AT3G56120

Specifically methylates the N1 position of guanosine-37 in various cytoplasmic and mitochondrial tRNAs. Methylation is not dependent on the nature of the nucleoside 5' of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
Physical Location & Seq
Forward (+)
20823146 .. 20826543
3398 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G56120.1

Sequence Viewer

Length: 1407 bp
ATGTTTGATGAAAGCAAGTTCGATGTCAATCTCAAGCTCTGGGCTCTTAGAATTCCCCGTGAACTCTGTAAAAGCGCATCTCGCATTCTCAATGGATACATGCTTAACATGCCGCGAATTAAGCCCATCACTGAAGATCCTACCTGTGAAAAGACTCGTTTGGTGATATTGTCCGAAAGTGTTAAAAATGCTGATTTGTCGGAGATACCCGAGGAAAAACTAAACCAGCTTAAGAAACTTAGTGAACTTGAGGTTGTTCCTCATTCGGTTACTCTTGGGTATTCCTATTGGAGTGCAGACCACCTTTTGAAGCAGATTCTACCAGATGGATTGGATATACCTTCCTCTTTTGAAACTATAGGTCATATTGCCCACTTAAATCTACATGATGAGCTCCTTCCATTCAAAGATGTTATAGCAAAGGTTATCTACGACAAAAATTATCCAAGGATCAAGACAATTGTTAATAAAGTTGGGACTATCAGTAATGAGTTTCGAGTTCCAAAGTTTGAAGTGTTAGCTGGAGAAAATGGGATGGAAACAGAAGTAAAGCAATATGGGGCTAGATTTAAGCTGGACTATGGCTTGGTTTATTGGAATTCAAGATTGGAACATGAGCACATGCGGCTTTCATCTTTGTTTAAACCTGGGGAAACCGTATGTGATATGTTTGCTGGTATTGGGCCTTTTGCTATTCCAGCTGCACAGAAAGGATGCTTTGTGTATGCAAATGATTTAAATCCAGACAGTGTTCGGTACTTGAAGATCAATGCAAAGTTCAATAAGGTTGATGATTTGATTTGTGTGCACAACATGGATGCTCGTAAATTTTTCTCTCACTTGATGGCGGTGTCAACTTGCGAGGATAATTTGCAATCAGTGGCTGATAATGATAAAACAAAGGAAGCAGCCGTGAGTCGAGGAGGTGAGACTAATTCCAGTGGAGAGGAAATACGTGAATCCAATGCAAGCATAAATGAGCCTCTTGGTGCAAATAAGAAGCCATCTGGTACTACAAAGACGGAAAATGGGGTAGGAAAAGACTGCAAGAGTATAGAAGGACACGCAAATAAGAGATTGAGACAAACGTTGCTTCCAATCGCAAAGCCGTGGGAACATATCGACCATGTTATTATGAACCTTCCAGCATCTGCCTTGCAGTTTCTTGATTCGTTCAGTAATGTTATTCAAAAGAAGTATTGGAAAGGACCTCTTCCATTAATTCATTGCTATTGTTTCATCCGTGCAAGCGAAACCACAGAGTTTATAATTGCAGAAGCTGAAACTGCTTTGAAGTTCCATATAGAAGATCCAGTCTTCCACAAGGTTAGAGATGTTGCTCCAAACAAGGCTATGTTTTGCCTAAGCTTTAGACTACCTGAAGCATGCTTGAAGCAAGAAGAGTAA
Functional Annotation
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families

Protein Analysis

468

Amino Acids

52.91

Weight (kDa)

6.45

Isoelectric Point (pI)

37.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TYW2_N_2 PF25133 101 - 178 2.8e-21 TYW2 N-terminal domain
TRM5-TYW2_MTfase PF02475 181 - 279 2.6e-26 TRM5/TYW2 methyltransferase domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

Orthologous Genes (Group: OG0016610)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G56120
fragaria_vesca FvH4_1g05380
malus_domestica MD02G1062400.v1.1
pyrus_communis pycom02g04360
rosa_chinensis RchiOBHm_Chr2g0091071
rosa_laevigata RLG00000016174
rosa_multiflora Rmu_sc0005171.1_g000009
rosa_roxburghii Rroxscaffold_2G00150620
rosa_rugosa Rorug02G0012300
rosa_samantha Rh2AG058400 Rh2BG056800 Rh2CG059000 Rh2DG058300
rosa_wichuraiana Rw2G005080

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1268
AccII CGCG 1 cut(s) 115
AciI CCGC 3 cut(s) 113, 625, 848
AclI AACGTT 1 cut(s) 1088
AclWI GGATC 3 cut(s) 131, 458, 1304
AcsI RAATTY 3 cut(s) 51, 598, 827
AcuI CTGAAG 2 cut(s) 153, 1401
AfaI GTAC 2 cut(s) 758, 1012
AflII CTTAAG 1 cut(s) 230
AjnI CCWGG 1 cut(s) 646
AjuI GAANNNNNNNTTGG 2 cut(s) 590, 622
AluBI AGCT 8 cut(s) 37, 229, 394, 521, 574, 701, 1280, 1368
AluI AGCT 8 cut(s) 37, 229, 394, 521, 574, 701, 1280, 1368
Alw21I GWGCWC 3 cut(s) 396, 621, 810
Alw26I GTCTC 2 cut(s) 923, 1075
Alw44I GTGCAC 1 cut(s) 806
AlwI GGATC 3 cut(s) 131, 458, 1304
AlwNI CAGNNNCTG 3 cut(s) 884, 1151, 1280
Ama87I CYCGRG 1 cut(s) 209
AoxI GGCC 1 cut(s) 683
ApaLI GTGCAC 1 cut(s) 806
ApeKI GCWGC 2 cut(s) 701, 908
ApoI RAATTY 3 cut(s) 51, 598, 827
AseI ATTAAT 1 cut(s) 1220
AspLEI GCGC 1 cut(s) 77
AspS9I GGNCC 2 cut(s) 683, 1208
AsuHPI GGTGA 2 cut(s) 175, 938
AvaI CYCGRG 1 cut(s) 209
AvaII GGWCC 1 cut(s) 1208
BaeGI GKGCMC 1 cut(s) 810
BanII GRGCYC 2 cut(s) 46, 396
BbsI GAAGAC 1 cut(s) 1309
Bbv12I GWGCWC 3 cut(s) 396, 621, 810
BbvI GCAGC 2 cut(s) 688, 920
BccI CCATC 5 cut(s) 134, 320, 529, 838, 1012
BceAI ACGGC 2 cut(s) 896, 1093
BciT130I CCWGG 1 cut(s) 648
BciVI GTATCC 1 cut(s) 89
BcoDI GTCTC 2 cut(s) 923, 1075
BfaI CTAG 1 cut(s) 564
BfmI CTRYAG 1 cut(s) 357
BfrI CTTAAG 1 cut(s) 230
BfuI GTATCC 1 cut(s) 89
BisI GCNGC 4 cut(s) 113, 626, 702, 909
BlsI GCNGC 4 cut(s) 114, 627, 703, 910
Bme1390I CCNGG 1 cut(s) 648
Bme18I GGWCC 1 cut(s) 1208
BmeT110I CYCGRG 1 cut(s) 209
BmgT120I GGNCC 2 cut(s) 683, 1208
BmrFI CCNGG 1 cut(s) 648
BmsI GCATC 4 cut(s) 86, 704, 808, 1157
BpiI GAAGAC 1 cut(s) 1309
BpmI CTGGAG 1 cut(s) 543
Bpu10I CCTNAGC 1 cut(s) 1364
BpuEI CTTGAG 2 cut(s) 17, 269
BsaAI YACGTR 1 cut(s) 956
BsaBI GATNNNNATC 2 cut(s) 27, 738
BsaJI CCNNGG 4 cut(s) 210, 446, 647, 1109
Bse1I ACTGG 2 cut(s) 939, 1313
Bse3DI GCAATG 1 cut(s) 1225
Bse8I GATNNNNATC 2 cut(s) 27, 738
BseBI CCWGG 1 cut(s) 648
BseDI CCNNGG 4 cut(s) 210, 446, 647, 1109
BseGI GGATG 4 cut(s) 540, 719, 823, 1239
BseJI GATNNNNATC 2 cut(s) 27, 738
BseMI GCAATG 1 cut(s) 1225
BseNI ACTGG 2 cut(s) 939, 1313
BseRI GAGGAG 1 cut(s) 936
BseSI GKGCMC 1 cut(s) 810
BseXI GCAGC 2 cut(s) 688, 920
BsgI GTGCAG 2 cut(s) 315, 687
Bsh1236I CGCG 1 cut(s) 115
BshFI GGCC 1 cut(s) 685
BsiHKAI GWGCWC 3 cut(s) 396, 621, 810
BsiHKCI CYCGRG 1 cut(s) 209
BslFI GGGAC 1 cut(s) 490
BsmAI GTCTC 2 cut(s) 923, 1075
BsmFI GGGAC 1 cut(s) 490
BsmI GAATGC 1 cut(s) 84
BsnI GGCC 1 cut(s) 685
BsoBI CYCGRG 1 cut(s) 209
Bsp1286I GDGCHC 4 cut(s) 46, 396, 621, 810
Bsp143I GATC 4 cut(s) 136, 450, 765, 1309
BspACI CCGC 3 cut(s) 113, 625, 848
BspANI GGCC 1 cut(s) 685
BspFNI CGCG 1 cut(s) 115
BspPI GGATC 3 cut(s) 131, 458, 1304
BspTI CTTAAG 1 cut(s) 230
BsrDI GCAATG 1 cut(s) 1225
BsrI ACTGG 2 cut(s) 939, 1313
BssECI CCNNGG 4 cut(s) 210, 446, 647, 1109
BssMI GATC 4 cut(s) 136, 450, 765, 1309
BssT1I CCWWGG 1 cut(s) 446
Bst2UI CCWGG 1 cut(s) 648
Bst4CI ACNGT 2 cut(s) 658, 749
Bst6I CTCTTC 2 cut(s) 1218, 1395
BstAFI CTTAAG 1 cut(s) 230
BstBAI YACGTR 1 cut(s) 956
BstC8I GCNNGC 3 cut(s) 970, 1249, 1387
BstDEI CTNAG 3 cut(s) 47, 239, 1364
BstDSI CCRYGG 1 cut(s) 1109
BstF5I GGATG 4 cut(s) 540, 719, 823, 1239
BstFNI CGCG 1 cut(s) 115
BstHHI GCGC 1 cut(s) 77
BstKTI GATC 4 cut(s) 139, 453, 768, 1312
BstMAI GTCTC 2 cut(s) 923, 1075
BstMBI GATC 4 cut(s) 136, 450, 765, 1309
BstMWI GCNNNNNNNGC 6 cut(s) 81, 109, 121, 625, 698, 1286
BstNI CCWGG 1 cut(s) 648
BstNSI RCATGY 4 cut(s) 103, 112, 625, 1389
BstSCI CCNGG 1 cut(s) 646
BstSFI CTRYAG 1 cut(s) 357
BstSLI GKGCMC 1 cut(s) 810
BstUI CGCG 1 cut(s) 115
BstV1I GCAGC 2 cut(s) 688, 920
BstV2I GAAGAC 1 cut(s) 1309
BstX2I RGATCY 2 cut(s) 136, 1309
BstYI RGATCY 2 cut(s) 136, 1309
BsuI GTATCC 1 cut(s) 89
BsuRI GGCC 1 cut(s) 685
BtgI CCRYGG 1 cut(s) 1109
BtsCI GGATG 4 cut(s) 540, 719, 823, 1239
BtsIMutI CAGTG 4 cut(s) 129, 754, 885, 946
Cac8I GCNNGC 3 cut(s) 970, 1249, 1387
CaiI CAGNNNCTG 3 cut(s) 884, 1151, 1280
CfoI GCGC 1 cut(s) 77
Cfr13I GGNCC 2 cut(s) 683, 1208
Csp6I GTAC 2 cut(s) 757, 1011
CviAII CATG 8 cut(s) 100, 109, 386, 614, 622, 814, 1127, 1386
CviQI GTAC 2 cut(s) 757, 1011
DdeI CTNAG 3 cut(s) 47, 239, 1364
DpnI GATC 4 cut(s) 138, 452, 767, 1311
DpnII GATC 4 cut(s) 136, 450, 765, 1309
DraI TTTAAA 2 cut(s) 643, 738
Eam1104I CTCTTC 2 cut(s) 1218, 1395
EarI CTCTTC 2 cut(s) 1218, 1395
Ecl136II GAGCTC 1 cut(s) 394
Eco130I CCWWGG 1 cut(s) 446
Eco24I GRGCYC 2 cut(s) 46, 396
Eco47I GGWCC 1 cut(s) 1208
Eco53kI GAGCTC 1 cut(s) 394
Eco57I CTGAAG 2 cut(s) 153, 1401
Eco88I CYCGRG 1 cut(s) 209
EcoICRI GAGCTC 1 cut(s) 394
EcoO109I RGGNCCY 1 cut(s) 1208
EcoRI GAATTC 2 cut(s) 51, 598
EcoRII CCWGG 1 cut(s) 646
EcoT14I CCWWGG 1 cut(s) 446
EcoT38I GRGCYC 2 cut(s) 46, 396
ErhI CCWWGG 1 cut(s) 446
FaeI CATG 8 cut(s) 103, 112, 389, 617, 625, 817, 1130, 1389
FalI AAGNNNNNCTT 2 cut(s) 1197, 1229
FaqI GGGAC 1 cut(s) 490
FatI CATG 8 cut(s) 99, 108, 385, 613, 621, 813, 1126, 1385
Fnu4HI GCNGC 4 cut(s) 113, 626, 702, 909
FokI GGATG 4 cut(s) 547, 726, 830, 1226
FriOI GRGCYC 2 cut(s) 46, 396
Fsp4HI GCNGC 4 cut(s) 113, 626, 702, 909
FspBI CTAG 1 cut(s) 564
GlaI GCGC 1 cut(s) 76
GluI GCNGC 4 cut(s) 113, 626, 702, 909
GsuI CTGGAG 1 cut(s) 543
HaeIII GGCC 1 cut(s) 685
HhaI GCGC 1 cut(s) 77
Hin1II CATG 8 cut(s) 103, 112, 389, 617, 625, 817, 1130, 1389
Hin6I GCGC 1 cut(s) 75
HinP1I GCGC 1 cut(s) 75
HincII GTYRAC 1 cut(s) 855
HindII GTYRAC 1 cut(s) 855
HindIII AAGCTT 1 cut(s) 1366
HinfI GANTC 5 cut(s) 154, 316, 916, 959, 1169
HphI GGTGA 2 cut(s) 175, 938
Hpy166II GTNNAC 4 cut(s) 62, 245, 808, 855
Hpy188I TCNGA 2 cut(s) 175, 202
Hpy188III TCNNGA 4 cut(s) 454, 603, 743, 1166
Hpy8I GTNNAC 4 cut(s) 62, 245, 808, 855
HpyAV CCTTC 4 cut(s) 351, 407, 1052, 1151
HpyCH4III ACNGT 2 cut(s) 658, 749
HpyCH4IV ACGT 2 cut(s) 955, 1088
HpyF10VI GCNNNNNNNGC 6 cut(s) 81, 109, 121, 625, 698, 1286
HpyF3I CTNAG 3 cut(s) 47, 239, 1364
HpySE526I ACGT 2 cut(s) 955, 1088
Hsp92II CATG 8 cut(s) 103, 112, 389, 617, 625, 817, 1130, 1389
HspAI GCGC 1 cut(s) 75
Kzo9I GATC 4 cut(s) 136, 450, 765, 1309
LmnI GCTCC 2 cut(s) 399, 1345
Lsp1109I GCAGC 2 cut(s) 688, 920
LweI GCATC 4 cut(s) 86, 704, 808, 1157
MaeI CTAG 1 cut(s) 564
MaeII ACGT 2 cut(s) 955, 1088
MaeIII GTNAC 1 cut(s) 268
MalI GATC 4 cut(s) 138, 452, 767, 1311
MboI GATC 4 cut(s) 136, 450, 765, 1309
MboII GAAGA 5 cut(s) 146, 775, 1205, 1309, 1319
MfeI CAATTG 1 cut(s) 459
MflI RGATCY 2 cut(s) 136, 1309
MhlI GDGCHC 4 cut(s) 46, 396, 621, 810
MlyI GAGTC 2 cut(s) 148, 925
MmeI TCCRAC 1 cut(s) 180
MspA1I CMGCKG 1 cut(s) 701
MspCI CTTAAG 1 cut(s) 230
MspR9I CCNGG 1 cut(s) 648
MssI GTTTAAAC 1 cut(s) 643
MunI CAATTG 1 cut(s) 459
Mva1269I GAATGC 1 cut(s) 84
MvaI CCWGG 1 cut(s) 648
MvnI CGCG 1 cut(s) 115
MwoI GCNNNNNNNGC 6 cut(s) 81, 109, 121, 625, 698, 1286
NdeII GATC 4 cut(s) 136, 450, 765, 1309
NlaIII CATG 8 cut(s) 103, 112, 389, 617, 625, 817, 1130, 1389
NspI RCATGY 4 cut(s) 103, 112, 625, 1389
PaeI GCATGC 1 cut(s) 1389
PctI GAATGC 1 cut(s) 84
PfeI GAWTC 3 cut(s) 316, 959, 1169
PkrI GCNGC 4 cut(s) 114, 627, 703, 910
PleI GAGTC 2 cut(s) 148, 924
PmeI GTTTAAAC 1 cut(s) 643
PpsI GAGTC 2 cut(s) 148, 924
Ppu21I YACGTR 1 cut(s) 956
PpuMI RGGWCCY 1 cut(s) 1208
PshBI ATTAAT 1 cut(s) 1220
PsiI TTATAA 1 cut(s) 1268
Psp124BI GAGCTC 1 cut(s) 396
Psp1406I AACGTT 1 cut(s) 1088
Psp5II RGGWCCY 1 cut(s) 1208
Psp6I CCWGG 1 cut(s) 646
PspGI CCWGG 1 cut(s) 646
PspPI GGNCC 2 cut(s) 683, 1208
PspPPI RGGWCCY 1 cut(s) 1208
PstNI CAGNNNCTG 3 cut(s) 884, 1151, 1280
PsuI RGATCY 2 cut(s) 136, 1309
PvuII CAGCTG 1 cut(s) 701
RsaI GTAC 2 cut(s) 758, 1012
RsaNI GTAC 2 cut(s) 757, 1011
SacI GAGCTC 1 cut(s) 396
SatI GCNGC 4 cut(s) 113, 626, 702, 909
Sau3AI GATC 4 cut(s) 136, 450, 765, 1309
Sau96I GGNCC 2 cut(s) 683, 1208
SchI GAGTC 2 cut(s) 148, 925
ScrFI CCNGG 1 cut(s) 648
SduI GDGCHC 4 cut(s) 46, 396, 621, 810
SfaNI GCATC 4 cut(s) 86, 704, 808, 1157
SfcI CTRYAG 1 cut(s) 357
SinI GGWCC 1 cut(s) 1208
SmiI ATTTAAAT 1 cut(s) 738
SmlI CTYRAG 3 cut(s) 32, 230, 248
SmoI CTYRAG 3 cut(s) 32, 230, 248
SphI GCATGC 1 cut(s) 1389
SsiI CCGC 3 cut(s) 113, 625, 848
SspMI CTAG 1 cut(s) 564
SstI GAGCTC 1 cut(s) 396
StyD4I CCNGG 1 cut(s) 646
StyI CCWWGG 1 cut(s) 446
SwaI ATTTAAAT 1 cut(s) 738
TaaI ACNGT 2 cut(s) 658, 749
TaiI ACGT 2 cut(s) 958, 1091
TaqI TCGA 4 cut(s) 21, 496, 919, 1122
TauI GCSGC 2 cut(s) 115, 628
TfiI GAWTC 3 cut(s) 316, 959, 1169
TscAI CASTG 4 cut(s) 136, 754, 885, 946
TseI GCWGC 2 cut(s) 701, 908
TspDTI ATGAA 5 cut(s) 24, 621, 1151, 1214, 1228
TspGWI ACGGA 2 cut(s) 1037, 1232
TspRI CASTG 4 cut(s) 136, 754, 885, 946
Vha464I CTTAAG 1 cut(s) 230
VneI GTGCAC 1 cut(s) 806
VpaK11BI GGWCC 1 cut(s) 1208
VspI ATTAAT 1 cut(s) 1220
XapI RAATTY 3 cut(s) 51, 598, 827
XceI RCATGY 4 cut(s) 103, 112, 625, 1389
XspI CTAG 1 cut(s) 564
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.