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: KDM3A |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 1946219 LUNG c.1595A>T p.Q532L COSMIC PASSENGER/OTHER Probably Damaging 2 587376 LARGE INTESTINE c.1429T>G p.L477V COSMIC PASSENGER/OTHER Benign 3 587376 LARGE INTESTINE c.1468A>C p.K490Q COSMIC PASSENGER/OTHER Possibly Damaging 4 587376 LARGE INTESTINE c.2703G>T p.K901N COSMIC PASSENGER/OTHER Possibly Damaging 5 587376 LARGE INTESTINE c.52C>A p.L18I COSMIC PASSENGER/OTHER Possibly Damaging 6 91T SKIN c.1000C>T p.P334S COSMIC PASSENGER/OTHER Probably Damaging 7 Br27P CENTRAL NERVOUS SYSTEM c.1400G>A p.C467Y COSMIC PASSENGER/OTHER Possibly Damaging 8 ESO-536 OESOPHAGUS c.2288A>G p.K763R COSMIC PASSENGER/OTHER Benign 9 GC8_T STOMACH c.1559T>A p.L520H COSMIC PASSENGER/OTHER Probably Damaging 10 GC8_T STOMACH c.1560C>T p.L520L COSMIC NP NP 11 GC8_T STOMACH c.3561A>G p.E1187E COSMIC NP NP 12 HCC100T LIVER c.99G>A p.W33* COSMIC NP NP 13 HCC2218 BREAST c.559G>C p.D187H COSMIC PASSENGER/OTHER Probably Damaging 14 HCC2998 LARGE INTESTINE c.2491A>C p.N831H COSMIC PASSENGER/OTHER Possibly Damaging 15 HCC61T LIVER c.3203A>C p.N1068T COSMIC PASSENGER/OTHER Probably Damaging 16 HCC75T LIVER c.3490_3491insT p.E1165fs*1 COSMIC NP NP 17 HF-23896 LUNG c.1595A>T p.Q532L COSMIC PASSENGER/OTHER Probably Damaging 18 HN_62624 UPPER AERODIGESTIVE TRACT c.3371C>G p.S1124C COSMIC PASSENGER/OTHER Probably Damaging 19 HN_63080 UPPER AERODIGESTIVE TRACT c.3851C>A p.S1284* COSMIC NP NP 20 LOXIMVI HAEMATOPOIETIC AND LYMPHOID TISSUE c.2188G>T p.A730S COSMIC PASSENGER/OTHER Possibly Damaging 21 LUAD-CHTN-MAD06-00668 LUNG c.16G>T p.G6* COSMIC NP NP 22 LUAD-CHTN-MAD06-00668 LUNG c.44G>T p.R15M COSMIC PASSENGER/OTHER Benign 23 LUAD-NYU704 LUNG c.2591C>T p.T864I COSMIC PASSENGER/OTHER Benign 24 LUAD-S01357 LUNG c.329delA p.Q110fs*5 COSMIC NP NP 25 LUAD-S01482 LUNG c.2219C>A p.S740Y COSMIC PASSENGER/OTHER Probably Damaging 26 P53 LIVER c.1663C>T p.R555C COSMIC PASSENGER/OTHER Probably Damaging 27 PD4128a BREAST c.1351_1358delAATGCACC p.N451fs*8 COSMIC NP NP 28 PD4601a NS c.3371C>G p.S1124C COSMIC PASSENGER/OTHER Probably Damaging 29 RK126_C01 LIVER c.1439G>T p.R480L COSMIC PASSENGER/OTHER Benign 30 SJMB008 CENTRAL NERVOUS SYSTEM c.2012A>G p.N671S COSMIC PASSENGER/OTHER Probably Damaging 31 T155 ENDOMETRIUM c.277A>C p.N93H COSMIC PASSENGER/OTHER Benign 32 T90 PROSTATE c.3267C>G p.N1089K COSMIC PASSENGER/OTHER Benign 33 TCGA-13-1498-01 OVARY c.2628C>G p.P876P COSMIC NP NP 34 TCGA-18-3407-01 LUNG c.2229G>A p.A743A COSMIC NP NP 35 TCGA-18-3411-01 LUNG c.713T>A p.L238Q COSMIC PASSENGER/OTHER Probably Damaging 36 TCGA-22-4593-01 LUNG c.3001G>T p.E1001* COSMIC NP NP 37 TCGA-39-5031-01 LUNG c.3933G>A p.L1311L COSMIC NP NP 38 TCGA-44-2656-01 LUNG c.3685C>T p.Q1229* COSMIC NP NP 39 TCGA-44-2656-01 LUNG c.448A>G p.I150V COSMIC PASSENGER/OTHER Benign 40 TCGA-66-2778-01 LUNG c.1122G>A p.Q374Q COSMIC NP NP 41 TCGA-A3-3324-01 KIDNEY c.1468A>C p.K490Q COSMIC PASSENGER/OTHER Possibly Damaging 42 TCGA-A5-A0GA-01 ENDOMETRIUM c.561C>A p.D187E COSMIC PASSENGER/OTHER Possibly Damaging 43 TCGA-A6-2672-01 LARGE INTESTINE c.614A>G p.Q205R COSMIC PASSENGER/OTHER Probably Damaging 44 TCGA-A6-3809-01 LARGE INTESTINE c.863C>A p.P288H COSMIC PASSENGER/OTHER Benign 45 TCGA-AA-3525-01 LARGE INTESTINE c.1091G>A p.C364Y COSMIC PASSENGER/OTHER Possibly Damaging 46 TCGA-AA-3861-01 LARGE INTESTINE c.441G>A p.L147L COSMIC NP NP 47 TCGA-AA-3864-01 LARGE INTESTINE c.1582G>A p.E528K COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-AA-3966-01 LARGE INTESTINE c.993delA p.I333fs*18 COSMIC NP NP 49 TCGA-AA-A00R-01 LARGE INTESTINE c.784C>T p.R262C COSMIC PASSENGER/OTHER Probably Damaging 50 TCGA-AA-A022-01 LARGE INTESTINE c.255G>A p.R85R COSMIC NP NP 51 TCGA-AD-6965-01 LARGE INTESTINE c.1401T>C p.C467C COSMIC NP NP 52 TCGA-AF-6136-01 LARGE INTESTINE c.1401T>C p.C467C COSMIC NP NP 53 TCGA-AG-A002-01 LARGE INTESTINE c.1432G>T p.A478S COSMIC PASSENGER/OTHER Benign 54 TCGA-AO-A03V-01 BREAST c.2486G>A p.S829N COSMIC PASSENGER/OTHER Possibly Damaging 55 TCGA-AP-A059-01 ENDOMETRIUM c.1438C>T p.R480* COSMIC NP NP 56 TCGA-AP-A059-01 ENDOMETRIUM c.2948A>C p.H983P COSMIC PASSENGER/OTHER Benign 57 TCGA-AX-A05Z-01 ENDOMETRIUM c.366A>C p.K122N COSMIC PASSENGER/OTHER Probably Damaging 58 TCGA-AX-A05Z-01 ENDOMETRIUM c.505G>T p.E169* COSMIC NP NP 59 TCGA-AX-A05Z-01 ENDOMETRIUM c.956C>T p.T319I COSMIC PASSENGER/OTHER Possibly Damaging 60 TCGA-AX-A064-01 ENDOMETRIUM c.2656C>A p.R886R COSMIC NP NP 61 TCGA-AX-A0IU-01 ENDOMETRIUM c.3205A>T p.I1069F COSMIC PASSENGER/OTHER Probably Damaging 62 TCGA-AX-A0J0-01 ENDOMETRIUM c.2533A>C p.I845L COSMIC PASSENGER/OTHER Benign 63 TCGA-AX-A0J1-01 ENDOMETRIUM c.2778G>A p.R926R COSMIC NP NP 64 TCGA-AX-A0J1-01 ENDOMETRIUM c.3661C>T p.R1221C COSMIC PASSENGER/OTHER Probably Damaging 65 TCGA-AZ-4315-01 LARGE INTESTINE c.3097C>T p.R1033C COSMIC PASSENGER/OTHER Probably Damaging 66 TCGA-AZ-4315-01 LARGE INTESTINE c.3896T>C p.V1299A COSMIC PASSENGER/OTHER Probably Damaging 67 TCGA-AZ-6599-01 LARGE INTESTINE c.2627C>A p.P876H COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-B0-5110-01 KIDNEY c.3307G>A p.A1103T COSMIC PASSENGER/OTHER Probably Damaging 69 TCGA-B0-5116-01 KIDNEY c.3639T>C p.Y1213Y COSMIC NP NP 70 TCGA-B2-5633-01 KIDNEY c.3915A>G p.K1305K COSMIC NP NP 71 TCGA-B5-A0JY-01 ENDOMETRIUM c.224G>T p.R75I COSMIC PASSENGER/OTHER Possibly Damaging 72 TCGA-B5-A11E-01 ENDOMETRIUM c.1974T>C p.V658V COSMIC NP NP 73 TCGA-BH-A1FC-01 BREAST c.2640C>T p.N880N COSMIC NP NP 74 TCGA-BP-5168-01 KIDNEY c.2876A>G p.N959S COSMIC PASSENGER/OTHER Benign 75 TCGA-BT-A3PH-01 URINARY TRACT c.2421C>T p.A807A COSMIC NP NP 76 TCGA-CA-6717-01 LARGE INTESTINE c.2628C>T p.P876P COSMIC NP NP 77 TCGA-CA-6717-01 LARGE INTESTINE c.2848C>T p.R950C COSMIC PASSENGER/OTHER Probably Damaging 78 TCGA-CA-6717-01 LARGE INTESTINE c.3747T>C p.H1249H COSMIC NP NP 79 TCGA-CA-6717-01 LARGE INTESTINE c.672C>T p.N224N COSMIC NP NP 80 TCGA-CF-A3MG-01 URINARY TRACT c.376G>A p.G126R COSMIC PASSENGER/OTHER Probably Damaging 81 TCGA-CM-5344-01 LARGE INTESTINE c.1401T>C p.C467C COSMIC NP NP 82 TCGA-D1-A103-01 ENDOMETRIUM c.505G>T p.E169* COSMIC NP NP 83 TCGA-D1-A103-01 ENDOMETRIUM c.727G>T p.V243F COSMIC PASSENGER/OTHER Possibly Damaging 84 TCGA-D1-A17M-01 ENDOMETRIUM c.187G>T p.V63L COSMIC PASSENGER/OTHER Benign 85 TCGA-D8-A1JL-01 BREAST c.3685C>G p.Q1229E COSMIC PASSENGER/OTHER Benign 86 TCGA-D8-A27L-01 BREAST c.2647G>A p.G883S COSMIC PASSENGER/OTHER Possibly Damaging 87 TCGA-E2-A150-01 BREAST c.2279T>G p.L760R COSMIC PASSENGER/OTHER Possibly Damaging 88 TCGA-E5-A2PC-01 URINARY TRACT c.70G>A p.D24N COSMIC PASSENGER/OTHER Benign 89 TCGA-EJ-5516-01 PROSTATE c.2143C>T p.H715Y COSMIC PASSENGER/OTHER Probably Damaging 90 TCGA-F4-6856-01 LARGE INTESTINE c.1664G>A p.R555H COSMIC PASSENGER/OTHER Probably Damaging 91 TCGA-FI-A2EW-01 ENDOMETRIUM c.2951A>C p.K984T COSMIC PASSENGER/OTHER Benign 92 TCGA-G4-6626-01 LARGE INTESTINE c.2626C>T p.P876S COSMIC PASSENGER/OTHER Benign 93 WA37 PROSTATE c.2422G>C p.G808R COSMIC PASSENGER/OTHER Benign
*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 (+)
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 (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PB017027 Pfam-B_17027 351 439 4.6e-47 PB006147 Pfam-B_6147 440 540 4.6e-20 PB003525 Pfam-B_3525 536 621 2.9e-08 PB007111 Pfam-B_7111 783 849 7.7e-38 PB014772 Pfam-B_14772 851 889 6.6e-26 PB015350 Pfam-B_15350 940 1012 2.1e-21 PB016670 Pfam-B_16670 1057 1106 1.4e-32 PB016202 Pfam-B_16202 1108 1153 1.3e-24 PF02373 JmjC 1155 1264 3.8e-17 2. Superfamily Domains:Domain ID Start Site End Site E-value 0047105 962 1132 1.51e-48 0053909 660 692 4.94e-03 -
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 KDM3A KDM3A KDM3A ENSP00000323659 Q9Y4C1 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9Y4C1 KDM3A ENSP00000323659 KDM3A Q9Y4C1 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM3A ENSP00000323659 611512 Q9Y4C1 PA164721293
