RCHIOBHM_CPG0501901

Bacterial RNA polymerase, alpha chain C terminal domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
Pt
OG0016509
Physical Location & Seq
Forward (+)
32174 .. 33715
1542 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ15682

Sequence Viewer

Length: 1395 bp
ATGGCAAAACCTATACCAAAAATTGGTTCACGTAGAAATAGACGTATTGGTTCACGTAAGAATGCGCGTAGAATACCAAAGGGAGTTATTCATGTTCAAGCAAGTTTCAACAATACCATTGTGACTGTTACAGATGTACGGGGTCGAGTAATTTCTTGGTCCTCCGCCGGTACTTGTGGATTCAAGGGTACAAGAAGAGGGACACCATTTGCCGCTCAAACCGCAGCGGGAAATGCTATTCGTACAGTGGTGGATCAAGGTATGCAACGAGCAGAAGTCATGATAAAAGGCCCGGGTCTCGGGAGAGATGCGGCATTAAGAGCTATTCGTAGAAGTGGCATACTATTAAGTTTCATACGGGATGTAACCCCTATGCCGCATAATGGCTGTAGGCCCCCCAAAAAAAGACGTAAAGTAACAGTATCTACTCGGACACTACAGTGGAAGTGTGTTGAATCAAGAGCAGACAGTAAGCGTCTTTATTATGGACGCTTTATTCTGGCCCCACTTATGAAAGGCCAAGCCGATACAATAGGCATCGCGATGCGAAGAGCTTTACTCGGAGAAATAGAAGGAACATGTATTACACGTGCAAGATCTGAGAAAATACCACACGAATATTCTACCATCGTAGGTATTCAAGAATCTGTACATGAAATTTTAATGAATTTGAAAGAAATTGTATTGAGAAGTAATCTGTATGGAACTCGTAATGCGTCTATTTGTGTCAAGGGTCCTGGGTATGTAACTGCTCAAGACATCATTTTACCACCCTCTGTAGAAATCGTTGATAATACACAGCATATAGCTAACCTAACAGAACCAATTAATTTGTGTATTCAATTACAAATCGAGAGGAATCGTGGATATCGTATAAAAACGCCAAATAACTTTCAAGACGGCAGTTATCCTATAGATGCTGTATTCATGCCCGTTCGAAATGCGAATCATAGTATTCATTCTTATGTGAATGGGAATGAAAAACAAGAGATACTCTTTATCGAAATATGGACAAATGGAAGTTTAACTCCTAAAGAAGCACTTCATGAAGCCTCCCGAAATTTGATTGATTTATTTATTCCCTTTTTACATGCCGAAGAAGAAAATTTCCATTTCGAAAACAATCAACACAAAGTTACTTTACCCCTTTTTACTTTTCATGATAAATTTGCTAATCCAAGGAAAAGTAAAACAGAAATCACATTGAAATATATTTTTATTGACCAATCAGAACTGCCCCCGAGGGTCTATAATTGCCTCAAACGGTCCAACATACATACATTATTGGACCTTTTGAATAACAGTCAAGAAGATCTTATAAAAATGAAACATTTGCGCATAGAAGATGTAAAACATATATTGAATATTCTAGAAAAAAAAAAGCATTTCGAATAA

Protein Analysis

464

Amino Acids

52.68

Weight (kDa)

9.97

Isoelectric Point (pI)

48.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ribosomal_S11 PF00411 28 - 137 2.6e-50 Ribosomal protein S11
RNA_pol_L PF01193 169 - 359 1.5e-14 RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_A_bac PF01000 202 - 310 4e-22 RNA polymerase Rpb3/RpoA insert domain
RNA_pol_A_CTD PF03118 401 - 458 3.3e-13 Bacterial RNA polymerase, alpha chain C terminal domain
HHH_XRCC3_RpoA PF26169 407 - 454 6.4e-07 XRCC3/RpoA-like, helix-hairpin-helix domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AanI TTATAA 1 cut(s) 1319
Acc16I TGCGCA 1 cut(s) 1337
AccB7I CCANNNNNTGG 1 cut(s) 23
AccBSI CCGCTC 1 cut(s) 215
AccII CGCG 2 cut(s) 67, 542
AciI CCGC 6 cut(s) 165, 213, 222, 227, 311, 377
AclWI GGATC 1 cut(s) 261
AcsI RAATTY 5 cut(s) 657, 667, 1060, 1105, 1166
AcvI CACGTG 1 cut(s) 590
AfaI GTAC 5 cut(s) 138, 172, 190, 244, 651
AfiI CCNNNNNNNGG 3 cut(s) 23, 299, 383
AflIII ACRYGT 2 cut(s) 578, 587
AjnI CCWGG 1 cut(s) 736
AjuI GAANNNNNNNTTGG 2 cut(s) 10, 42
AleI CACNNNNGTG 1 cut(s) 439
AluBI AGCT 3 cut(s) 323, 554, 809
AluI AGCT 3 cut(s) 323, 554, 809
Alw26I GTCTC 1 cut(s) 302
AlwI GGATC 1 cut(s) 261
Ama87I CYCGRG 3 cut(s) 292, 299, 1240
AoxI GGCC 4 cut(s) 289, 392, 501, 517
ApeKI GCWGC 1 cut(s) 224
ApoI RAATTY 5 cut(s) 657, 667, 1060, 1105, 1166
AseI ATTAAT 1 cut(s) 828
Asp700I GAANNNNTTC 1 cut(s) 1041
AspLEI GCGC 2 cut(s) 67, 1338
AspS9I GGNCC 7 cut(s) 159, 290, 393, 502, 734, 1266, 1288
AsuC2I CCSGG 2 cut(s) 293, 294
AsuII TTCGAA 3 cut(s) 937, 1116, 1389
AvaI CYCGRG 3 cut(s) 292, 299, 1240
AvaII GGWCC 4 cut(s) 159, 734, 1266, 1288
BbrPI CACGTG 1 cut(s) 590
BbvI GCAGC 1 cut(s) 236
BccI CCATC 1 cut(s) 635
BceAI ACGGC 1 cut(s) 916
BciT130I CCWGG 1 cut(s) 738
BcnI CCSGG 2 cut(s) 293, 294
BcoDI GTCTC 1 cut(s) 302
BfaI CTAG 1 cut(s) 1370
BfmI CTRYAG 4 cut(s) 388, 437, 777, 912
BglII AGATCT 2 cut(s) 596, 1312
BisI GCNGC 4 cut(s) 213, 225, 312, 377
BlsI GCNGC 4 cut(s) 214, 226, 313, 378
Bme1390I CCNGG 3 cut(s) 293, 294, 738
Bme18I GGWCC 4 cut(s) 159, 734, 1266, 1288
BmeT110I CYCGRG 3 cut(s) 292, 299, 1240
BmgT120I GGNCC 7 cut(s) 159, 290, 393, 502, 734, 1266, 1288
BmiI GGNNCC 3 cut(s) 395, 504, 735
BmrFI CCNGG 3 cut(s) 293, 294, 738
BmsI GCATC 4 cut(s) 298, 534, 546, 907
BplI GAGNNNNNCTC 2 cut(s) 543, 575
Bpu14I TTCGAA 3 cut(s) 937, 1116, 1389
BpuEI CTTGAG 1 cut(s) 738
BpuMI CCSGG 2 cut(s) 293, 294
BsaAI YACGTR 3 cut(s) 32, 56, 590
BsaI GGTCTC 1 cut(s) 302
BsaJI CCNNGG 4 cut(s) 292, 737, 1178, 1241
Bsc4I CCNNNNNNNGG 3 cut(s) 23, 299, 383
Bse118I RCCGGY 1 cut(s) 167
BseBI CCWGG 1 cut(s) 738
BseDI CCNNGG 4 cut(s) 292, 737, 1178, 1241
BseGI GGATG 1 cut(s) 367
BseLI CCNNNNNNNGG 3 cut(s) 23, 299, 383
BseMII CTCAG 1 cut(s) 591
BseXI GCAGC 1 cut(s) 236
Bsh1236I CGCG 2 cut(s) 67, 542
BshFI GGCC 4 cut(s) 291, 394, 503, 519
BsiHKCI CYCGRG 3 cut(s) 292, 299, 1240
BsiSI CCGG 2 cut(s) 168, 293
BslFI GGGAC 1 cut(s) 214
BslI CCNNNNNNNGG 3 cut(s) 23, 299, 383
BsmAI GTCTC 1 cut(s) 302
BsmFI GGGAC 1 cut(s) 214
BsmI GAATGC 1 cut(s) 67
BsnI GGCC 4 cut(s) 291, 394, 503, 519
Bso31I GGTCTC 1 cut(s) 302
BsoBI CYCGRG 3 cut(s) 292, 299, 1240
Bsp119I TTCGAA 3 cut(s) 937, 1116, 1389
Bsp1407I TGTACA 1 cut(s) 649
Bsp143I GATC 3 cut(s) 253, 596, 1312
Bsp68I TCGCGA 1 cut(s) 542
BspACI CCGC 6 cut(s) 165, 213, 222, 227, 311, 377
BspANI GGCC 4 cut(s) 291, 394, 503, 519
BspCNI CTCAG 1 cut(s) 592
BspFNI CGCG 2 cut(s) 67, 542
BspHI TCATGA 3 cut(s) 279, 1045, 1159
BspLI GGNNCC 3 cut(s) 395, 504, 735
BspPI GGATC 1 cut(s) 261
BspQI GCTCTTC 1 cut(s) 544
BspT104I TTCGAA 3 cut(s) 937, 1116, 1389
BspTNI GGTCTC 1 cut(s) 302
BsrBI CCGCTC 1 cut(s) 215
BsrFI RCCGGY 1 cut(s) 167
BsrGI TGTACA 1 cut(s) 649
BssAI RCCGGY 1 cut(s) 167
BssECI CCNNGG 4 cut(s) 292, 737, 1178, 1241
BssMI GATC 3 cut(s) 253, 596, 1312
BssT1I CCWWGG 1 cut(s) 1178
Bst2UI CCWGG 1 cut(s) 738
Bst4CI ACNGT 7 cut(s) 127, 247, 421, 441, 470, 1266, 1304
Bst6I CTCTTC 2 cut(s) 190, 544
BstAUI TGTACA 1 cut(s) 649
BstBAI YACGTR 3 cut(s) 32, 56, 590
BstBI TTCGAA 3 cut(s) 937, 1116, 1389
BstDEI CTNAG 1 cut(s) 600
BstF5I GGATG 1 cut(s) 367
BstFNI CGCG 2 cut(s) 67, 542
BstHHI GCGC 2 cut(s) 67, 1338
BstKTI GATC 3 cut(s) 256, 599, 1315
BstMAI GTCTC 1 cut(s) 302
BstMBI GATC 3 cut(s) 253, 596, 1312
BstMWI GCNNNNNNNGC 3 cut(s) 221, 233, 320
BstNI CCWGG 1 cut(s) 738
BstNSI RCATGY 2 cut(s) 582, 1094
BstSCI CCNGG 3 cut(s) 291, 292, 736
BstSFI CTRYAG 4 cut(s) 388, 437, 777, 912
BstUI CGCG 2 cut(s) 67, 542
BstV1I GCAGC 1 cut(s) 236
BstX2I RGATCY 2 cut(s) 596, 1312
BstYI RGATCY 2 cut(s) 596, 1312
BsuRI GGCC 4 cut(s) 291, 394, 503, 519
BtgZI GCGATG 2 cut(s) 523, 557
BtsCI GGATG 1 cut(s) 367
BtsIMutI CAGTG 2 cut(s) 252, 446
BtuMI TCGCGA 1 cut(s) 542
CciI TCATGA 3 cut(s) 279, 1045, 1159
CfoI GCGC 2 cut(s) 67, 1338
Cfr10I RCCGGY 1 cut(s) 167
Cfr13I GGNCC 7 cut(s) 159, 290, 393, 502, 734, 1266, 1288
Cfr9I CCCGGG 1 cut(s) 292
CseI GACGC 3 cut(s) 464, 498, 705
Csp6I GTAC 5 cut(s) 137, 171, 189, 243, 650
CviAII CATG 8 cut(s) 92, 280, 579, 653, 928, 1046, 1091, 1160
CviQI GTAC 5 cut(s) 137, 171, 189, 243, 650
DdeI CTNAG 1 cut(s) 600
DpnI GATC 3 cut(s) 255, 598, 1314
DpnII GATC 3 cut(s) 253, 596, 1312
Eam1104I CTCTTC 2 cut(s) 190, 544
EarI CTCTTC 2 cut(s) 190, 544
EciI GGCGGA 1 cut(s) 154
Eco130I CCWWGG 1 cut(s) 1178
Eco31I GGTCTC 1 cut(s) 302
Eco32I GATATC 1 cut(s) 869
Eco47I GGWCC 4 cut(s) 159, 734, 1266, 1288
Eco72I CACGTG 1 cut(s) 590
Eco88I CYCGRG 3 cut(s) 292, 299, 1240
EcoO109I RGGNCCY 2 cut(s) 393, 734
EcoRII CCWGG 1 cut(s) 736
EcoRV GATATC 1 cut(s) 869
EcoT14I CCWWGG 1 cut(s) 1178
ErhI CCWWGG 1 cut(s) 1178
FaeI CATG 8 cut(s) 95, 283, 582, 656, 931, 1049, 1094, 1163
FalI AAGNNNNNCTT 4 cut(s) 1026, 1058, 1299, 1331
FaqI GGGAC 1 cut(s) 214
FatI CATG 8 cut(s) 91, 279, 578, 652, 927, 1045, 1090, 1159
FauI CCCGC 1 cut(s) 220
Fnu4HI GCNGC 4 cut(s) 213, 225, 312, 377
FokI GGATG 1 cut(s) 374
Fsp4HI GCNGC 4 cut(s) 213, 225, 312, 377
FspBI CTAG 1 cut(s) 1370
FspI TGCGCA 1 cut(s) 1337
GlaI GCGC 2 cut(s) 66, 1337
GluI GCNGC 4 cut(s) 213, 225, 312, 377
HaeIII GGCC 4 cut(s) 291, 394, 503, 519
HapII CCGG 2 cut(s) 168, 293
HgaI GACGC 3 cut(s) 464, 498, 705
HhaI GCGC 2 cut(s) 67, 1338
Hin1II CATG 8 cut(s) 95, 283, 582, 656, 931, 1049, 1094, 1163
Hin6I GCGC 2 cut(s) 65, 1336
HinP1I GCGC 2 cut(s) 65, 1336
HinfI GANTC 5 cut(s) 180, 455, 644, 859, 946
HpaII CCGG 2 cut(s) 168, 293
Hpy166II GTNNAC 2 cut(s) 29, 53
Hpy188I TCNGA 4 cut(s) 432, 563, 601, 1231
Hpy8I GTNNAC 2 cut(s) 29, 53
HpyAV CCTTC 1 cut(s) 566
HpyCH4III ACNGT 7 cut(s) 127, 247, 421, 441, 470, 1266, 1304
HpyCH4IV ACGT 5 cut(s) 31, 43, 55, 409, 589
HpyCH4V TGCA 2 cut(s) 265, 593
HpyF10VI GCNNNNNNNGC 3 cut(s) 221, 233, 320
HpyF3I CTNAG 1 cut(s) 600
HpySE526I ACGT 5 cut(s) 31, 43, 55, 409, 589
Hsp92II CATG 8 cut(s) 95, 283, 582, 656, 931, 1049, 1094, 1163
HspAI GCGC 2 cut(s) 65, 1336
Kzo9I GATC 3 cut(s) 253, 596, 1312
LguI GCTCTTC 1 cut(s) 544
LpnPI CCDG 5 cut(s) 181, 306, 485, 723, 750
Lsp1109I GCAGC 1 cut(s) 236
LweI GCATC 4 cut(s) 298, 534, 546, 907
MaeI CTAG 1 cut(s) 1370
MaeII ACGT 5 cut(s) 31, 43, 55, 409, 589
MaeIII GTNAC 6 cut(s) 121, 127, 364, 415, 745, 1135
MalI GATC 3 cut(s) 255, 598, 1314
MbiI CCGCTC 1 cut(s) 215
MboI GATC 3 cut(s) 253, 596, 1312
MboII GAAGA 6 cut(s) 207, 561, 1109, 1112, 1322, 1355
MflI RGATCY 2 cut(s) 596, 1312
MmeI TCCRAC 1 cut(s) 1293
MnlI CCTC 7 cut(s) 172, 191, 784, 849, 1063, 1236, 1268
MroXI GAANNNNTTC 1 cut(s) 1041
MseI TTAA 5 cut(s) 317, 347, 662, 828, 1025
MslI CAYNNNNRTG 3 cut(s) 439, 542, 963
MspA1I CMGCKG 1 cut(s) 227
MspI CCGG 2 cut(s) 168, 293
MspR9I CCNGG 3 cut(s) 293, 294, 738
Mva1269I GAATGC 1 cut(s) 67
MvaI CCWGG 1 cut(s) 738
MvnI CGCG 2 cut(s) 67, 542
MwoI GCNNNNNNNGC 3 cut(s) 221, 233, 320
NciI CCSGG 2 cut(s) 293, 294
NdeII GATC 3 cut(s) 253, 596, 1312
NlaIII CATG 8 cut(s) 95, 283, 582, 656, 931, 1049, 1094, 1163
NlaIV GGNNCC 3 cut(s) 395, 504, 735
NmuCI GTSAC 1 cut(s) 121
NruI TCGCGA 1 cut(s) 542
NsbI TGCGCA 1 cut(s) 1337
NspI RCATGY 2 cut(s) 582, 1094
NspV TTCGAA 3 cut(s) 937, 1116, 1389
OliI CACNNNNGTG 1 cut(s) 439
PagI TCATGA 3 cut(s) 279, 1045, 1159
PciI ACATGT 1 cut(s) 578
PciSI GCTCTTC 1 cut(s) 544
PcsI WCGNNNNNNNCGW 1 cut(s) 868
PctI GAATGC 1 cut(s) 67
PdmI GAANNNNTTC 1 cut(s) 1041
PfeI GAWTC 5 cut(s) 180, 455, 644, 859, 946
PflMI CCANNNNNTGG 1 cut(s) 23
PkrI GCNGC 4 cut(s) 214, 226, 313, 378
PmaCI CACGTG 1 cut(s) 590
PmlI CACGTG 1 cut(s) 590
Ppu21I YACGTR 3 cut(s) 32, 56, 590
PpuMI RGGWCCY 1 cut(s) 734
PscI ACATGT 1 cut(s) 578
PshBI ATTAAT 1 cut(s) 828
PsiI TTATAA 1 cut(s) 1319
Psp5II RGGWCCY 1 cut(s) 734
Psp6I CCWGG 1 cut(s) 736
PspCI CACGTG 1 cut(s) 590
PspGI CCWGG 1 cut(s) 736
PspN4I GGNNCC 3 cut(s) 395, 504, 735
PspPI GGNCC 7 cut(s) 159, 290, 393, 502, 734, 1266, 1288
PspPPI RGGWCCY 1 cut(s) 734
PsrI GAACNNNNNNTAC 2 cut(s) 568, 600
PsuI RGATCY 2 cut(s) 596, 1312
RruI TCGCGA 1 cut(s) 542
RsaI GTAC 5 cut(s) 138, 172, 190, 244, 651
RsaNI GTAC 5 cut(s) 137, 171, 189, 243, 650
RseI CAYNNNNRTG 3 cut(s) 439, 542, 963
SapI GCTCTTC 1 cut(s) 544
SaqAI TTAA 5 cut(s) 317, 347, 662, 828, 1025
SatI GCNGC 4 cut(s) 213, 225, 312, 377
Sau3AI GATC 3 cut(s) 253, 596, 1312
Sau96I GGNCC 7 cut(s) 159, 290, 393, 502, 734, 1266, 1288
ScrFI CCNGG 3 cut(s) 293, 294, 738
SfaNI GCATC 4 cut(s) 298, 534, 546, 907
SfcI CTRYAG 4 cut(s) 388, 437, 777, 912
SfuI TTCGAA 3 cut(s) 937, 1116, 1389
SinI GGWCC 4 cut(s) 159, 734, 1266, 1288
SmaI CCCGGG 1 cut(s) 294
SmiMI CAYNNNNRTG 3 cut(s) 439, 542, 963
SmlI CTYRAG 1 cut(s) 753
SmoI CTYRAG 1 cut(s) 753
SsiI CCGC 6 cut(s) 165, 213, 222, 227, 311, 377
SspI AATATT 2 cut(s) 620, 1366
SspMI CTAG 1 cut(s) 1370
StyD4I CCNGG 3 cut(s) 291, 292, 736
StyI CCWWGG 1 cut(s) 1178
TaaI ACNGT 7 cut(s) 127, 247, 421, 441, 470, 1266, 1304
TaiI ACGT 5 cut(s) 34, 46, 58, 412, 592
TaqI TCGA 6 cut(s) 145, 852, 937, 1002, 1116, 1389
TatI WGTACW 1 cut(s) 649
TauI GCSGC 3 cut(s) 215, 314, 379
TfiI GAWTC 5 cut(s) 180, 455, 644, 859, 946
Tru1I TTAA 5 cut(s) 317, 347, 662, 828, 1025
Tru9I TTAA 5 cut(s) 317, 347, 662, 828, 1025
TscAI CASTG 2 cut(s) 252, 446
TseFI GTSAC 1 cut(s) 121
TseI GCWGC 1 cut(s) 224
Tsp45I GTSAC 1 cut(s) 121
TspMI CCCGGG 1 cut(s) 292
TspRI CASTG 2 cut(s) 252, 446
Van91I CCANNNNNTGG 1 cut(s) 23
VpaK11BI GGWCC 4 cut(s) 159, 734, 1266, 1288
VspI ATTAAT 1 cut(s) 828
XapI RAATTY 5 cut(s) 657, 667, 1060, 1105, 1166
XbaI TCTAGA 1 cut(s) 1369
XceI RCATGY 2 cut(s) 582, 1094
XmaI CCCGGG 1 cut(s) 292
XmnI GAANNNNTTC 1 cut(s) 1041
XspI CTAG 1 cut(s) 1370
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.