Rroxscaffold_2G00119010

Bacterial RNA polymerase, alpha chain C terminal domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0016509
Physical Location & Seq
Forward (+)
50820805 .. 50821800
996 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00119010.1

Sequence Viewer

Length: 996 bp
ATGGTTCGAGAGAAAGTAACAGTATCTACTCGGACACTACAGTGGAAGTGTGTTGAATCAAGAGCAGACAGTAAGCGTCTTTATTATGGACGCTTTATTCTGGCCCCACTTATGAAAGGCCAAGCCGATACAATAGGCATCGCGATGCGAAGAGCTTTACTCGGAGAAATAGAAGGAACATGTATTACACGTGCAAGATCTGAGAAAATACCACACGAATATTCTACCATCGTAGGTATTCAAGAATCTGTACATGAAATTTTAATGAATTTGAAAGAAATTGTATTGAGAAGTAATCTGTATGGAACTCGTAATGCGTCTATTTGTGTCAAGGGTCCTGGGTATGTAACTGCTCAAGACATCATTTTACCACCCTCTGTAGAAATCGTTGATAATACACAGCATATAGCTAACCTAACAGAACCAATTAATTTGTGTATTCAATTACAAATCGAGAGGAATCGTGGATATCGTATAAAAACGCCAAATAACTTTCAAGACGGCAGTTATCCTATAGATGCTGTATTCATGCCCGTTCGAAATGCGAATCATAGTATTCATTCTTATGTGAATGGGAATGAAAAACAAGAGATACTCTTTATCGAAATATGGACAAATGGAAGTTTAACTCCTAAAGAAGCACTTCATGAAGCCTCCCGAAATTTGATTGATTTATTTATTCCCTTTTTACATGCCGAAGAAGAAAATTTTCATTTCGAAAACAATCAACACAAAGTTACTTTACCCCTTTTTACTTTTCATGATAAATTTGCTAATCCAAGGAAAAGTAAAACAGAAATCATATTGAAATCTATTTTTATTGACCAATCAGAACTGCCCCCGAGGGTCTATAATTGCCTCAAACGGTCCAACATACATACATTATTGGACCTTTTGAATAACAGTCAAGAAGATCTTATAAAAATGAAACATTTGCGCATAGAAGATGTAAAACATATATTGAATATTCTAGAAAGAAAAAAGCATTTCGAATAA

Protein Analysis

331

Amino Acids

38.23

Weight (kDa)

8.49

Isoelectric Point (pI)

50.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_L PF01193 36 - 226 6.5e-15 RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_A_bac PF01000 69 - 177 2.1e-22 RNA polymerase Rpb3/RpoA insert domain
RNA_pol_A_CTD PF03118 269 - 325 4.1e-13 Bacterial RNA polymerase, alpha chain C terminal domain
HHH_XRCC3_RpoA PF26169 274 - 321 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
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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)
AanI TTATAA 1 cut(s) 920
Acc16I TGCGCA 1 cut(s) 938
AccII CGCG 1 cut(s) 143
AcsI RAATTY 5 cut(s) 258, 268, 661, 706, 767
AcvI CACGTG 1 cut(s) 191
AfaI GTAC 1 cut(s) 252
AflIII ACRYGT 2 cut(s) 179, 188
AgsI TTSAA 8 cut(s) 56, 242, 274, 443, 497, 808, 898, 964
AjnI CCWGG 1 cut(s) 337
AleI CACNNNNGTG 1 cut(s) 40
AluBI AGCT 2 cut(s) 155, 410
AluI AGCT 2 cut(s) 155, 410
Ama87I CYCGRG 1 cut(s) 841
AoxI GGCC 2 cut(s) 102, 118
ApoI RAATTY 5 cut(s) 258, 268, 661, 706, 767
AseI ATTAAT 1 cut(s) 429
Asp700I GAANNNNTTC 2 cut(s) 642, 708
AspLEI GCGC 1 cut(s) 939
AspS9I GGNCC 4 cut(s) 103, 335, 867, 889
AsuII TTCGAA 3 cut(s) 538, 717, 990
AvaI CYCGRG 1 cut(s) 841
AvaII GGWCC 3 cut(s) 335, 867, 889
BbrPI CACGTG 1 cut(s) 191
BccI CCATC 1 cut(s) 236
BceAI ACGGC 1 cut(s) 517
BciT130I CCWGG 1 cut(s) 339
BfaI CTAG 1 cut(s) 971
BfmI CTRYAG 3 cut(s) 38, 378, 513
BglII AGATCT 2 cut(s) 197, 913
Bme1390I CCNGG 1 cut(s) 339
Bme18I GGWCC 3 cut(s) 335, 867, 889
BmeT110I CYCGRG 1 cut(s) 841
BmgT120I GGNCC 4 cut(s) 103, 335, 867, 889
BmiI GGNNCC 2 cut(s) 105, 336
BmrFI CCNGG 1 cut(s) 339
BmsI GCATC 3 cut(s) 135, 147, 508
BplI GAGNNNNNCTC 2 cut(s) 144, 176
Bpu14I TTCGAA 3 cut(s) 538, 717, 990
BpuEI CTTGAG 1 cut(s) 339
BsaAI YACGTR 1 cut(s) 191
BsaJI CCNNGG 3 cut(s) 338, 779, 842
BseBI CCWGG 1 cut(s) 339
BseDI CCNNGG 3 cut(s) 338, 779, 842
BseMII CTCAG 1 cut(s) 192
Bsh1236I CGCG 1 cut(s) 143
BshFI GGCC 2 cut(s) 104, 120
BsiHKCI CYCGRG 1 cut(s) 841
BsnI GGCC 2 cut(s) 104, 120
BsoBI CYCGRG 1 cut(s) 841
Bsp119I TTCGAA 3 cut(s) 538, 717, 990
Bsp1407I TGTACA 1 cut(s) 250
Bsp143I GATC 2 cut(s) 197, 913
Bsp68I TCGCGA 1 cut(s) 143
BspANI GGCC 2 cut(s) 104, 120
BspCNI CTCAG 1 cut(s) 193
BspFNI CGCG 1 cut(s) 143
BspHI TCATGA 2 cut(s) 646, 760
BspLI GGNNCC 2 cut(s) 105, 336
BspQI GCTCTTC 1 cut(s) 145
BspT104I TTCGAA 3 cut(s) 538, 717, 990
BsrGI TGTACA 1 cut(s) 250
BssECI CCNNGG 3 cut(s) 338, 779, 842
BssMI GATC 2 cut(s) 197, 913
BssT1I CCWWGG 1 cut(s) 779
Bst2UI CCWGG 1 cut(s) 339
Bst4CI ACNGT 5 cut(s) 22, 42, 71, 867, 905
Bst6I CTCTTC 1 cut(s) 145
BstAUI TGTACA 1 cut(s) 250
BstBAI YACGTR 1 cut(s) 191
BstBI TTCGAA 3 cut(s) 538, 717, 990
BstDEI CTNAG 1 cut(s) 201
BstFNI CGCG 1 cut(s) 143
BstHHI GCGC 1 cut(s) 939
BstKTI GATC 2 cut(s) 200, 916
BstMBI GATC 2 cut(s) 197, 913
BstNI CCWGG 1 cut(s) 339
BstNSI RCATGY 2 cut(s) 183, 695
BstSCI CCNGG 1 cut(s) 337
BstSFI CTRYAG 3 cut(s) 38, 378, 513
BstUI CGCG 1 cut(s) 143
BstX2I RGATCY 2 cut(s) 197, 913
BstYI RGATCY 2 cut(s) 197, 913
BsuRI GGCC 2 cut(s) 104, 120
BtgZI GCGATG 2 cut(s) 124, 158
BtsIMutI CAGTG 1 cut(s) 47
BtuMI TCGCGA 1 cut(s) 143
CciI TCATGA 2 cut(s) 646, 760
CfoI GCGC 1 cut(s) 939
Cfr13I GGNCC 4 cut(s) 103, 335, 867, 889
CseI GACGC 3 cut(s) 65, 99, 306
Csp6I GTAC 1 cut(s) 251
CviAII CATG 6 cut(s) 180, 254, 529, 647, 692, 761
CviJI RGCY 6 cut(s) 104, 120, 125, 155, 410, 653
CviKI_1 RGCY 6 cut(s) 104, 120, 125, 155, 410, 653
CviQI GTAC 1 cut(s) 251
DdeI CTNAG 1 cut(s) 201
DpnI GATC 2 cut(s) 199, 915
DpnII GATC 2 cut(s) 197, 913
Eam1104I CTCTTC 1 cut(s) 145
EarI CTCTTC 1 cut(s) 145
Eco130I CCWWGG 1 cut(s) 779
Eco32I GATATC 1 cut(s) 470
Eco47I GGWCC 3 cut(s) 335, 867, 889
Eco72I CACGTG 1 cut(s) 191
Eco88I CYCGRG 1 cut(s) 841
EcoO109I RGGNCCY 1 cut(s) 335
EcoRII CCWGG 1 cut(s) 337
EcoRV GATATC 1 cut(s) 470
EcoT14I CCWWGG 1 cut(s) 779
ErhI CCWWGG 1 cut(s) 779
FaeI CATG 6 cut(s) 183, 257, 532, 650, 695, 764
FalI AAGNNNNNCTT 4 cut(s) 627, 659, 900, 932
FatI CATG 6 cut(s) 179, 253, 528, 646, 691, 760
FspBI CTAG 1 cut(s) 971
FspI TGCGCA 1 cut(s) 938
GlaI GCGC 1 cut(s) 938
HaeIII GGCC 2 cut(s) 104, 120
HgaI GACGC 3 cut(s) 65, 99, 306
HhaI GCGC 1 cut(s) 939
Hin1II CATG 6 cut(s) 183, 257, 532, 650, 695, 764
Hin6I GCGC 1 cut(s) 937
HinP1I GCGC 1 cut(s) 937
HinfI GANTC 4 cut(s) 56, 245, 460, 547
Hpy188I TCNGA 4 cut(s) 33, 164, 202, 832
HpyAV CCTTC 1 cut(s) 167
HpyCH4III ACNGT 5 cut(s) 22, 42, 71, 867, 905
HpyCH4IV ACGT 1 cut(s) 190
HpyCH4V TGCA 1 cut(s) 194
HpyF3I CTNAG 1 cut(s) 201
HpySE526I ACGT 1 cut(s) 190
Hsp92II CATG 6 cut(s) 183, 257, 532, 650, 695, 764
HspAI GCGC 1 cut(s) 937
Kzo9I GATC 2 cut(s) 197, 913
LguI GCTCTTC 1 cut(s) 145
LpnPI CCDG 3 cut(s) 86, 324, 351
LweI GCATC 3 cut(s) 135, 147, 508
MaeI CTAG 1 cut(s) 971
MaeII ACGT 1 cut(s) 190
MaeIII GTNAC 3 cut(s) 16, 346, 736
MalI GATC 2 cut(s) 199, 915
MboI GATC 2 cut(s) 197, 913
MboII GAAGA 5 cut(s) 162, 710, 713, 923, 956
MflI RGATCY 2 cut(s) 197, 913
MmeI TCCRAC 1 cut(s) 894
MnlI CCTC 5 cut(s) 385, 450, 664, 837, 869
MroXI GAANNNNTTC 2 cut(s) 642, 708
MseI TTAA 3 cut(s) 263, 429, 626
MslI CAYNNNNRTG 3 cut(s) 40, 143, 564
MspR9I CCNGG 1 cut(s) 339
MvaI CCWGG 1 cut(s) 339
MvnI CGCG 1 cut(s) 143
NdeII GATC 2 cut(s) 197, 913
NlaIII CATG 6 cut(s) 183, 257, 532, 650, 695, 764
NlaIV GGNNCC 2 cut(s) 105, 336
NruI TCGCGA 1 cut(s) 143
NsbI TGCGCA 1 cut(s) 938
NspI RCATGY 2 cut(s) 183, 695
NspV TTCGAA 3 cut(s) 538, 717, 990
OliI CACNNNNGTG 1 cut(s) 40
PagI TCATGA 2 cut(s) 646, 760
PciI ACATGT 1 cut(s) 179
PciSI GCTCTTC 1 cut(s) 145
PcsI WCGNNNNNNNCGW 1 cut(s) 469
PdmI GAANNNNTTC 2 cut(s) 642, 708
PfeI GAWTC 4 cut(s) 56, 245, 460, 547
PmaCI CACGTG 1 cut(s) 191
PmlI CACGTG 1 cut(s) 191
Ppu21I YACGTR 1 cut(s) 191
PpuMI RGGWCCY 1 cut(s) 335
PscI ACATGT 1 cut(s) 179
PshBI ATTAAT 1 cut(s) 429
PsiI TTATAA 1 cut(s) 920
Psp5II RGGWCCY 1 cut(s) 335
Psp6I CCWGG 1 cut(s) 337
PspCI CACGTG 1 cut(s) 191
PspGI CCWGG 1 cut(s) 337
PspN4I GGNNCC 2 cut(s) 105, 336
PspPI GGNCC 4 cut(s) 103, 335, 867, 889
PspPPI RGGWCCY 1 cut(s) 335
PsrI GAACNNNNNNTAC 2 cut(s) 169, 201
PsuI RGATCY 2 cut(s) 197, 913
RruI TCGCGA 1 cut(s) 143
RsaI GTAC 1 cut(s) 252
RsaNI GTAC 1 cut(s) 251
RseI CAYNNNNRTG 3 cut(s) 40, 143, 564
SapI GCTCTTC 1 cut(s) 145
SaqAI TTAA 3 cut(s) 263, 429, 626
Sau3AI GATC 2 cut(s) 197, 913
Sau96I GGNCC 4 cut(s) 103, 335, 867, 889
ScrFI CCNGG 1 cut(s) 339
SetI ASST 6 cut(s) 157, 193, 238, 412, 417, 894
SfaNI GCATC 3 cut(s) 135, 147, 508
SfcI CTRYAG 3 cut(s) 38, 378, 513
SfuI TTCGAA 3 cut(s) 538, 717, 990
SinI GGWCC 3 cut(s) 335, 867, 889
SmiMI CAYNNNNRTG 3 cut(s) 40, 143, 564
SmlI CTYRAG 1 cut(s) 354
SmoI CTYRAG 1 cut(s) 354
SspI AATATT 2 cut(s) 221, 967
SspMI CTAG 1 cut(s) 971
StyD4I CCNGG 1 cut(s) 337
StyI CCWWGG 1 cut(s) 779
TaaI ACNGT 5 cut(s) 22, 42, 71, 867, 905
TaiI ACGT 1 cut(s) 193
TaqI TCGA 6 cut(s) 7, 453, 538, 603, 717, 990
TatI WGTACW 1 cut(s) 250
TfiI GAWTC 4 cut(s) 56, 245, 460, 547
Tru1I TTAA 3 cut(s) 263, 429, 626
Tru9I TTAA 3 cut(s) 263, 429, 626
TscAI CASTG 1 cut(s) 47
TspRI CASTG 1 cut(s) 47
VpaK11BI GGWCC 3 cut(s) 335, 867, 889
VspI ATTAAT 1 cut(s) 429
XapI RAATTY 5 cut(s) 258, 268, 661, 706, 767
XbaI TCTAGA 1 cut(s) 970
XceI RCATGY 2 cut(s) 183, 695
XmnI GAANNNNTTC 2 cut(s) 642, 708
XspI CTAG 1 cut(s) 971
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.