Rh5AG182400

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0002579
Physical Location & Seq
Forward (+)
20699884 .. 20702306
2423 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG182400.1

Sequence Viewer

Length: 561 bp
ATGGCTACCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGGAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTACCGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCATACCGCATTCGGCCAAAACACTGACCTCGACCACCTCACCATCTGCGCCTCTCTCCGCTCCAATTCTAAGAACAAGCTATGGATAAATAATGAAATAAGGAACTCTTGTAAACTGATATTGCTGATGATTCTAAGAAAATTATTCATTGTGTCTTCAACTCTGTTTTGTTGTGGAGGGTTTATTTACAAGACTCAAGTTATGGGAAAGCGTGGTATTGATGCATTGCCTGGCATGACAATTGTATCTGCTTACTTAGAAACTGTGAGCATTACCAACATAATTTACATAGCAAGTACTAGTGATTATTGCCTTATGGCTTGTATATTACCTAATTGCTTATGGATGCGAGATTAA

Protein Analysis

186

Amino Acids

20.43

Weight (kDa)

7.54

Isoelectric Point (pI)

45.77

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_N PF03871 34 - 97 1.2e-16 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)
AatII GACGTC 1 cut(s) 81
AccBSI CCGCTC 1 cut(s) 264
AciI CCGC 4 cut(s) 39, 56, 210, 262
AcoI YGGCCR 1 cut(s) 217
AcyI GRCGYC 2 cut(s) 24, 78
AfaI GTAC 3 cut(s) 113, 130, 502
AflIII ACRYGT 1 cut(s) 117
AgeI ACCGGT 1 cut(s) 108
AgsI TTSAA 1 cut(s) 363
AhlI ACTAGT 1 cut(s) 503
AjnI CCWGG 1 cut(s) 433
AluBI AGCT 3 cut(s) 96, 105, 283
AluI AGCT 3 cut(s) 96, 105, 283
Alw26I GTCTC 1 cut(s) 126
AoxI GGCC 2 cut(s) 49, 217
AsiGI ACCGGT 1 cut(s) 108
AspLEI GCGC 1 cut(s) 254
AspS9I GGNCC 1 cut(s) 178
AsuC2I CCSGG 1 cut(s) 53
AsuHPI GGTGA 2 cut(s) 145, 235
AvaII GGWCC 1 cut(s) 178
BaeI ACNNNNGTAYC 2 cut(s) 432, 465
BbsI GAAGAC 1 cut(s) 351
BccI CCATC 2 cut(s) 130, 254
BceAI ACGGC 1 cut(s) 11
BciT130I CCWGG 1 cut(s) 435
BcnI CCSGG 1 cut(s) 53
BcoDI GTCTC 1 cut(s) 126
BcuI ACTAGT 1 cut(s) 503
BfaI CTAG 1 cut(s) 504
BlpI GCTNAGC 1 cut(s) 146
BmcAI AGTACT 1 cut(s) 502
Bme1390I CCNGG 2 cut(s) 53, 435
Bme18I GGWCC 1 cut(s) 178
BmgT120I GGNCC 1 cut(s) 178
BmrFI CCNGG 2 cut(s) 53, 435
BmsI GCATC 4 cut(s) 50, 132, 415, 540
BpiI GAAGAC 1 cut(s) 351
Bpu1102I GCTNAGC 1 cut(s) 146
BpuEI CTTGAG 1 cut(s) 384
BpuMI CCSGG 1 cut(s) 53
BsaAI YACGTR 1 cut(s) 118
BsaHI GRCGYC 2 cut(s) 24, 78
BsaJI CCNNGG 2 cut(s) 9, 154
BsaWI WCCGGW 1 cut(s) 108
Bse118I RCCGGY 1 cut(s) 108
Bse3DI GCAATG 1 cut(s) 428
BseBI CCWGG 1 cut(s) 435
BseDI CCNNGG 2 cut(s) 9, 154
BseGI GGATG 2 cut(s) 65, 555
BseMI GCAATG 1 cut(s) 428
BseMII CTCAG 2 cut(s) 137, 189
BseRI GAGGAG 1 cut(s) 60
Bsh1285I CGRYCG 1 cut(s) 154
BshFI GGCC 2 cut(s) 51, 219
BshTI ACCGGT 1 cut(s) 108
BsiEI CGRYCG 1 cut(s) 154
BsiSI CCGG 2 cut(s) 52, 109
BsiWI CGTACG 1 cut(s) 128
BsmAI GTCTC 1 cut(s) 126
BsmI GAATGC 1 cut(s) 212
BsnI GGCC 2 cut(s) 51, 219
Bsp1720I GCTNAGC 1 cut(s) 146
BspACI CCGC 4 cut(s) 39, 56, 210, 262
BspANI GGCC 2 cut(s) 51, 219
BspCNI CTCAG 2 cut(s) 138, 190
BsrBI CCGCTC 1 cut(s) 264
BsrDI GCAATG 1 cut(s) 428
BsrFI RCCGGY 1 cut(s) 108
BssAI RCCGGY 1 cut(s) 108
BssECI CCNNGG 2 cut(s) 9, 154
BssNI GRCGYC 2 cut(s) 24, 78
Bst2UI CCWGG 1 cut(s) 435
Bst4CI ACNGT 3 cut(s) 10, 133, 469
BstACI GRCGYC 2 cut(s) 24, 78
BstBAI YACGTR 1 cut(s) 118
BstDEI CTNAG 5 cut(s) 146, 198, 273, 338, 460
BstDSI CCRYGG 1 cut(s) 9
BstF5I GGATG 2 cut(s) 65, 555
BstHHI GCGC 1 cut(s) 254
BstMAI GTCTC 1 cut(s) 126
BstMCI CGRYCG 1 cut(s) 154
BstMWI GCNNNNNNNGC 3 cut(s) 69, 102, 156
BstNI CCWGG 1 cut(s) 435
BstSCI CCNGG 2 cut(s) 51, 433
BstV2I GAAGAC 1 cut(s) 351
BsuRI GGCC 2 cut(s) 51, 219
BtgI CCRYGG 1 cut(s) 9
BtsCI GGATG 2 cut(s) 65, 555
BtsIMutI CAGTG 2 cut(s) 195, 225
CfoI GCGC 1 cut(s) 254
Cfr10I RCCGGY 1 cut(s) 108
Cfr13I GGNCC 1 cut(s) 178
CseI GACGC 1 cut(s) 32
Csp6I GTAC 3 cut(s) 112, 129, 501
CspAI ACCGGT 1 cut(s) 108
CviAII CATG 2 cut(s) 64, 439
CviJI RGCY 9 cut(s) 5, 51, 72, 96, 105, 159, 219, 283, 524
CviKI_1 RGCY 9 cut(s) 5, 51, 72, 96, 105, 159, 219, 283, 524
CviQI GTAC 3 cut(s) 112, 129, 501
DdeI CTNAG 5 cut(s) 146, 198, 273, 338, 460
EaeI YGGCCR 1 cut(s) 217
Eco47I GGWCC 1 cut(s) 178
EcoRII CCWGG 1 cut(s) 433
EcoT22I ATGCAT 2 cut(s) 65, 430
FaeI CATG 2 cut(s) 67, 442
FalI AAGNNNNNCTT 2 cut(s) 295, 327
FatI CATG 2 cut(s) 63, 438
FauI CCCGC 1 cut(s) 49
FokI GGATG 1 cut(s) 72
FspBI CTAG 1 cut(s) 504
GlaI GCGC 1 cut(s) 253
HaeIII GGCC 2 cut(s) 51, 219
HapII CCGG 2 cut(s) 52, 109
HgaI GACGC 1 cut(s) 32
HhaI GCGC 1 cut(s) 254
Hin1I GRCGYC 2 cut(s) 24, 78
Hin1II CATG 2 cut(s) 67, 442
Hin6I GCGC 1 cut(s) 252
HinP1I GCGC 1 cut(s) 252
HinfI GANTC 3 cut(s) 173, 334, 397
HpaII CCGG 2 cut(s) 52, 109
HphI GGTGA 2 cut(s) 145, 235
Hpy166II GTNNAC 1 cut(s) 317
Hpy188I TCNGA 1 cut(s) 178
Hpy8I GTNNAC 1 cut(s) 317
Hpy99I CGWCG 6 cut(s) 26, 80, 83, 86, 129, 170
HpyCH4III ACNGT 3 cut(s) 10, 133, 469
HpyCH4IV ACGT 3 cut(s) 78, 117, 165
HpyCH4V TGCA 2 cut(s) 63, 428
HpyF10VI GCNNNNNNNGC 3 cut(s) 69, 102, 156
HpyF3I CTNAG 5 cut(s) 146, 198, 273, 338, 460
HpySE526I ACGT 3 cut(s) 78, 117, 165
Hsp92I GRCGYC 2 cut(s) 24, 78
Hsp92II CATG 2 cut(s) 67, 442
HspAI GCGC 1 cut(s) 252
LmnI GCTCC 2 cut(s) 93, 269
LpnPI CCDG 4 cut(s) 65, 122, 420, 447
LweI GCATC 4 cut(s) 50, 132, 415, 540
MaeI CTAG 1 cut(s) 504
MaeII ACGT 3 cut(s) 78, 117, 165
MbiI CCGCTC 1 cut(s) 264
MboII GAAGA 1 cut(s) 351
MfeI CAATTG 1 cut(s) 444
MluCI AATT 5 cut(s) 268, 344, 444, 486, 538
MlyI GAGTC 2 cut(s) 167, 391
MnlI CCTC 9 cut(s) 38, 41, 83, 149, 191, 242, 251, 265, 374
Mph1103I ATGCAT 2 cut(s) 65, 430
MseI TTAA 1 cut(s) 559
MspI CCGG 2 cut(s) 52, 109
MspR9I CCNGG 2 cut(s) 53, 435
MunI CAATTG 1 cut(s) 444
Mva1269I GAATGC 1 cut(s) 212
MvaI CCWGG 1 cut(s) 435
MwoI GCNNNNNNNGC 3 cut(s) 69, 102, 156
NciI CCSGG 1 cut(s) 53
NlaIII CATG 2 cut(s) 67, 442
NsiI ATGCAT 2 cut(s) 65, 430
PctI GAATGC 1 cut(s) 212
PfeI GAWTC 1 cut(s) 334
Pfl23II CGTACG 1 cut(s) 128
PflFI GACNNNGTC 1 cut(s) 80
PinAI ACCGGT 1 cut(s) 108
PleI GAGTC 2 cut(s) 167, 391
PpsI GAGTC 2 cut(s) 167, 391
Ppu21I YACGTR 1 cut(s) 118
Psp6I CCWGG 1 cut(s) 433
PspGI CCWGG 1 cut(s) 433
PspLI CGTACG 1 cut(s) 128
PspPI GGNCC 1 cut(s) 178
PsyI GACNNNGTC 1 cut(s) 80
RsaI GTAC 3 cut(s) 113, 130, 502
RsaNI GTAC 3 cut(s) 112, 129, 501
SaqAI TTAA 1 cut(s) 559
Sau96I GGNCC 1 cut(s) 178
ScaI AGTACT 1 cut(s) 502
SchI GAGTC 2 cut(s) 167, 391
ScrFI CCNGG 2 cut(s) 53, 435
SfaNI GCATC 4 cut(s) 50, 132, 415, 540
SinI GGWCC 1 cut(s) 178
SmlI CTYRAG 1 cut(s) 399
SmoI CTYRAG 1 cut(s) 399
SpeI ACTAGT 1 cut(s) 503
Sse9I AATT 5 cut(s) 268, 344, 444, 486, 538
SsiI CCGC 4 cut(s) 39, 56, 210, 262
SspMI CTAG 1 cut(s) 504
StyD4I CCNGG 2 cut(s) 51, 433
TaaI ACNGT 3 cut(s) 10, 133, 469
TaiI ACGT 3 cut(s) 81, 120, 168
TaqI TCGA 1 cut(s) 234
TaqII GACCGA 1 cut(s) 168
TasI AATT 5 cut(s) 268, 344, 444, 486, 538
TatI WGTACW 1 cut(s) 500
TfiI GAWTC 1 cut(s) 334
Tru1I TTAA 1 cut(s) 559
Tru9I TTAA 1 cut(s) 559
TscAI CASTG 2 cut(s) 202, 232
TspDTI ATGAA 2 cut(s) 312, 340
TspRI CASTG 2 cut(s) 202, 232
Tth111I GACNNNGTC 1 cut(s) 80
VpaK11BI GGWCC 1 cut(s) 178
XspI CTAG 1 cut(s) 504
ZraI GACGTC 1 cut(s) 79
ZrmI AGTACT 1 cut(s) 502
Zsp2I ATGCAT 2 cut(s) 65, 430
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.