CASM | YJL124C | LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD | 10851237 |
| LSM11 | FLJ38273 | LSM11, U7 small nuclear RNA associated | - | HPRD | 12975319 |
| LSM2 | C6orf28 | G7b | YBL026W | snRNP | LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD,BioGRID | 10851237 |
| LSM3 | SMX4 | USS2 | YLR438C | LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD | 10851237 |
| LSM4 | YER112W | LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD,BioGRID | 10851237 |
| LSM5 | FLJ12710 | YER146W | LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD | 10851237 |
| LSM6 | YDR378C | LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD,BioGRID | 10851237 |
| LSM7 | YNL147W | LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) | - | HPRD,BioGRID | 10851237 |
| OSTF1 | FLJ20559 | OSF | SH3P2 | bA235O14.1 | osteoclast stimulating factor 1 | - | HPRD | 11551898 |
| POP7 | 0610037N12Rik | RPP2 | RPP20 | processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae) | Rpp20 interacts with SMN | BIND | 14715275 |
| PPP4C | PP4 | PPH3 | PPX | protein phosphatase 4 (formerly X), catalytic subunit | Affinity Capture-Western | BioGRID | 12668731 |
| SIP1 | GEMIN2 | SIP1-delta | survival of motor neuron protein interacting protein 1 | - | HPRD,BioGRID | 9323129 |
| SMN1 | BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541 | survival of motor neuron 1, telomeric | Two-hybrid | BioGRID | 16189514 |
| SMN1 | BCD541 | SMA | SMA1 | SMA2 | SMA3 | SMA4 | SMA@ | SMN | SMNT | T-BCD541 | survival of motor neuron 1, telomeric | hSMN interacts with a second hSMN molecule. | BIND | 14715275 |
| SMN2 | BCD541 | C-BCD541 | FLJ76644 | MGC20996 | MGC5208 | SMNC | survival of motor neuron 2, centromeric | Co-fractionation Co-purification | BioGRID | 10942426 |
| SNRPB | COD | SNRPB1 | SmB/SmB' | snRNP-B | small nuclear ribonucleoprotein polypeptides B and B1 | SMN interacts with SmB'. | BIND | 15494309 |
| SNRPB | COD | SNRPB1 | SmB/SmB' | snRNP-B | small nuclear ribonucleoprotein polypeptides B and B1 | - | HPRD | 11720283 |
| SNRPB | COD | SNRPB1 | SmB/SmB' | snRNP-B | small nuclear ribonucleoprotein polypeptides B and B1 | - | HPRD,BioGRID | 9323129|11720283 |
| SNRPD1 | HsT2456 | SMD1 | SNRPD | small nuclear ribonucleoprotein D1 polypeptide 16kDa | Co-fractionation Co-purification Reconstituted Complex | BioGRID | 9323129 |10851237 |10942426 |
| SNRPD2 | SMD2 | SNRPD1 | small nuclear ribonucleoprotein D2 polypeptide 16.5kDa | Co-fractionation Co-purification | BioGRID | 10942426 |
| SNRPD3 | SMD3 | small nuclear ribonucleoprotein D3 polypeptide 18kDa | Reconstituted Complex | BioGRID | 10851237 |
| SNRPE | B-raf | SME | small nuclear ribonucleoprotein polypeptide E | Reconstituted Complex | BioGRID | 9323129 |
| SNUPN | KPNBL | RNUT1 | Snurportin1 | snurportin 1 | Reconstituted Complex | BioGRID | 12095920 |
| STXBP3 | MUNC18-3 | MUNC18C | PSP | UNC-18C | syntaxin binding protein 3 | - | HPRD | 12065586 |
| SYNCRIP | GRY-RBP | HNRPQ1 | NSAP1 | RP1-3J17.2 | dJ3J17.2 | hnRNP-Q | pp68 | synaptotagmin binding, cytoplasmic RNA interacting protein | - | HPRD | 11773003 |
| TP53 | FLJ92943 | LFS1 | TRP53 | p53 | tumor protein p53 | - | HPRD,BioGRID | 11704667 |
| UNC119 | HRG4 | unc-119 homolog (C. elegans) | Two-hybrid | BioGRID | 16169070 |
| WDYHV1 | C8orf32 | FLJ10204 | WDYHV motif containing 1 | Two-hybrid | BioGRID | 16189514 |
| ZRANB2 | DKFZp686J1831 | DKFZp686N09117 | FLJ41119 | ZIS | ZIS1 | ZIS2 | ZNF265 | zinc finger, RAN-binding domain containing 2 | - | HPRD | 11448987 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME METABOLISM OF NON CODING RNA | 49 | 29 | All SZGR 2.0 genes in this pathway |
| REACTOME METABOLISM OF RNA | 330 | 155 | All SZGR 2.0 genes in this pathway |
| MOHANKUMAR TLX1 TARGETS UP | 414 | 287 | All SZGR 2.0 genes in this pathway |
| GOLDRATH HOMEOSTATIC PROLIFERATION | 171 | 102 | All SZGR 2.0 genes in this pathway |
| IVANOVA HEMATOPOIESIS EARLY PROGENITOR | 532 | 309 | All SZGR 2.0 genes in this pathway |
| MUELLER PLURINET | 299 | 189 | 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 |