RchiOBHm_Chr3g0472601

DNA-directed RNA polymerases I, II, and III subunit RPABC1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0003607
Physical Location & Seq
Forward (+)
18523373 .. 18524422
1050 bp
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UTR
Exon/CDS
Intron
PRQ43829

Sequence Viewer

Length: 438 bp
ATGGCTGCCGTGGTCTTGAACGAAGCCGTTTCGGGTGGCGGTAGAGGCCGGCCGGGATGCATGACGAGCCATGGAGGAGGAGGAGGAAGGAGCTTGGAGAGCTACAGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCTACTCGGACCTCACTCGCTCATTCACTAAGTTCCGTACCGCGTTCGGCCAAAACCCTGACCTCGACCTCCTCACCATCTGCGTCTCTCTCAGCTCCAATTCCAAGAACAAGATTATGGTCATGTTCTGTGGAACTGATGAAATCAGAAAGGCGAGTGTTCGTGCCATTCATGCTATCCTCCTGAACAAGGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTCGAAAAGAACTGGTAAACTATCCTCACAAAGTTGA

Protein Analysis

145

Amino Acids

15.8

Weight (kDa)

9.96

Isoelectric Point (pI)

50.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_N PF03871 33 - 112 4.9e-21 RNA polymerase Rpb5, N-terminal domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 209
AciI CCGC 2 cut(s) 39, 207
AcoI YGGCCR 2 cut(s) 50, 214
AfaI GTAC 3 cut(s) 110, 127, 205
AfiI CCNNNNNNNGG 1 cut(s) 355
AflIII ACRYGT 1 cut(s) 114
AgsI TTSAA 1 cut(s) 19
AluBI AGCT 4 cut(s) 93, 102, 261, 366
AluI AGCT 4 cut(s) 93, 102, 261, 366
Alw26I GTCTC 2 cut(s) 123, 256
AoxI GGCC 3 cut(s) 46, 50, 214
ApeKI GCWGC 1 cut(s) 5
AspS9I GGNCC 1 cut(s) 175
AsuC2I CCSGG 1 cut(s) 54
AsuHPI GGTGA 2 cut(s) 142, 232
AvaII GGWCC 1 cut(s) 175
BccI CCATC 2 cut(s) 127, 251
BceAI ACGGC 1 cut(s) 11
BcnI CCSGG 1 cut(s) 54
BcoDI GTCTC 2 cut(s) 123, 256
BfmI CTRYAG 1 cut(s) 103
BisI GCNGC 1 cut(s) 6
BlpI GCTNAGC 1 cut(s) 143
BlsI GCNGC 1 cut(s) 7
Bme1390I CCNGG 1 cut(s) 54
Bme18I GGWCC 1 cut(s) 175
BmgT120I GGNCC 1 cut(s) 175
BmrFI CCNGG 1 cut(s) 54
BmsI GCATC 3 cut(s) 47, 129, 363
Bpu1102I GCTNAGC 1 cut(s) 143
BpuMI CCSGG 1 cut(s) 54
BsaAI YACGTR 1 cut(s) 115
BsaJI CCNNGG 3 cut(s) 9, 70, 151
Bsc4I CCNNNNNNNGG 1 cut(s) 355
Bse118I RCCGGY 1 cut(s) 48
Bse1I ACTGG 1 cut(s) 418
BseDI CCNNGG 3 cut(s) 9, 70, 151
BseGI GGATG 1 cut(s) 62
BseLI CCNNNNNNNGG 1 cut(s) 355
BseMII CTCAG 2 cut(s) 134, 271
BseNI ACTGG 1 cut(s) 418
BseRI GAGGAG 5 cut(s) 90, 93, 96, 227, 391
BseX3I CGGCCG 1 cut(s) 50
Bsh1236I CGCG 1 cut(s) 209
Bsh1285I CGRYCG 2 cut(s) 53, 151
BshFI GGCC 3 cut(s) 48, 52, 216
BsiEI CGRYCG 2 cut(s) 53, 151
BsiSI CCGG 2 cut(s) 49, 53
BsiWI CGTACG 1 cut(s) 125
BslI CCNNNNNNNGG 1 cut(s) 355
BsmAI GTCTC 2 cut(s) 123, 256
BsmBI CGTCTC 1 cut(s) 256
BsnI GGCC 3 cut(s) 48, 52, 216
Bsp1720I GCTNAGC 1 cut(s) 143
Bsp19I CCATGG 1 cut(s) 70
BspACI CCGC 2 cut(s) 39, 207
BspANI GGCC 3 cut(s) 48, 52, 216
BspCNI CTCAG 2 cut(s) 135, 270
BspFNI CGCG 1 cut(s) 209
BsrFI RCCGGY 1 cut(s) 48
BsrI ACTGG 1 cut(s) 418
BssAI RCCGGY 1 cut(s) 48
BssECI CCNNGG 3 cut(s) 9, 70, 151
BssT1I CCWWGG 1 cut(s) 70
Bst4CI ACNGT 1 cut(s) 130
BstBAI YACGTR 1 cut(s) 115
BstC8I GCNNGC 1 cut(s) 50
BstDEI CTNAG 3 cut(s) 143, 195, 257
BstDSI CCRYGG 2 cut(s) 9, 70
BstENI CCTNNNNNAGG 1 cut(s) 353
BstF5I GGATG 1 cut(s) 62
BstFNI CGCG 1 cut(s) 209
BstMAI GTCTC 2 cut(s) 123, 256
BstMCI CGRYCG 2 cut(s) 53, 151
BstMWI GCNNNNNNNGC 6 cut(s) 45, 66, 99, 153, 338, 382
BstSCI CCNGG 1 cut(s) 52
BstSFI CTRYAG 1 cut(s) 103
BstUI CGCG 1 cut(s) 209
BstZI CGGCCG 1 cut(s) 50
BsuRI GGCC 3 cut(s) 48, 52, 216
BtgI CCRYGG 2 cut(s) 9, 70
BtsCI GGATG 1 cut(s) 62
Cac8I GCNNGC 1 cut(s) 50
Cfr10I RCCGGY 1 cut(s) 48
Cfr13I GGNCC 1 cut(s) 175
CseI GACGC 1 cut(s) 238
Csp6I GTAC 3 cut(s) 109, 126, 204
CviAII CATG 4 cut(s) 61, 71, 289, 338
CviQI GTAC 3 cut(s) 109, 126, 204
DdeI CTNAG 3 cut(s) 143, 195, 257
EaeI YGGCCR 2 cut(s) 50, 214
EagI CGGCCG 1 cut(s) 50
EclXI CGGCCG 1 cut(s) 50
Eco130I CCWWGG 1 cut(s) 70
Eco47I GGWCC 1 cut(s) 175
Eco52I CGGCCG 1 cut(s) 50
EcoNI CCTNNNNNAGG 1 cut(s) 353
EcoT14I CCWWGG 1 cut(s) 70
EcoT22I ATGCAT 1 cut(s) 62
ErhI CCWWGG 1 cut(s) 70
Esp3I CGTCTC 1 cut(s) 256
FaeI CATG 4 cut(s) 64, 74, 292, 341
FaiI YATR 6 cut(s) 62, 72, 284, 290, 339, 362
FatI CATG 4 cut(s) 60, 70, 288, 337
Fnu4HI GCNGC 1 cut(s) 6
FokI GGATG 1 cut(s) 69
FseI GGCCGGCC 1 cut(s) 52
Fsp4HI GCNGC 1 cut(s) 6
GluI GCNGC 1 cut(s) 6
HaeIII GGCC 3 cut(s) 48, 52, 216
HapII CCGG 2 cut(s) 49, 53
HgaI GACGC 1 cut(s) 238
Hin1II CATG 4 cut(s) 64, 74, 292, 341
HpaII CCGG 2 cut(s) 49, 53
HphI GGTGA 2 cut(s) 142, 232
Hpy166II GTNNAC 1 cut(s) 419
Hpy188I TCNGA 3 cut(s) 175, 314, 372
Hpy188III TCNNGA 2 cut(s) 16, 349
Hpy8I GTNNAC 1 cut(s) 419
Hpy99I CGWCG 2 cut(s) 126, 167
HpyAV CCTTC 1 cut(s) 81
HpyCH4III ACNGT 1 cut(s) 130
HpyCH4IV ACGT 2 cut(s) 114, 162
HpyCH4V TGCA 2 cut(s) 60, 385
HpyF10VI GCNNNNNNNGC 6 cut(s) 45, 66, 99, 153, 338, 382
HpyF3I CTNAG 3 cut(s) 143, 195, 257
HpySE526I ACGT 2 cut(s) 114, 162
Hsp92II CATG 4 cut(s) 64, 74, 292, 341
KroI GCCGGC 1 cut(s) 48
KroNI GCCGGC 1 cut(s) 50
LmnI GCTCC 2 cut(s) 90, 266
LpnPI CCDG 7 cut(s) 62, 66, 91, 237, 362, 395, 399
LweI GCATC 3 cut(s) 47, 129, 363
MaeII ACGT 2 cut(s) 114, 162
MluCI AATT 1 cut(s) 265
Mph1103I ATGCAT 1 cut(s) 62
MroNI GCCGGC 1 cut(s) 48
MspI CCGG 2 cut(s) 49, 53
MspR9I CCNGG 1 cut(s) 54
MvnI CGCG 1 cut(s) 209
MwoI GCNNNNNNNGC 6 cut(s) 45, 66, 99, 153, 338, 382
NaeI GCCGGC 1 cut(s) 50
NciI CCSGG 1 cut(s) 54
NcoI CCATGG 1 cut(s) 70
NgoMIV GCCGGC 1 cut(s) 48
NlaIII CATG 4 cut(s) 64, 74, 292, 341
NsiI ATGCAT 1 cut(s) 62
PdiI GCCGGC 1 cut(s) 50
Pfl23II CGTACG 1 cut(s) 125
PkrI GCNGC 1 cut(s) 7
Ppu21I YACGTR 1 cut(s) 115
PspLI CGTACG 1 cut(s) 125
PspPI GGNCC 1 cut(s) 175
RigI GGCCGGCC 1 cut(s) 52
RsaI GTAC 3 cut(s) 110, 127, 205
RsaNI GTAC 3 cut(s) 109, 126, 204
SatI GCNGC 1 cut(s) 6
Sau96I GGNCC 1 cut(s) 175
ScrFI CCNGG 1 cut(s) 54
SfaNI GCATC 3 cut(s) 47, 129, 363
SfcI CTRYAG 1 cut(s) 103
SinI GGWCC 1 cut(s) 175
Sse9I AATT 1 cut(s) 265
SsiI CCGC 2 cut(s) 39, 207
StyD4I CCNGG 1 cut(s) 52
StyI CCWWGG 1 cut(s) 70
TaaI ACNGT 1 cut(s) 130
TaiI ACGT 2 cut(s) 117, 165
TaqI TCGA 2 cut(s) 231, 404
TaqII GACCGA 1 cut(s) 165
TasI AATT 1 cut(s) 265
TseI GCWGC 1 cut(s) 5
TspDTI ATGAA 3 cut(s) 321, 326, 410
TspGWI ACGGA 1 cut(s) 191
VpaK11BI GGWCC 1 cut(s) 175
XagI CCTNNNNNAGG 1 cut(s) 353
Zsp2I ATGCAT 1 cut(s) 62
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.