RLG00000000282

RNA polymerase Rpb1, domain 5

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr1
OG0017067
Physical Location & Seq
Reverse (-)
351651 .. 353754
2104 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000000282

Sequence Viewer

Length: 1431 bp
ATGGATAAGATATTCCGACACAATGGCATCTTGATACCGCCAGGAACAAATTCTAAGGAATCAAAAAAGCGGAACAATTGGATTTATGTCCAATGGATCACACCCACCAAGAAAAAGTATTTTGTTTTGGTTCGACCCGTAATCATATATGAAATTGCGGACGGTATAAATTTAGCAACACTTTTCCCCCAGGATCCATTGCGGGAAAGGGATAATCTAGAACTTCGAGTTGTAAATTATATACTTTATGGAAATGGCAAACCAATTCGGGGAATTTCCGGCACAAGTATTCAATTAGTTCGGACCTGTTTAATCTTGAACTGGGACAAAAACAAAAAAAGTTCTTCTATCGAAGAGGCCCACGCTTCCTTTGTTGAAGTAAGTGCGAATGGTCTGATTCAAGATTTCCTCAGAATCAACTTAGTGAAATCCCATACTTCGTATATCCGAAAAAGGAATGATCCATTAGGTTCAGGATTGATCTCTGATAATAGGTCGGATCCCAAAAAAGGATCGCCCCTAAAATCGGGTCAAGTTATAGTCGTTCAACTTGACTCTTTAGTAATAAGATCGGCGAAGCCTTATTTAGCTACTCCAGGAGCAACTGTTCATGGACATTATGGAGAAATCCTTTCCGAAGGAGATACATTAGTTACATTTATATATGAAAAATCTCGATCTGGTGATATAACGCAAGGTCTTCCAAAAGTAGAACAGGTTTTAGAGGTACGTTCGATTGATTCAATATCGATGAACCTAGAAAAGAGAGTTGAGGGTTGGAATGAGTGTATAACAAGAATTCTTGGAATTCCTTGGGGATTCTTGATTGGCGCTGAGCTAACTATAGCGCAAAGTCGTATCTCTTTGGTTAATAAGATCCAAAAAGTTTATAGATCCCAGGGGGTACAGATCCATAATAGGCATATCGAAATCATTGTACGTCAAATAACATCAAAAGTGTTGGTTTCAGAAGATGGAATGTCTAATGTTTTTTCACCCGGAGAACTAATTGGATTGCTGCGAGCTGAACGAACGGGGCGCGCTTTAGAAGAAGCGATTTGTTACCGAGCCATATTATTAGGAATAACGAAAGCATCTCTAAATACTCAAAGTTTCATATCCGAAGCAAGTTTTCAAGAAACTGCTCGAGTTTTAGCAAAAGCTGCCCTCCGGGGTCGTATCGATTGGTTGAAAGGTCTGAAAGAGAACGTTGTTCTAGGAGGGATGATACCCGTTGGTACCGGATTCAAAGGATTCGTGCCCCGTTCAAGGCAACATAACAACATTTCTTTGGAAACCAAAAATAAGAGTTTATTCGAGGGGGAAATGAGAGATATTTTGGTCCACCACAGAGAATTATTTGATTTTTGCATTTCAAAAAATTTACATGATACATCAGAACAATCTTTTTTCGGATTTAATGATTCCTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00190 ko00195 ko00230 ko00240 ko01100 ko03020 map00190 map00195 map00230 map00240 map01100 map03020
Pfam Domains
Protein Families
RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5 Ribosomal_S2

Protein Analysis

477

Amino Acids

53.42

Weight (kDa)

9.49

Isoelectric Point (pI)

41.19

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb1_5 PF04998 280 - 368 4.2e-08 RNA polymerase Rpb1, domain 5
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)
Acc65I GGTACC 1 cut(s) 1238
AccB1I GGYRCC 1 cut(s) 1238
AccII CGCG 1 cut(s) 1041
AciI CCGC 4 cut(s) 38, 70, 158, 202
AclI AACGTT 1 cut(s) 1209
AcsI RAATTY 6 cut(s) 49, 169, 273, 798, 807, 1381
AfaI GTAC 4 cut(s) 729, 906, 939, 1240
AfiI CCNNNNNNNGG 4 cut(s) 269, 509, 526, 1269
AjnI CCWGG 4 cut(s) 40, 189, 595, 897
AloI GAACNNNNNNTCC 2 cut(s) 591, 623
AluBI AGCT 4 cut(s) 590, 838, 1025, 1163
AluI AGCT 4 cut(s) 590, 838, 1025, 1163
Ama87I CYCGRG 1 cut(s) 1146
AoxI GGCC 1 cut(s) 357
ApeKI GCWGC 2 cut(s) 1018, 1163
ApoI RAATTY 6 cut(s) 49, 169, 273, 798, 807, 1381
Asp700I GAANNNNTTC 1 cut(s) 49
Asp718I GGTACC 1 cut(s) 1238
AspLEI GCGC 4 cut(s) 833, 850, 1041, 1043
AspS9I GGNCC 3 cut(s) 303, 358, 1342
AsuC2I CCSGG 2 cut(s) 999, 1172
AsuHPI GGTGA 2 cut(s) 695, 987
AvaI CYCGRG 1 cut(s) 1146
AvaII GGWCC 2 cut(s) 303, 1342
BaeGI GKGCMC 1 cut(s) 1263
BaeI ACNNNNGTAYC 2 cut(s) 636, 669
BamHI GGATCC 2 cut(s) 193, 499
BanI GGYRCC 1 cut(s) 1238
BbsI GAAGAC 1 cut(s) 692
BbvI GCAGC 2 cut(s) 1005, 1150
BccI CCATC 1 cut(s) 968
BciT130I CCWGG 4 cut(s) 42, 191, 597, 899
BcnI CCSGG 2 cut(s) 999, 1172
BfaI CTAG 3 cut(s) 218, 758, 1217
BfmI CTRYAG 1 cut(s) 843
BfoI RGCGCY 1 cut(s) 834
BisI GCNGC 2 cut(s) 1019, 1164
BlpI GCTNAGC 1 cut(s) 834
BlsI GCNGC 2 cut(s) 1020, 1165
Bme1390I CCNGG 6 cut(s) 42, 191, 597, 899, 999, 1172
Bme18I GGWCC 2 cut(s) 303, 1342
BmeT110I CYCGRG 1 cut(s) 1146
BmgT120I GGNCC 3 cut(s) 303, 358, 1342
BmiI GGNNCC 3 cut(s) 195, 501, 1240
BmrFI CCNGG 6 cut(s) 42, 191, 597, 899, 999, 1172
BmrI ACTGGG 1 cut(s) 331
BmsI GCATC 2 cut(s) 36, 1103
BmuI ACTGGG 1 cut(s) 331
BpiI GAAGAC 1 cut(s) 692
BpmI CTGGAG 1 cut(s) 579
Bpu1102I GCTNAGC 1 cut(s) 834
BpuMI CCSGG 2 cut(s) 999, 1172
Bsa29I ATCGAT 2 cut(s) 749, 1182
BsaJI CCNNGG 5 cut(s) 189, 812, 897, 898, 1171
BsaWI WCCGGW 1 cut(s) 1241
BsaXI ACNNNNNCTCC 2 cut(s) 591, 621
Bsc4I CCNNNNNNNGG 4 cut(s) 269, 509, 526, 1269
Bse1I ACTGG 1 cut(s) 326
Bse3DI GCAATG 1 cut(s) 197
BseBI CCWGG 4 cut(s) 42, 191, 597, 899
BseCI ATCGAT 2 cut(s) 749, 1182
BseDI CCNNGG 5 cut(s) 189, 812, 897, 898, 1171
BseGI GGATG 1 cut(s) 1230
BseLI CCNNNNNNNGG 4 cut(s) 269, 509, 526, 1269
BseMI GCAATG 1 cut(s) 197
BseMII CTCAG 2 cut(s) 424, 825
BseNI ACTGG 1 cut(s) 326
BsePI GCGCGC 1 cut(s) 1039
BseSI GKGCMC 1 cut(s) 1263
BseXI GCAGC 2 cut(s) 1005, 1150
Bsh1236I CGCG 1 cut(s) 1041
BshFI GGCC 1 cut(s) 359
BshNI GGYRCC 1 cut(s) 1238
BshVI ATCGAT 2 cut(s) 749, 1182
BsiHKCI CYCGRG 1 cut(s) 1146
BsiSI CCGG 4 cut(s) 279, 999, 1171, 1242
BslFI GGGAC 1 cut(s) 338
BslI CCNNNNNNNGG 4 cut(s) 269, 509, 526, 1269
BsmFI GGGAC 1 cut(s) 338
BsnI GGCC 1 cut(s) 359
BsoBI CYCGRG 1 cut(s) 1146
Bsp1286I GDGCHC 1 cut(s) 1263
Bsp1720I GCTNAGC 1 cut(s) 834
BspACI CCGC 4 cut(s) 38, 70, 158, 202
BspANI GGCC 1 cut(s) 359
BspCNI CTCAG 2 cut(s) 423, 826
BspDI ATCGAT 2 cut(s) 749, 1182
BspFNI CGCG 1 cut(s) 1041
BspLI GGNNCC 3 cut(s) 195, 501, 1240
BspT107I GGYRCC 1 cut(s) 1238
BsrDI GCAATG 1 cut(s) 197
BsrI ACTGG 1 cut(s) 326
BssECI CCNNGG 5 cut(s) 189, 812, 897, 898, 1171
BssHII GCGCGC 1 cut(s) 1039
BssT1I CCWWGG 1 cut(s) 812
Bst2UI CCWGG 4 cut(s) 42, 191, 597, 899
Bst4CI ACNGT 2 cut(s) 164, 607
Bst6I CTCTTC 1 cut(s) 348
BstAPI GCANNNNNTGC 1 cut(s) 1163
BstC8I GCNNGC 2 cut(s) 1023, 1041
BstDEI CTNAG 4 cut(s) 54, 410, 421, 834
BstF5I GGATG 1 cut(s) 1230
BstFNI CGCG 1 cut(s) 1041
BstH2I RGCGCY 1 cut(s) 834
BstHHI GCGC 4 cut(s) 833, 850, 1041, 1043
BstMWI GCNNNNNNNGC 1 cut(s) 1163
BstNI CCWGG 4 cut(s) 42, 191, 597, 899
BstSCI CCNGG 6 cut(s) 40, 189, 595, 897, 997, 1170
BstSFI CTRYAG 1 cut(s) 843
BstSLI GKGCMC 1 cut(s) 1263
BstUI CGCG 1 cut(s) 1041
BstV1I GCAGC 2 cut(s) 1005, 1150
BstV2I GAAGAC 1 cut(s) 692
BstX2I RGATCY 5 cut(s) 193, 499, 876, 893, 909
BstYI RGATCY 5 cut(s) 193, 499, 876, 893, 909
Bsu15I ATCGAT 2 cut(s) 749, 1182
BsuRI GGCC 1 cut(s) 359
BsuTUI ATCGAT 2 cut(s) 749, 1182
BtsCI GGATG 1 cut(s) 1230
Cac8I GCNNGC 2 cut(s) 1023, 1041
CfoI GCGC 4 cut(s) 833, 850, 1041, 1043
Cfr13I GGNCC 3 cut(s) 303, 358, 1342
ClaI ATCGAT 2 cut(s) 749, 1182
Csp6I GTAC 4 cut(s) 728, 905, 938, 1239
CviAII CATG 2 cut(s) 611, 1388
CviJI RGCY 7 cut(s) 359, 580, 590, 838, 1025, 1070, 1163
CviKI_1 RGCY 7 cut(s) 359, 580, 590, 838, 1025, 1070, 1163
CviQI GTAC 4 cut(s) 728, 905, 938, 1239
DdeI CTNAG 4 cut(s) 54, 410, 421, 834
Eam1104I CTCTTC 1 cut(s) 348
EarI CTCTTC 1 cut(s) 348
Eco130I CCWWGG 1 cut(s) 812
Eco47I GGWCC 2 cut(s) 303, 1342
Eco88I CYCGRG 1 cut(s) 1146
EcoRI GAATTC 2 cut(s) 798, 807
EcoRII CCWGG 4 cut(s) 40, 189, 595, 897
EcoT14I CCWWGG 1 cut(s) 812
ErhI CCWWGG 1 cut(s) 812
FaeI CATG 2 cut(s) 614, 1391
FaqI GGGAC 1 cut(s) 338
FatI CATG 2 cut(s) 610, 1387
FauI CCCGC 1 cut(s) 195
Fnu4HI GCNGC 2 cut(s) 1019, 1164
FokI GGATG 1 cut(s) 1237
Fsp4HI GCNGC 2 cut(s) 1019, 1164
FspBI CTAG 3 cut(s) 218, 758, 1217
GlaI GCGC 4 cut(s) 832, 849, 1040, 1042
GluI GCNGC 2 cut(s) 1019, 1164
GsuI CTGGAG 1 cut(s) 579
HaeII RGCGCY 1 cut(s) 834
HaeIII GGCC 1 cut(s) 359
HapII CCGG 4 cut(s) 279, 999, 1171, 1242
HhaI GCGC 4 cut(s) 833, 850, 1041, 1043
Hin1II CATG 2 cut(s) 614, 1391
Hin6I GCGC 4 cut(s) 831, 848, 1039, 1041
HinP1I GCGC 4 cut(s) 831, 848, 1039, 1041
HinfI GANTC 9 cut(s) 59, 397, 414, 554, 740, 819, 1245, 1254, 1424
HpaII CCGG 4 cut(s) 279, 999, 1171, 1242
HphI GGTGA 2 cut(s) 695, 987
Hpy166II GTNNAC 1 cut(s) 1345
Hpy188III TCNNGA 8 cut(s) 31, 218, 316, 401, 474, 675, 823, 1136
Hpy8I GTNNAC 1 cut(s) 1345
HpyAV CCTTC 1 cut(s) 632
HpyCH4III ACNGT 2 cut(s) 164, 607
HpyCH4IV ACGT 3 cut(s) 730, 940, 1209
HpyCH4V TGCA 1 cut(s) 1371
HpyF10VI GCNNNNNNNGC 1 cut(s) 1163
HpyF3I CTNAG 4 cut(s) 54, 410, 421, 834
HpySE526I ACGT 3 cut(s) 730, 940, 1209
Hsp92II CATG 2 cut(s) 614, 1391
HspAI GCGC 4 cut(s) 831, 848, 1039, 1041
KpnI GGTACC 1 cut(s) 1242
LmnI GCTCC 1 cut(s) 599
Lsp1109I GCAGC 2 cut(s) 1005, 1150
LweI GCATC 2 cut(s) 36, 1103
MaeI CTAG 3 cut(s) 218, 758, 1217
MaeII ACGT 3 cut(s) 730, 940, 1209
MaeIII GTNAC 2 cut(s) 652, 1061
MboII GAAGA 5 cut(s) 336, 365, 692, 983, 1061
MfeI CAATTG 1 cut(s) 76
MflI RGATCY 5 cut(s) 193, 499, 876, 893, 909
MhlI GDGCHC 1 cut(s) 1263
MlyI GAGTC 1 cut(s) 548
MmeI TCCRAC 3 cut(s) 40, 477, 758
MnlI CCTC 7 cut(s) 349, 419, 718, 766, 1178, 1214, 1312
MroXI GAANNNNTTC 1 cut(s) 49
MseI TTAA 3 cut(s) 311, 870, 1419
MspI CCGG 4 cut(s) 279, 999, 1171, 1242
MspR9I CCNGG 6 cut(s) 42, 191, 597, 899, 999, 1172
MunI CAATTG 1 cut(s) 76
MvaI CCWGG 4 cut(s) 42, 191, 597, 899
MvnI CGCG 1 cut(s) 1041
MwoI GCNNNNNNNGC 1 cut(s) 1163
NciI CCSGG 2 cut(s) 999, 1172
NlaIII CATG 2 cut(s) 614, 1391
NlaIV GGNNCC 3 cut(s) 195, 501, 1240
PaeR7I CTCGAG 1 cut(s) 1146
PasI CCCWGGG 1 cut(s) 898
PauI GCGCGC 1 cut(s) 1039
PdmI GAANNNNTTC 1 cut(s) 49
PfeI GAWTC 8 cut(s) 59, 397, 414, 740, 819, 1245, 1254, 1424
PfoI TCCNGGA 1 cut(s) 595
PkrI GCNGC 2 cut(s) 1020, 1165
PleI GAGTC 1 cut(s) 548
PpsI GAGTC 1 cut(s) 548
Psp1406I AACGTT 1 cut(s) 1209
Psp6I CCWGG 4 cut(s) 40, 189, 595, 897
PspGI CCWGG 4 cut(s) 40, 189, 595, 897
PspN4I GGNNCC 3 cut(s) 195, 501, 1240
PspPI GGNCC 3 cut(s) 303, 358, 1342
PspXI VCTCGAGB 1 cut(s) 1146
PsuI RGATCY 5 cut(s) 193, 499, 876, 893, 909
PteI GCGCGC 1 cut(s) 1039
RsaI GTAC 4 cut(s) 729, 906, 939, 1240
RsaNI GTAC 4 cut(s) 728, 905, 938, 1239
SaqAI TTAA 3 cut(s) 311, 870, 1419
SatI GCNGC 2 cut(s) 1019, 1164
Sau96I GGNCC 3 cut(s) 303, 358, 1342
SchI GAGTC 1 cut(s) 548
ScrFI CCNGG 6 cut(s) 42, 191, 597, 899, 999, 1172
SduI GDGCHC 1 cut(s) 1263
SfaNI GCATC 2 cut(s) 36, 1103
SfcI CTRYAG 1 cut(s) 843
Sfr274I CTCGAG 1 cut(s) 1146
SinI GGWCC 2 cut(s) 303, 1342
SlaI CTCGAG 1 cut(s) 1146
SmlI CTYRAG 1 cut(s) 1146
SmoI CTYRAG 1 cut(s) 1146
SsiI CCGC 4 cut(s) 38, 70, 158, 202
SspMI CTAG 3 cut(s) 218, 758, 1217
StyD4I CCNGG 6 cut(s) 40, 189, 595, 897, 997, 1170
StyI CCWWGG 1 cut(s) 812
TaaI ACNGT 2 cut(s) 164, 607
TaiI ACGT 3 cut(s) 733, 943, 1212
TfiI GAWTC 8 cut(s) 59, 397, 414, 740, 819, 1245, 1254, 1424
Tru1I TTAA 3 cut(s) 311, 870, 1419
Tru9I TTAA 3 cut(s) 311, 870, 1419
TseI GCWGC 2 cut(s) 1018, 1163
TspDTI ATGAA 5 cut(s) 165, 599, 681, 767, 1105
VpaK11BI GGWCC 2 cut(s) 303, 1342
XapI RAATTY 6 cut(s) 49, 169, 273, 798, 807, 1381
XbaI TCTAGA 1 cut(s) 217
XhoI CTCGAG 1 cut(s) 1146
XmnI GAANNNNTTC 1 cut(s) 49
XspI CTAG 3 cut(s) 218, 758, 1217
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.