RLG00000000071

Bacterial RNA polymerase, alpha chain C terminal domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Unknown
OG0016509
Physical Location & Seq
Reverse (-)
405296 .. 406780
1485 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000000071

Sequence Viewer

Length: 684 bp
ATGGCAAAACCTATACCAAAAATTGGTTCACGTAGAAATAGACGTATTGGTTCACGTAAGAATGCGCGTAGAATACCAAAGGGAGTTATTCATGTTCAAGCAAGTTTCAACAATACCATTGTGACTGTTACAGATGTACGGGGTCGAGTAATTTCTTGGTCCTCCGCCGGTACTTGTGGATTCAAGGGTACAAGAAGAGGGACACCATTTGCCGCTCAAACCGCAGCGGGAAATGCTATTCGTACAGTGGTGGATCAAGGTATGCAACGAGCAGAAGTCATGATAAAAGGCCCGGGTCTCGGGAGAGATGCGGCATTAAGAGCTATTCGTAGAAGTGGCATACTATTAAGTTTCATACGGGATTGGAAGTGTGTTGAATCAAGAGCAGACAGTAAGCGTCTTTATTATGGACGCTTTATTCTGGCCCCACTTATGAAAGGCCAAGCCGATACAATAGGCATCGCGATGCGAAGAGCTTTACTCGGAGAAATAGAAGGAACATGTATTACACGTGCAAGATCTGAGAAAATACCACACGAATATTCTACCATCGTAGGTATTCAAGAATCTGTACATGAAATTTTAATGAATTTGAAAGAAATTGTATTGAGAAGTAATCTGTATGGAACTCGTAATGCGTCTATTTGTGTCAAGGGTCCTGGAACTGCCCCCGAGGGTCTATAA

Protein Analysis

228

Amino Acids

24.84

Weight (kDa)

11.12

Isoelectric Point (pI)

38.27

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ribosomal_S11 PF00411 28 - 122 3.2e-39 Ribosomal protein S11
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0016509)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00750
fragaria_vesca FvH4_c3g00200
pyrus_communis pycom12397g00170
rosa_chinensis RchiOBHm_CPg0501901
rosa_laevigata RLG00000000055 RLG00000000071 RLG00000000177 RLG00000000219 RLG00000037103
rosa_roxburghii Rroxscaffold_2G00119010
rosa_rugosa RorugMtG0002700.1
rosa_samantha Rh1CG032700
rosa_wichuraiana Rw7G013550 Rw7G013560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 23
AccBSI CCGCTC 1 cut(s) 215
AccII CGCG 2 cut(s) 67, 464
AciI CCGC 5 cut(s) 165, 213, 222, 227, 311
AclWI GGATC 1 cut(s) 261
AcsI RAATTY 2 cut(s) 579, 589
AcvI CACGTG 1 cut(s) 512
AfaI GTAC 5 cut(s) 138, 172, 190, 244, 573
AfiI CCNNNNNNNGG 2 cut(s) 23, 299
AflIII ACRYGT 2 cut(s) 500, 509
AgsI TTSAA 6 cut(s) 98, 109, 184, 377, 563, 595
AjnI CCWGG 1 cut(s) 658
AjuI GAANNNNNNNTTGG 2 cut(s) 10, 42
AluBI AGCT 2 cut(s) 323, 476
AluI AGCT 2 cut(s) 323, 476
Alw26I GTCTC 1 cut(s) 302
AlwI GGATC 1 cut(s) 261
Ama87I CYCGRG 3 cut(s) 292, 299, 671
AoxI GGCC 3 cut(s) 289, 423, 439
ApeKI GCWGC 1 cut(s) 224
ApoI RAATTY 2 cut(s) 579, 589
AspLEI GCGC 1 cut(s) 67
AspS9I GGNCC 4 cut(s) 159, 290, 424, 656
AsuC2I CCSGG 2 cut(s) 293, 294
AvaI CYCGRG 3 cut(s) 292, 299, 671
AvaII GGWCC 2 cut(s) 159, 656
BbrPI CACGTG 1 cut(s) 512
BbvI GCAGC 1 cut(s) 236
BccI CCATC 1 cut(s) 557
BciT130I CCWGG 1 cut(s) 660
BcnI CCSGG 2 cut(s) 293, 294
BcoDI GTCTC 1 cut(s) 302
BglII AGATCT 1 cut(s) 518
BisI GCNGC 3 cut(s) 213, 225, 312
BlsI GCNGC 3 cut(s) 214, 226, 313
Bme1390I CCNGG 3 cut(s) 293, 294, 660
Bme18I GGWCC 2 cut(s) 159, 656
BmeT110I CYCGRG 3 cut(s) 292, 299, 671
BmgT120I GGNCC 4 cut(s) 159, 290, 424, 656
BmiI GGNNCC 2 cut(s) 426, 657
BmrFI CCNGG 3 cut(s) 293, 294, 660
BmsI GCATC 3 cut(s) 298, 456, 468
BplI GAGNNNNNCTC 2 cut(s) 465, 497
BpuMI CCSGG 2 cut(s) 293, 294
BsaAI YACGTR 3 cut(s) 32, 56, 512
BsaI GGTCTC 1 cut(s) 302
BsaJI CCNNGG 2 cut(s) 292, 672
Bsc4I CCNNNNNNNGG 2 cut(s) 23, 299
Bse118I RCCGGY 1 cut(s) 167
BseBI CCWGG 1 cut(s) 660
BseDI CCNNGG 2 cut(s) 292, 672
BseLI CCNNNNNNNGG 2 cut(s) 23, 299
BseMII CTCAG 1 cut(s) 513
BseXI GCAGC 1 cut(s) 236
Bsh1236I CGCG 2 cut(s) 67, 464
BshFI GGCC 3 cut(s) 291, 425, 441
BsiHKCI CYCGRG 3 cut(s) 292, 299, 671
BsiSI CCGG 2 cut(s) 168, 293
BslFI GGGAC 1 cut(s) 214
BslI CCNNNNNNNGG 2 cut(s) 23, 299
BsmAI GTCTC 1 cut(s) 302
BsmFI GGGAC 1 cut(s) 214
BsmI GAATGC 1 cut(s) 67
BsnI GGCC 3 cut(s) 291, 425, 441
Bso31I GGTCTC 1 cut(s) 302
BsoBI CYCGRG 3 cut(s) 292, 299, 671
Bsp1407I TGTACA 1 cut(s) 571
Bsp143I GATC 2 cut(s) 253, 518
Bsp68I TCGCGA 1 cut(s) 464
BspACI CCGC 5 cut(s) 165, 213, 222, 227, 311
BspANI GGCC 3 cut(s) 291, 425, 441
BspCNI CTCAG 1 cut(s) 514
BspFNI CGCG 2 cut(s) 67, 464
BspHI TCATGA 1 cut(s) 279
BspLI GGNNCC 2 cut(s) 426, 657
BspPI GGATC 1 cut(s) 261
BspQI GCTCTTC 1 cut(s) 466
BspTNI GGTCTC 1 cut(s) 302
BsrBI CCGCTC 1 cut(s) 215
BsrFI RCCGGY 1 cut(s) 167
BsrGI TGTACA 1 cut(s) 571
BssAI RCCGGY 1 cut(s) 167
BssECI CCNNGG 2 cut(s) 292, 672
BssMI GATC 2 cut(s) 253, 518
Bst2UI CCWGG 1 cut(s) 660
Bst4CI ACNGT 3 cut(s) 127, 247, 392
Bst6I CTCTTC 2 cut(s) 190, 466
BstAUI TGTACA 1 cut(s) 571
BstBAI YACGTR 3 cut(s) 32, 56, 512
BstDEI CTNAG 1 cut(s) 522
BstFNI CGCG 2 cut(s) 67, 464
BstHHI GCGC 1 cut(s) 67
BstKTI GATC 2 cut(s) 256, 521
BstMAI GTCTC 1 cut(s) 302
BstMBI GATC 2 cut(s) 253, 518
BstMWI GCNNNNNNNGC 3 cut(s) 221, 233, 320
BstNI CCWGG 1 cut(s) 660
BstNSI RCATGY 1 cut(s) 504
BstSCI CCNGG 3 cut(s) 291, 292, 658
BstUI CGCG 2 cut(s) 67, 464
BstV1I GCAGC 1 cut(s) 236
BstX2I RGATCY 1 cut(s) 518
BstYI RGATCY 1 cut(s) 518
BsuRI GGCC 3 cut(s) 291, 425, 441
BtgZI GCGATG 2 cut(s) 445, 479
BtsIMutI CAGTG 1 cut(s) 252
BtuMI TCGCGA 1 cut(s) 464
CciI TCATGA 1 cut(s) 279
CfoI GCGC 1 cut(s) 67
Cfr10I RCCGGY 1 cut(s) 167
Cfr13I GGNCC 4 cut(s) 159, 290, 424, 656
Cfr9I CCCGGG 1 cut(s) 292
CseI GACGC 3 cut(s) 386, 420, 627
Csp6I GTAC 5 cut(s) 137, 171, 189, 243, 572
CviAII CATG 4 cut(s) 92, 280, 501, 575
CviJI RGCY 6 cut(s) 291, 323, 425, 441, 446, 476
CviKI_1 RGCY 6 cut(s) 291, 323, 425, 441, 446, 476
CviQI GTAC 5 cut(s) 137, 171, 189, 243, 572
DdeI CTNAG 1 cut(s) 522
DpnI GATC 2 cut(s) 255, 520
DpnII GATC 2 cut(s) 253, 518
Eam1104I CTCTTC 2 cut(s) 190, 466
EarI CTCTTC 2 cut(s) 190, 466
EciI GGCGGA 1 cut(s) 154
Eco31I GGTCTC 1 cut(s) 302
Eco47I GGWCC 2 cut(s) 159, 656
Eco72I CACGTG 1 cut(s) 512
Eco88I CYCGRG 3 cut(s) 292, 299, 671
EcoO109I RGGNCCY 1 cut(s) 656
EcoRII CCWGG 1 cut(s) 658
FaeI CATG 4 cut(s) 95, 283, 504, 578
FaqI GGGAC 1 cut(s) 214
FatI CATG 4 cut(s) 91, 279, 500, 574
FauI CCCGC 1 cut(s) 220
Fnu4HI GCNGC 3 cut(s) 213, 225, 312
Fsp4HI GCNGC 3 cut(s) 213, 225, 312
GlaI GCGC 1 cut(s) 66
GluI GCNGC 3 cut(s) 213, 225, 312
HaeIII GGCC 3 cut(s) 291, 425, 441
HapII CCGG 2 cut(s) 168, 293
HgaI GACGC 3 cut(s) 386, 420, 627
HhaI GCGC 1 cut(s) 67
Hin1II CATG 4 cut(s) 95, 283, 504, 578
Hin6I GCGC 1 cut(s) 65
HinP1I GCGC 1 cut(s) 65
HinfI GANTC 3 cut(s) 180, 377, 566
HpaII CCGG 2 cut(s) 168, 293
Hpy166II GTNNAC 2 cut(s) 29, 53
Hpy188I TCNGA 2 cut(s) 485, 523
Hpy188III TCNNGA 5 cut(s) 280, 301, 381, 463, 563
Hpy8I GTNNAC 2 cut(s) 29, 53
HpyAV CCTTC 1 cut(s) 488
HpyCH4III ACNGT 3 cut(s) 127, 247, 392
HpyCH4IV ACGT 4 cut(s) 31, 43, 55, 511
HpyCH4V TGCA 2 cut(s) 265, 515
HpyF10VI GCNNNNNNNGC 3 cut(s) 221, 233, 320
HpyF3I CTNAG 1 cut(s) 522
HpySE526I ACGT 4 cut(s) 31, 43, 55, 511
Hsp92II CATG 4 cut(s) 95, 283, 504, 578
HspAI GCGC 1 cut(s) 65
Kzo9I GATC 2 cut(s) 253, 518
LguI GCTCTTC 1 cut(s) 466
LpnPI CCDG 5 cut(s) 181, 306, 407, 645, 672
Lsp1109I GCAGC 1 cut(s) 236
LweI GCATC 3 cut(s) 298, 456, 468
MaeII ACGT 4 cut(s) 31, 43, 55, 511
MaeIII GTNAC 2 cut(s) 121, 127
MalI GATC 2 cut(s) 255, 520
MbiI CCGCTC 1 cut(s) 215
MboI GATC 2 cut(s) 253, 518
MboII GAAGA 2 cut(s) 207, 483
MflI RGATCY 1 cut(s) 518
MluCI AATT 5 cut(s) 21, 150, 579, 589, 600
MnlI CCTC 3 cut(s) 172, 191, 667
MseI TTAA 3 cut(s) 317, 347, 584
MslI CAYNNNNRTG 1 cut(s) 464
MspA1I CMGCKG 1 cut(s) 227
MspI CCGG 2 cut(s) 168, 293
MspR9I CCNGG 3 cut(s) 293, 294, 660
Mva1269I GAATGC 1 cut(s) 67
MvaI CCWGG 1 cut(s) 660
MvnI CGCG 2 cut(s) 67, 464
MwoI GCNNNNNNNGC 3 cut(s) 221, 233, 320
NciI CCSGG 2 cut(s) 293, 294
NdeII GATC 2 cut(s) 253, 518
NlaIII CATG 4 cut(s) 95, 283, 504, 578
NlaIV GGNNCC 2 cut(s) 426, 657
NmuCI GTSAC 1 cut(s) 121
NruI TCGCGA 1 cut(s) 464
NspI RCATGY 1 cut(s) 504
PagI TCATGA 1 cut(s) 279
PciI ACATGT 1 cut(s) 500
PciSI GCTCTTC 1 cut(s) 466
PctI GAATGC 1 cut(s) 67
PfeI GAWTC 3 cut(s) 180, 377, 566
PflMI CCANNNNNTGG 1 cut(s) 23
PfoI TCCNGGA 1 cut(s) 658
PkrI GCNGC 3 cut(s) 214, 226, 313
PmaCI CACGTG 1 cut(s) 512
PmlI CACGTG 1 cut(s) 512
Ppu21I YACGTR 3 cut(s) 32, 56, 512
PpuMI RGGWCCY 1 cut(s) 656
PscI ACATGT 1 cut(s) 500
Psp5II RGGWCCY 1 cut(s) 656
Psp6I CCWGG 1 cut(s) 658
PspCI CACGTG 1 cut(s) 512
PspGI CCWGG 1 cut(s) 658
PspN4I GGNNCC 2 cut(s) 426, 657
PspPI GGNCC 4 cut(s) 159, 290, 424, 656
PspPPI RGGWCCY 1 cut(s) 656
PsrI GAACNNNNNNTAC 2 cut(s) 490, 522
PsuI RGATCY 1 cut(s) 518
RruI TCGCGA 1 cut(s) 464
RsaI GTAC 5 cut(s) 138, 172, 190, 244, 573
RsaNI GTAC 5 cut(s) 137, 171, 189, 243, 572
RseI CAYNNNNRTG 1 cut(s) 464
SapI GCTCTTC 1 cut(s) 466
SaqAI TTAA 3 cut(s) 317, 347, 584
SatI GCNGC 3 cut(s) 213, 225, 312
Sau3AI GATC 2 cut(s) 253, 518
Sau96I GGNCC 4 cut(s) 159, 290, 424, 656
ScrFI CCNGG 3 cut(s) 293, 294, 660
SetI ASST 9 cut(s) 13, 34, 46, 58, 262, 325, 478, 514, 559
SfaNI GCATC 3 cut(s) 298, 456, 468
SinI GGWCC 2 cut(s) 159, 656
SmaI CCCGGG 1 cut(s) 294
SmiMI CAYNNNNRTG 1 cut(s) 464
Sse9I AATT 5 cut(s) 21, 150, 579, 589, 600
SsiI CCGC 5 cut(s) 165, 213, 222, 227, 311
SspI AATATT 1 cut(s) 542
StyD4I CCNGG 3 cut(s) 291, 292, 658
TaaI ACNGT 3 cut(s) 127, 247, 392
TaiI ACGT 4 cut(s) 34, 46, 58, 514
TaqI TCGA 1 cut(s) 145
TasI AATT 5 cut(s) 21, 150, 579, 589, 600
TatI WGTACW 1 cut(s) 571
TauI GCSGC 2 cut(s) 215, 314
TfiI GAWTC 3 cut(s) 180, 377, 566
Tru1I TTAA 3 cut(s) 317, 347, 584
Tru9I TTAA 3 cut(s) 317, 347, 584
TscAI CASTG 1 cut(s) 252
TseFI GTSAC 1 cut(s) 121
TseI GCWGC 1 cut(s) 224
Tsp45I GTSAC 1 cut(s) 121
TspDTI ATGAA 5 cut(s) 80, 343, 449, 591, 602
TspMI CCCGGG 1 cut(s) 292
TspRI CASTG 1 cut(s) 252
Van91I CCANNNNNTGG 1 cut(s) 23
VpaK11BI GGWCC 2 cut(s) 159, 656
XapI RAATTY 2 cut(s) 579, 589
XceI RCATGY 1 cut(s) 504
XmaI CCCGGG 1 cut(s) 292
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.