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: SMARCD3 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 090 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1012G>A p.D338N COSMIC NP NP 2 090-02-1TD HAEMATOPOIETIC AND LYMPHOID TISSUE c.1012G>A p.D338N COSMIC NP NP 3 587260 LARGE INTESTINE c.745C>T p.Q249* COSMIC NP NP 4 587332 LARGE INTESTINE c.1056G>T p.E352D COSMIC NP NP 5 587376 LARGE INTESTINE c.569C>A p.S190Y COSMIC NP NP 6 CA3 LARGE INTESTINE c.800G>A p.R267H COSMIC NP NP 7 Case5 OVARY c.1078A>T p.S360C COSMIC NP NP 8 H2009 LUNG c.481G>C p.D161H COSMIC NP NP 9 H2009 LUNG c.730G>A p.D244N COSMIC NP NP 10 HCC139T LIVER c.319C>A p.Q107K COSMIC NP NP 11 HX12T LIVER c.857C>A p.S286Y COSMIC NP NP 12 LUAD-RT-S01702 LUNG c.669C>T p.D223D COSMIC NP NP 13 LUAD-RT-S01770 LUNG c.1080C>T p.S360S COSMIC NP NP 14 NCI-H2009 LUNG c.481G>C p.D161H COSMIC NP NP 15 OV207 OVARY c.1402C>T p.R468C COSMIC NP NP 16 PGBM11PT CENTRAL NERVOUS SYSTEM c.27delC p.T10fs*125 COSMIC NP NP 17 T155 ENDOMETRIUM c.465G>A p.A155A COSMIC NP NP 18 TARGET-30-PATESI AUTONOMIC GANGLIA c.669C>T p.D223D COSMIC NP NP 19 TCGA-13-0885-01 OVARY c.844A>T p.R282W COSMIC NP NP 20 TCGA-29-1693-01 OVARY c.942G>T p.Q314H COSMIC NP NP 21 TCGA-37-3789-01 LUNG c.465G>T p.A155A COSMIC NP NP 22 TCGA-44-2656-01 LUNG c.463G>T p.A155S COSMIC NP NP 23 TCGA-91-6847-01 LUNG c.1335C>T p.A445A COSMIC NP NP 24 TCGA-95-7947-01 LUNG c.521A>C p.E174A COSMIC NP NP 25 TCGA-A6-6648-01 LARGE INTESTINE c.740C>T p.P247L COSMIC NP NP 26 TCGA-AA-3516-01 LARGE INTESTINE c.514C>T p.R172W COSMIC NP NP 27 TCGA-AA-3710-01 LARGE INTESTINE c.670G>A p.G224S COSMIC NP NP 28 TCGA-AA-3864-01 LARGE INTESTINE c.1028C>T p.A343V COSMIC NP NP 29 TCGA-AA-A010-01 LARGE INTESTINE c.465G>A p.A155A COSMIC NP NP 30 TCGA-AD-5900-01 LARGE INTESTINE c.412A>G p.M138V COSMIC NP NP 31 TCGA-AG-3612-01 LARGE INTESTINE c.1392G>A p.S464S COSMIC NP NP 32 TCGA-AG-3892-01 LARGE INTESTINE c.465G>A p.A155A COSMIC NP NP 33 TCGA-AN-A0AS-01 BREAST c.1363delC p.Q455fs*>16 COSMIC NP NP 34 TCGA-AP-A051-01 ENDOMETRIUM c.1213G>T p.G405C COSMIC NP NP 35 TCGA-AP-A059-01 ENDOMETRIUM c.992T>G p.V331G COSMIC NP NP 36 TCGA-AX-A05Z-01 ENDOMETRIUM c.428A>C p.K143T COSMIC NP NP 37 TCGA-AX-A05Z-01 ENDOMETRIUM c.579G>T p.K193N COSMIC NP NP 38 TCGA-AX-A0J1-01 ENDOMETRIUM c.1297C>T p.R433W COSMIC NP NP 39 TCGA-AY-6196-01 LARGE INTESTINE c.844A>G p.R282G COSMIC NP NP 40 TCGA-AZ-6598-01 LARGE INTESTINE c.987C>T p.N329N COSMIC NP NP 41 TCGA-B5-A0JY-01 ENDOMETRIUM c.1146G>A p.T382T COSMIC NP NP 42 TCGA-B5-A11E-01 ENDOMETRIUM c.981C>T p.V327V COSMIC NP NP 43 TCGA-BH-A18U-01 BREAST c.932A>G p.E311G COSMIC NP NP 44 TCGA-BS-A0UV-01 ENDOMETRIUM c.486C>T p.S162S COSMIC NP NP 45 TCGA-CI-6619-01 LARGE INTESTINE c.800G>A p.R267H COSMIC NP NP 46 TCGA-CK-5915-01 LARGE INTESTINE c.844A>G p.R282G COSMIC NP NP 47 TCGA-CM-6162-01 LARGE INTESTINE c.1295G>A p.R432H COSMIC NP NP 48 TCGA-D1-A16X-01 ENDOMETRIUM c.424C>T p.R142W COSMIC NP NP 49 TCGA-DI-A0WH-01 ENDOMETRIUM c.1111_1113delGAG p.E371delE COSMIC NP NP 50 TCGA-E2-A1B0-01 BREAST c.1130G>A p.S377N COSMIC NP NP 51 TCGA-GV-A3QI-01 URINARY TRACT c.414G>A p.M138I COSMIC NP NP
*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.Gene essentiality data is not present in COLT database!! -
Tertiary structure (+)
Users must enabled the Java in their browser to see structure.
Users can also download Java from here.Modelled Structure Structures available in PDB Structure is not available in PDB -
Structure Domains (+)
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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 SMARCD3 SMARCD3 SMARCD3 ENSP00000262188 Q6STE5 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q6STE5 SMARCD3 ENSP00000262188 SMARCD3 Q6STE5 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SMARCD3 ENSP00000262188 601737 Q6STE5 PA35958
