dbEM
A Database of Epigenetic Modifiers
Cite: Nanda JS, Kumar R, Raghava GP. (2016) dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. Sci Rep. 6:19340.
Protein: SMARCC1 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 1T SKIN c.3147C>T p.T1049T COSMIC NP NP 2 587276 LARGE INTESTINE c.1954C>T p.R652C COSMIC CANCER Probably Damaging 3 587278 LARGE INTESTINE c.1708C>T p.H570Y COSMIC CANCER Probably Damaging 4 587338 LARGE INTESTINE c.1075A>G p.K359E COSMIC PASSENGER/OTHER Benign 5 587376 LARGE INTESTINE c.2090G>A p.S697N COSMIC CANCER Possibly Damaging 6 587376 LARGE INTESTINE c.2424A>C p.Q808H COSMIC PASSENGER/OTHER Possibly Damaging 7 587376 LARGE INTESTINE c.2518G>T p.E840* COSMIC NP NP 8 8031704 PANCREAS c.2472G>A p.V824V COSMIC NP NP 9 BN38T LIVER c.1687C>T p.P563S COSMIC CANCER Probably Damaging 10 ESO-0013 OESOPHAGUS c.3181T>G p.L1061V COSMIC PASSENGER/OTHER Benign 11 ESO-191 OESOPHAGUS c.2531C>T p.T844I COSMIC PASSENGER/OTHER Benign 12 H2171 LUNG c.1928A>T p.N643I COSMIC PASSENGER/OTHER Benign 13 HN_0-046 UPPER AERODIGESTIVE TRACT c.2301C>G p.P767P COSMIC NP NP 14 LAU165 SKIN c.2175C>T p.V725V COSMIC NP NP 15 LC_C28 LUNG c.3010C>T p.H1004Y COSMIC PASSENGER/OTHER Probably Damaging 16 LUAD-CHTN-3090415 LUNG c.772A>G p.I258V COSMIC CANCER Benign 17 LUAD-CHTN-3090416 LUNG c.1176G>T p.K392N COSMIC CANCER Probably Damaging 18 LUAD-D01382 LUNG c.2120A>T p.D707V COSMIC CANCER Probably Damaging 19 LUAD-RT-S01777 LUNG c.2441_2444delAAAA p.K814fs*10 COSMIC NP NP 20 LUAD-S01341 LUNG c.1141G>A p.E381K COSMIC CANCER Possibly Damaging 21 MOLT-4 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1696C>A p.L566I COSMIC CANCER Possibly Damaging 22 MZ7-mel SKIN c.1495C>T p.R499C COSMIC CANCER Possibly Damaging 23 NCI-H2171 LUNG c.1928A>T p.N643I COSMIC PASSENGER/OTHER Benign 24 PR-00-1165 PROSTATE c.3213C>T p.N1071N COSMIC NP NP 25 RK022_C01 LIVER c.1367C>G p.S456* COSMIC NP NP 26 S00945 LUNG c.2021C>T p.S674L COSMIC CANCER Benign 27 TCGA-05-4427-01 LUNG c.2177G>T p.R726L COSMIC CANCER Possibly Damaging 28 TCGA-29-1693-01 OVARY c.2242T>C p.S748P COSMIC PASSENGER/OTHER Possibly Damaging 29 TCGA-34-5231-01 LUNG c.1926G>C p.W642C COSMIC CANCER Probably Damaging 30 TCGA-37-4141-01 LUNG c.1108G>T p.D370Y COSMIC PASSENGER/OTHER Probably Damaging 31 TCGA-44-4112-01 LUNG c.2669G>C p.R890T COSMIC CANCER Probably Damaging 32 TCGA-44-6777-01 LUNG c.828C>T p.F276F COSMIC NP NP 33 TCGA-55-8089-01 LUNG c.2415T>A p.D805E COSMIC PASSENGER/OTHER Benign 34 TCGA-64-5775-01 LUNG c.2072C>T p.S691L COSMIC CANCER Benign 35 TCGA-66-2744-01 LUNG c.1205G>T p.G402V COSMIC CANCER Probably Damaging 36 TCGA-A5-A0R7-01 ENDOMETRIUM c.1847G>T p.G616V COSMIC CANCER Probably Damaging 37 TCGA-A8-A0AB-01 BREAST c.2607C>G p.A869A COSMIC NP NP 38 TCGA-AA-3664-01 LARGE INTESTINE c.2860G>A p.A954T COSMIC PASSENGER/OTHER Probably Damaging 39 TCGA-AA-3984-01 LARGE INTESTINE c.781A>C p.K261Q COSMIC PASSENGER/OTHER Possibly Damaging 40 TCGA-AA-A01R-01 LARGE INTESTINE c.1364C>T p.A455V COSMIC CANCER Probably Damaging 41 TCGA-AP-A051-01 ENDOMETRIUM c.2682C>T p.S894S COSMIC NP NP 42 TCGA-AP-A054-01 ENDOMETRIUM c.2759T>G p.I920S COSMIC CANCER Probably Damaging 43 TCGA-AX-A05Z-01 ENDOMETRIUM c.1472G>A p.R491Q COSMIC CANCER Probably Damaging 44 TCGA-AZ-6601-01 LARGE INTESTINE c.443A>T p.N148I COSMIC PASSENGER/OTHER Probably Damaging 45 TCGA-B0-5098-01 KIDNEY c.2490A>G p.S830S COSMIC NP NP 46 TCGA-B5-A0JY-01 ENDOMETRIUM c.2530A>G p.T844A COSMIC PASSENGER/OTHER Benign 47 TCGA-B6-A0WW-01 BREAST c.1554T>C p.D518D COSMIC NP NP 48 TCGA-BG-A0VX-01 ENDOMETRIUM c.2840_2881del42 p.L947_Q960del14 COSMIC NP NP 49 TCGA-BH-A0HP-01 BREAST c.2332G>C p.E778Q COSMIC CANCER Benign 50 TCGA-BK-A0C9-01 ENDOMETRIUM c.1197T>C p.P399P COSMIC NP NP 51 TCGA-BS-A0TE-01 ENDOMETRIUM c.1657A>G p.T553A COSMIC CANCER Probably Damaging 52 TCGA-BS-A0UF-01 ENDOMETRIUM c.2518G>T p.E840* COSMIC NP NP 53 TCGA-BS-A0UF-01 ENDOMETRIUM c.852T>G p.D284E COSMIC PASSENGER/OTHER Probably Damaging 54 TCGA-BS-A0UV-01 ENDOMETRIUM c.1180G>T p.D394Y COSMIC CANCER Probably Damaging 55 TCGA-BS-A0UV-01 ENDOMETRIUM c.1714C>T p.R572* COSMIC NP NP 56 TCGA-BS-A0UV-01 ENDOMETRIUM c.2016G>T p.E672D COSMIC PASSENGER/OTHER Benign 57 TCGA-BS-A0UV-01 ENDOMETRIUM c.569G>A p.R190Q COSMIC PASSENGER/OTHER Probably Damaging 58 TCGA-BT-A20N-01 URINARY TRACT c.760G>A p.E254K COSMIC CANCER Benign 59 TCGA-C4-A0F6-01 URINARY TRACT c.850G>A p.D284N COSMIC PASSENGER/OTHER Probably Damaging 60 TCGA-C8-A1HM-01 BREAST c.1561G>T p.A521S COSMIC CANCER Probably Damaging 61 TCGA-CA-6717-01 LARGE INTESTINE c.2040T>G p.P680P COSMIC NP NP 62 TCGA-CM-4743-01 LARGE INTESTINE c.3131C>T p.S1044F COSMIC PASSENGER/OTHER Benign 63 TCGA-CM-6678-01 LARGE INTESTINE c.1928A>G p.N643S COSMIC PASSENGER/OTHER Benign 64 TCGA-D1-A101-01 ENDOMETRIUM c.1805G>A p.R602H COSMIC CANCER Probably Damaging 65 TCGA-D1-A103-01 ENDOMETRIUM c.1371G>T p.W457C COSMIC CANCER Probably Damaging 66 TCGA-D1-A15X-01 ENDOMETRIUM c.1535G>A p.R512Q COSMIC CANCER Probably Damaging 67 TCGA-D1-A16F-01 ENDOMETRIUM c.2883G>A p.Q961Q COSMIC NP NP 68 TCGA-D1-A177-01 ENDOMETRIUM c.2541A>G p.E847E COSMIC NP NP 69 TCGA-D5-5540-01 LARGE INTESTINE c.1929C>T p.N643N COSMIC NP NP 70 TCGA-D5-6532-01 LARGE INTESTINE c.823_824delAT p.I275fs*3 COSMIC NP NP 71 TCGA-DC-6157-01 LARGE INTESTINE c.1497T>C p.R499R COSMIC NP NP 72 TCGA-DK-A1AC-01 URINARY TRACT c.2551G>A p.D851N COSMIC PASSENGER/OTHER Benign 73 TCGA-G4-6293-01 LARGE INTESTINE c.1928A>G p.N643S COSMIC PASSENGER/OTHER Benign 74 TCGA-G4-6315-01 LARGE INTESTINE c.1495C>T p.R499C COSMIC CANCER Possibly Damaging 75 YURTHE SKIN c.2059_2060CC>TT p.P687F COSMIC CANCER Probably Damaging 76 YUWAND SKIN c.2168C>T p.S723F COSMIC CANCER Probably Damaging 77 ccRCC-99 KIDNEY c.439C>G p.R147G COSMIC PASSENGER/OTHER Probably Damaging 78 pfg017T STOMACH c.890G>A p.R297H COSMIC PASSENGER/OTHER Probably Damaging 79 tumor_4163639 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1545G>C p.L515F COSMIC CANCER Probably Damaging
*NP: Not Predicted -
Copy number variation and expression profile (+)
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Gene Essentiality Data (+)
Note: Lower the GARP score (more negative), higher the essentiality of the gene. P-value tells about the significane of GARP score.test -
Tertiary structure (+)
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Structure Domains (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PB001849 Pfam-B_1849 31 206 4.6e-13 PB001566 Pfam-B_1566 295 969 1.4e-05 PF04433 SWIRM 450 537 7.2e-33 PF00249 Myb_DNA-binding 622 663 7.6e-09 PB000903 Pfam-B_903 729 1100 7e-09 PB000276 Pfam-B_276 755 972 0.00095 PB000265 Pfam-B_265 776 1066 0.00031 PB002122 Pfam-B_2122 777 997 3.4e-05 PB014233 Pfam-B_14233 865 944 2.1e-15 2. Superfamily Domains:Domain ID Start Site End Site E-value 0052200 445 550 5.73e-35 0040338 167 220 2.01e-14 0050538 619 672 2.02e-12 -
Sequence Alignment (+)
Users must enabled the Java in their browser to see sequence alignments.
Users can also download Java from here.1. Sequence alignment with 1000 genome variations:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 2. Mutants are not present in CCLE!!3. Sequence alignment with COSMIC mutants:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 4. Sequence alignment with homologus proteins:
Click on button to get Sequence alignment with Coverage, Consensus and Quality -
Sequence Profiles (+)
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Post Translational Modifications (+)
$x "); for($d=2;$d<$l777;$d++) { fwrite($FP6,$row6[$d]); fwrite($FP7,"$row6[$d] "); fwrite($FP6,"\t"); } fwrite($FP6,"\n"); fwrite($FP7,""); } fclose($FP6); echo""; } else{echo"
"; ##### table ##### $ptm_tr=file_get_contents("$dir/ptm"); if($ptm_tr != '') { echo"S. No. Position Amino acid Type Post translational modifications are not found!!";} ?> -
Other Databases Link (+)
Proteomics DB COSMIC Gene Atlas STRING PIR SMARCC1 SMARCC1 SMARCC1 ENSP00000254480 Q92922 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q92922 SMARCC1 ENSP00000254480 SMARCC1 Q92922 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SMARCC1 ENSP00000254480 601732 Q92922 PA35954
