Rorug01G0334900

RNA-directed DNA methylation 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000001
OG0010432
Physical Location & Seq
Reverse (-)
45302609 .. 45306762
4154 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug01G0334900.1

Sequence Viewer

Length: 1443 bp
ATGGACACTCTTGACTCACAACTAGAGATGGATTTAGTCATAGCAGTGAGAGATAAGGATCCTGATACTGCAATAATTAAGAGACTTTCGGAGAAGCTGCACCTCAGAACCATCAACGATCTGAAACAAGAGTCACTTGCTTTCCATGAATTGGTTATAGCAAGTGGCGGAGATCTAGGGGACCAGTTTGAACAGATGCAAGCTCTTTTTAAGAAGCTAAATGACTATGTGGTGACAGAAAACCCAGAAATTGACAGCTCTGAACGTGACAAGGGCACGATCAAGCACAGATCTCCAGTTATTCCAGATGATTTCCGGTGTCCAATATCTCTAGAATTGATGAAAGATCCTGTCATTGTATCTACTGGACAGACATATGAAAGATCCTGTATTCAGAAGTGGTTGGATGCTGGACACAAAACCTGTCCCAAAACACAGCAGACACTATTGCACACGGCCATAACCCCAAACTATGTTCTGAAGAGTCTAATTGCTTTGTGGTGCGAGAGCAATGGCGTTGAGCTACCCAAAAAGCAAGGGAATAAAAGCAAAAAACCAGGATGCAGTGTTTCAGACTGTGATCGTGCTTCTATTGATTCTTTATTAGAAAAATTGGCAAAGGGGAGTTCAGATGAACAAAGAGCAGCTGCTGGAGAGCTCCGCTTGCTGGCAAAAAGGAATGCAGATAATAGAGTGTGTATTGCTGATGCAGGAGCCATCCCACTCCTTGTTGAGCTTCTATCCTCCCCAGATCCTCGGACCCAAGAGCACGCCGTTACAGCACTCCTTAACCTTTCAATAAATGAGAGTAACAAGGGAGCAATTGTCATTGCAGGAGCTATACCTGATATAGTAGAAGTTTTGAAAAATGGTAGCATGGAGGCTAGAGAAAATGCAGCTGCAACCCTTTTCAGCTTGTCTGTAGTAGATGAGAACAAGGTGCAAATTGGAGCTGCTGGGGCTATCCCAGCCCTTATCAAATTGCTCTGCGAGGGGACTCCAAGAGGAAAAAAGGATGCTGCTACAGCTATATTCAATCTTTCGATCTACCAGGGAAACAAGGCCAGGGCTGTAAGGGCTGGTATTGTGACCCCGCTGATGAGATTGCTCAAGGATGCGGGAAGTGGGATGGTGGATGAAGCTCTTGCAATCCTGGCCATTCTGGCGAGCCATCACGAAGGAAAGGTGGCAATTGCTCAAGCTGAGGCAATCCCAGTTTTGGTGGAAGTTATACGAACTGGTTTCCCACGGAACCGGGAGAATGCTGCTGCTGTGTTATGGTCATTATGCACAGGTGATTTGCAGCAATTGAAACTAGCAAGGGAACTTGGTGCAGAAGAAGCATTGCAGGAACTTTCAGAAAATGGCACTGATAGGGCCAAGAGAAAAGCTGGAAATGTTTTAGAGCTCCTTCAACGAATCGATGACCCTGCTAGTCCATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RdDM_RDM1

Protein Analysis

480

Amino Acids

51.92

Weight (kDa)

5.67

Isoelectric Point (pI)

26.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
U-box PF04564 101 - 171 1.4e-21 U-box domain
ARM_ARMC5 PF24768 180 - 372 3.2e-10 ARMC5
ARM_PUB PF25598 198 - 472 3.4e-24 Plant U-box protein ARM repeat region
Arm PF00514 227 - 266 1.4e-11 Armadillo/beta-catenin-like repeat
ARM_ARMC5 PF24768 264 - 431 2.3e-09 ARMC5
Arm PF00514 310 - 348 1.2e-06 Armadillo/beta-catenin-like repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 151
AciI CCGC 4 cut(s) 168, 661, 1094, 1118
AclWI GGATC 5 cut(s) 53, 66, 341, 378, 746
AcoI YGGCCR 2 cut(s) 456, 1155
AcuI CTGAAG 1 cut(s) 500
AfiI CCNNNNNNNGG 3 cut(s) 151, 667, 1219
AgsI TTSAA 6 cut(s) 191, 798, 865, 1036, 1312, 1415
AjnI CCWGG 4 cut(s) 556, 1050, 1064, 1152
Alw21I GWGCWC 3 cut(s) 660, 771, 1410
Alw26I GTCTC 1 cut(s) 76
AlwI GGATC 5 cut(s) 53, 66, 341, 378, 746
AlwNI CAGNNNCTG 1 cut(s) 650
AoxI GGCC 4 cut(s) 456, 1062, 1155, 1377
AspS9I GGNCC 3 cut(s) 181, 759, 1377
AsuC2I CCSGG 1 cut(s) 1256
AsuHPI GGTGA 2 cut(s) 244, 1307
AvaII GGWCC 2 cut(s) 181, 759
BaeGI GKGCMC 1 cut(s) 278
BalI TGGCCA 1 cut(s) 1157
BamHI GGATCC 1 cut(s) 58
BanII GRGCYC 2 cut(s) 660, 1410
Bbv12I GWGCWC 3 cut(s) 660, 771, 1410
BbvCI CCTCAGC 1 cut(s) 1203
BccI CCATC 5 cut(s) 22, 119, 725, 1123, 1179
BceAI ACGGC 2 cut(s) 471, 758
BcgI CGANNNNNNTGC 1 cut(s) 1412
BciT130I CCWGG 4 cut(s) 558, 1052, 1066, 1154
BcnI CCSGG 1 cut(s) 1256
BcoDI GTCTC 1 cut(s) 76
BfaI CTAG 6 cut(s) 23, 176, 332, 885, 1316, 1434
BfmI CTRYAG 2 cut(s) 921, 1023
BglI GCCNNNNNGGC 1 cut(s) 1163
BglII AGATCT 2 cut(s) 172, 290
Bme1390I CCNGG 5 cut(s) 558, 1052, 1066, 1154, 1256
Bme18I GGWCC 2 cut(s) 181, 759
BmgT120I GGNCC 3 cut(s) 181, 759, 1377
BmiI GGNNCC 5 cut(s) 60, 182, 715, 761, 1253
BmrFI CCNGG 5 cut(s) 558, 1052, 1066, 1154, 1256
BmrI ACTGGG 1 cut(s) 1208
BmsI GCATC 6 cut(s) 186, 397, 551, 697, 1006, 1105
BmuI ACTGGG 1 cut(s) 1208
BpmI CTGGAG 2 cut(s) 279, 672
Bpu10I CCTNAGC 1 cut(s) 1203
BpuEI CTTGAG 2 cut(s) 1094, 1182
BpuMI CCSGG 1 cut(s) 1256
Bsa29I ATCGAT 1 cut(s) 1422
BsaBI GATNNNNATC 1 cut(s) 57
BsaJI CCNNGG 4 cut(s) 755, 1051, 1065, 1247
BsaWI WCCGGW 1 cut(s) 315
BsaXI ACNNNNNCTCC 2 cut(s) 810, 840
Bsc4I CCNNNNNNNGG 3 cut(s) 151, 667, 1219
Bse1I ACTGG 5 cut(s) 184, 296, 370, 1214, 1243
Bse3DI GCAATG 3 cut(s) 517, 828, 1343
Bse8I GATNNNNATC 1 cut(s) 57
BseBI CCWGG 4 cut(s) 558, 1052, 1066, 1154
BseCI ATCGAT 1 cut(s) 1422
BseDI CCNNGG 4 cut(s) 755, 1051, 1065, 1247
BseGI GGATG 7 cut(s) 412, 566, 717, 1021, 1120, 1134, 1141
BseJI GATNNNNATC 1 cut(s) 57
BseLI CCNNNNNNNGG 3 cut(s) 151, 667, 1219
BseMI GCAATG 3 cut(s) 517, 828, 1343
BseMII CTCAG 2 cut(s) 118, 1194
BseNI ACTGG 5 cut(s) 184, 296, 370, 1214, 1243
BseSI GKGCMC 1 cut(s) 278
BseYI CCCAGC 2 cut(s) 956, 967
BsgI GTGCAG 2 cut(s) 83, 1353
BshFI GGCC 4 cut(s) 458, 1064, 1157, 1379
BshVI ATCGAT 1 cut(s) 1422
BsiHKAI GWGCWC 3 cut(s) 660, 771, 1410
BsiSI CCGG 2 cut(s) 316, 1255
BslFI GGGAC 3 cut(s) 194, 411, 1009
BslI CCNNNNNNNGG 3 cut(s) 151, 667, 1219
BsmAI GTCTC 1 cut(s) 76
BsmFI GGGAC 3 cut(s) 194, 411, 1009
BsmI GAATGC 2 cut(s) 685, 1267
BsnI GGCC 4 cut(s) 458, 1064, 1157, 1379
Bsp1286I GDGCHC 4 cut(s) 278, 660, 771, 1410
BspACI CCGC 4 cut(s) 168, 661, 1094, 1118
BspANI GGCC 4 cut(s) 458, 1064, 1157, 1379
BspCNI CTCAG 2 cut(s) 117, 1195
BspDI ATCGAT 1 cut(s) 1422
BspLI GGNNCC 5 cut(s) 60, 182, 715, 761, 1253
BspPI GGATC 5 cut(s) 53, 66, 341, 378, 746
BsrDI GCAATG 3 cut(s) 517, 828, 1343
BsrI ACTGG 5 cut(s) 184, 296, 370, 1214, 1243
BssECI CCNNGG 4 cut(s) 755, 1051, 1065, 1247
Bst2UI CCWGG 4 cut(s) 558, 1052, 1066, 1154
Bst4CI ACNGT 1 cut(s) 578
Bst6I CTCTTC 1 cut(s) 476
BstC8I GCNNGC 5 cut(s) 201, 665, 669, 771, 1168
BstDEI CTNAG 2 cut(s) 104, 1203
BstDSI CCRYGG 1 cut(s) 1247
BstF5I GGATG 7 cut(s) 412, 566, 717, 1021, 1120, 1134, 1141
BstMAI GTCTC 1 cut(s) 76
BstMWI GCNNNNNNNGC 9 cut(s) 664, 779, 959, 968, 1025, 1076, 1154, 1163, 1340
BstNI CCWGG 4 cut(s) 558, 1052, 1066, 1154
BstSCI CCNGG 5 cut(s) 556, 1050, 1064, 1152, 1254
BstSFI CTRYAG 2 cut(s) 921, 1023
BstSLI GKGCMC 1 cut(s) 278
BstX2I RGATCY 6 cut(s) 58, 172, 290, 346, 383, 751
BstYI RGATCY 6 cut(s) 58, 172, 290, 346, 383, 751
Bsu15I ATCGAT 1 cut(s) 1422
BsuRI GGCC 4 cut(s) 458, 1064, 1157, 1379
BsuTUI ATCGAT 1 cut(s) 1422
BtgI CCRYGG 1 cut(s) 1247
BtsCI GGATG 7 cut(s) 412, 566, 717, 1021, 1120, 1134, 1141
BtsI GCAGTG 2 cut(s) 51, 571
BtsIMutI CAGTG 3 cut(s) 51, 571, 1368
Cac8I GCNNGC 5 cut(s) 201, 665, 669, 771, 1168
CaiI CAGNNNCTG 1 cut(s) 650
Cfr13I GGNCC 3 cut(s) 181, 759, 1377
ClaI ATCGAT 1 cut(s) 1422
CviAII CATG 2 cut(s) 146, 877
DdeI CTNAG 2 cut(s) 104, 1203
EaeI YGGCCR 2 cut(s) 456, 1155
Eam1104I CTCTTC 1 cut(s) 476
EarI CTCTTC 1 cut(s) 476
EciI GGCGGA 1 cut(s) 183
Ecl136II GAGCTC 2 cut(s) 658, 1408
Eco24I GRGCYC 2 cut(s) 660, 1410
Eco47I GGWCC 2 cut(s) 181, 759
Eco53kI GAGCTC 2 cut(s) 658, 1408
Eco57I CTGAAG 1 cut(s) 500
EcoICRI GAGCTC 2 cut(s) 658, 1408
EcoRII CCWGG 4 cut(s) 556, 1050, 1064, 1152
EcoT38I GRGCYC 2 cut(s) 660, 1410
FaeI CATG 2 cut(s) 149, 880
FalI AAGNNNNNCTT 2 cut(s) 120, 152
FaqI GGGAC 3 cut(s) 194, 411, 1009
FatI CATG 2 cut(s) 145, 876
FauI CCCGC 2 cut(s) 1101, 1111
FauNDI CATATG 1 cut(s) 376
FokI GGATG 7 cut(s) 419, 573, 704, 1028, 1127, 1141, 1148
FriOI GRGCYC 2 cut(s) 660, 1410
FspBI CTAG 6 cut(s) 23, 176, 332, 885, 1316, 1434
GsaI CCCAGC 2 cut(s) 960, 971
GsuI CTGGAG 2 cut(s) 279, 672
HaeIII GGCC 4 cut(s) 458, 1064, 1157, 1379
HapII CCGG 2 cut(s) 316, 1255
Hin1II CATG 2 cut(s) 149, 880
HinfI GANTC 6 cut(s) 14, 131, 484, 596, 997, 1419
HpaII CCGG 2 cut(s) 316, 1255
HphI GGTGA 2 cut(s) 244, 1307
Hpy188III TCNNGA 5 cut(s) 11, 62, 305, 332, 1175
HpyAV CCTTC 2 cut(s) 1172, 1421
HpyCH4III ACNGT 1 cut(s) 578
HpyCH4IV ACGT 1 cut(s) 265
HpyF10VI GCNNNNNNNGC 9 cut(s) 664, 779, 959, 968, 1025, 1076, 1154, 1163, 1340
HpyF3I CTNAG 2 cut(s) 104, 1203
HpySE526I ACGT 1 cut(s) 265
Hsp92II CATG 2 cut(s) 149, 880
LmnI GCTCC 6 cut(s) 663, 713, 818, 836, 950, 1413
LweI GCATC 6 cut(s) 186, 397, 551, 697, 1006, 1105
MaeI CTAG 6 cut(s) 23, 176, 332, 885, 1316, 1434
MaeII ACGT 1 cut(s) 265
MaeIII GTNAC 6 cut(s) 132, 232, 266, 775, 809, 1087
MboII GAAGA 2 cut(s) 493, 1349
MfeI CAATTG 3 cut(s) 822, 1191, 1307
MflI RGATCY 6 cut(s) 58, 172, 290, 346, 383, 751
MhlI GDGCHC 4 cut(s) 278, 660, 771, 1410
MlsI TGGCCA 1 cut(s) 1157
MluNI TGGCCA 1 cut(s) 1157
MlyI GAGTC 4 cut(s) 8, 140, 493, 991
MmeI TCCRAC 1 cut(s) 384
MnlI CCTC 7 cut(s) 113, 754, 765, 874, 985, 998, 1198
Mox20I TGGCCA 1 cut(s) 1157
MscI TGGCCA 1 cut(s) 1157
MseI TTAA 3 cut(s) 78, 210, 789
MslI CAYNNNNRTG 1 cut(s) 44
Msp20I TGGCCA 1 cut(s) 1157
MspA1I CMGCKG 3 cut(s) 647, 899, 1096
MspI CCGG 2 cut(s) 316, 1255
MspR9I CCNGG 5 cut(s) 558, 1052, 1066, 1154, 1256
MunI CAATTG 3 cut(s) 822, 1191, 1307
Mva1269I GAATGC 2 cut(s) 685, 1267
MvaI CCWGG 4 cut(s) 558, 1052, 1066, 1154
MwoI GCNNNNNNNGC 9 cut(s) 664, 779, 959, 968, 1025, 1076, 1154, 1163, 1340
NciI CCSGG 1 cut(s) 1256
NdeI CATATG 1 cut(s) 376
NlaIII CATG 2 cut(s) 149, 880
NlaIV GGNNCC 5 cut(s) 60, 182, 715, 761, 1253
NmuCI GTSAC 4 cut(s) 132, 232, 266, 1087
PctI GAATGC 2 cut(s) 685, 1267
PfeI GAWTC 2 cut(s) 596, 1419
PflMI CCANNNNNTGG 1 cut(s) 151
PleI GAGTC 4 cut(s) 8, 139, 492, 991
PpsI GAGTC 4 cut(s) 8, 139, 492, 991
Psp124BI GAGCTC 2 cut(s) 660, 1410
Psp6I CCWGG 4 cut(s) 556, 1050, 1064, 1152
PspFI CCCAGC 2 cut(s) 956, 967
PspGI CCWGG 4 cut(s) 556, 1050, 1064, 1152
PspN4I GGNNCC 5 cut(s) 60, 182, 715, 761, 1253
PspPI GGNCC 3 cut(s) 181, 759, 1377
PstNI CAGNNNCTG 1 cut(s) 650
PsuI RGATCY 6 cut(s) 58, 172, 290, 346, 383, 751
PvuII CAGCTG 2 cut(s) 647, 899
RseI CAYNNNNRTG 1 cut(s) 44
SacI GAGCTC 2 cut(s) 660, 1410
SaqAI TTAA 3 cut(s) 78, 210, 789
Sau96I GGNCC 3 cut(s) 181, 759, 1377
SchI GAGTC 4 cut(s) 8, 140, 493, 991
ScrFI CCNGG 5 cut(s) 558, 1052, 1066, 1154, 1256
SduI GDGCHC 4 cut(s) 278, 660, 771, 1410
SfaNI GCATC 6 cut(s) 186, 397, 551, 697, 1006, 1105
SfcI CTRYAG 2 cut(s) 921, 1023
SinI GGWCC 2 cut(s) 181, 759
SmiMI CAYNNNNRTG 1 cut(s) 44
SmlI CTYRAG 2 cut(s) 1109, 1197
SmoI CTYRAG 2 cut(s) 1109, 1197
SsiI CCGC 4 cut(s) 168, 661, 1094, 1118
SspMI CTAG 6 cut(s) 23, 176, 332, 885, 1316, 1434
SstI GAGCTC 2 cut(s) 660, 1410
StyD4I CCNGG 5 cut(s) 556, 1050, 1064, 1152, 1254
TaaI ACNGT 1 cut(s) 578
TaiI ACGT 1 cut(s) 268
TaqI TCGA 2 cut(s) 1043, 1422
TfiI GAWTC 2 cut(s) 596, 1419
Tru1I TTAA 3 cut(s) 78, 210, 789
Tru9I TTAA 3 cut(s) 78, 210, 789
TscAI CASTG 3 cut(s) 51, 571, 1375
TseFI GTSAC 4 cut(s) 132, 232, 266, 1087
Tsp45I GTSAC 4 cut(s) 132, 232, 266, 1087
TspDTI ATGAA 5 cut(s) 162, 356, 393, 648, 1152
TspGWI ACGGA 1 cut(s) 1264
TspRI CASTG 3 cut(s) 51, 571, 1375
Van91I CCANNNNNTGG 1 cut(s) 151
VpaK11BI GGWCC 2 cut(s) 181, 759
XbaI TCTAGA 1 cut(s) 331
XspI CTAG 6 cut(s) 23, 176, 332, 885, 1316, 1434
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.