Rorug07G0183300

RNA polymerase-associated protein CTR9 homolog

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000007
OG0004249
Physical Location & Seq
Reverse (-)
15282057 .. 15285951
3895 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug07G0183300.1

Sequence Viewer

Length: 909 bp
ATGACCTATGAGGAGAATGTTGATCGAGGAGAGGTGGAGCCGGAGCTGATCGTTAGAATTGGGGGCGGTGAGGATGATGAGAAGGGGAGAGGGGACTATGTGAAGCTCAGGGAGTGTCCCGGCGAGGCTGAGGAGGAGTCGTCGTCGTCGTCGTCTTCGCCCAAGGGATTATGGTGTTTGTGGTATTGGGTTAGGTTGGTGTTGCTGTTCATGTGCCTGGGGTTGTTGGCTGGGGTTTTTCTCAAATGGGTCGGGCCTTTTCTGATGGATACGGAGGTTATTCCAATTATTAACTGGGAGACAAAAACATTCAGTCCTCCAGTGCTTGCTATTCTGGTCTTTGCTTCTGTGGCATTGTTTCCTACCATACTATTACCATCTTCACCTTCTATGTGGGTGGCTGGAATGACTTTTGGTTATGGCTATGGATTTCTTCTCATTATATCAGCAGCAGCTATTGGTATATCACTTCCATATTTCATTAGCTATCTCTTCTACCATAAAATTCAGGGATGGTTAGAAAAATATCCAAAGAGAGCTTCCATTCTAAGATCAGCTGGCGAAGGAAACTGGTTTCACCAGTTTCGAGCTGTAGCATTAATCAGGATTTCTCCATTCCCTTATATTATATATAACTACTGTGCTGTGGCTACCAATGTCAAGTATGGTCCGTACCTCTTGGGGTCCTTGGCAGGAATGGTTCCAGAAACATTCGTTGCCATTTACACTGGGATCTTAATACGGACATTGGCAGATGCTTCACATGAGCACCACGGCCTTTCAGCCCCTCAGATAATCTTCACTGTTGTTGGCTTTGCTTTGGCTGTGGCTACCACAATTTTCTTCACAGTGTATGCAAAAAAGCAGCTCAAGGAATTGCAGAAGGAAGATGAGCCACTGTTGCAATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000122 GO:0000428 GO:0000785 GO:0000993 GO:0001098 GO:0001099 GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0006325 GO:0006355 GO:0006357 GO:0006464 GO:0006479 GO:0006807 GO:0006996 GO:0008023 GO:0008150 GO:0008152 GO:0008213 GO:0009889 GO:0009890 GO:0009891 GO:0009892 GO:0009893 GO:0009909 GO:0009910 GO:0009987 GO:0010468 GO:0010556 GO:0010557 GO:0010558 GO:0010604 GO:0010605 GO:0010628 GO:0010629 GO:0010638 GO:0016020 GO:0016043 GO:0016569 GO:0016570 GO:0016571 GO:0016591 GO:0016593 GO:0018022 GO:0018023 GO:0018193 GO:0018205 GO:0019219 GO:0019222 GO:0019538 GO:0019899 GO:0030880 GO:0031056 GO:0031058 GO:0031060 GO:0031062 GO:0031323 GO:0031324 GO:0031325 GO:0031326 GO:0031327 GO:0031328 GO:0031399 GO:0031401 GO:0031974 GO:0031981 GO:0032259 GO:0032268 GO:0032270 GO:0032784 GO:0032786 GO:0032968 GO:0032991 GO:0033043 GO:0033044 GO:0034243 GO:0034968 GO:0035327 GO:0036211 GO:0043170 GO:0043175 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043412 GO:0043414 GO:0044237 GO:0044238 GO:0044260 GO:0044267 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044877 GO:0045892 GO:0045893 GO:0045934 GO:0045935 GO:0045944 GO:0048518 GO:0048519 GO:0048522 GO:0048523 GO:0048580 GO:0048581 GO:0048831 GO:0050789 GO:0050793 GO:0050794 GO:0051093 GO:0051128 GO:0051130 GO:0051171 GO:0051172 GO:0051173 GO:0051239 GO:0051241 GO:0051246 GO:0051247 GO:0051252 GO:0051253 GO:0051254 GO:0051276 GO:0051568 GO:0051569 GO:0051571 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070063 GO:0071704 GO:0071840 GO:0080090 GO:0080182 GO:1901564 GO:1902275 GO:1902494 GO:1902679 GO:1902680 GO:1903506 GO:1903507 GO:1903508 GO:1905269 GO:1990234 GO:2000026 GO:2000112 GO:2000113 GO:2000241 GO:2000242 GO:2001141 GO:2001252
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
TPR_1 TPR_16 TPR_2 TPR_6 TPR_8

Protein Analysis

302

Amino Acids

33.72

Weight (kDa)

5.61

Isoelectric Point (pI)

44.7

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
VTT_dom PF09335 125 - 245 1.9e-15 VTT 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)
AciI CCGC 1 cut(s) 66
AclWI GGATC 1 cut(s) 740
AcsI RAATTY 1 cut(s) 504
AfaI GTAC 1 cut(s) 674
AjnI CCWGG 1 cut(s) 216
AjuI GAANNNNNNNTTGG 2 cut(s) 523, 555
AluBI AGCT 8 cut(s) 46, 106, 455, 486, 539, 557, 590, 868
AluI AGCT 8 cut(s) 46, 106, 455, 486, 539, 557, 590, 868
Alw21I GWGCWC 1 cut(s) 771
Alw26I GTCTC 1 cut(s) 293
AlwI GGATC 1 cut(s) 740
AoxI GGCC 2 cut(s) 254, 775
ApeKI GCWGC 3 cut(s) 449, 452, 865
ApoI RAATTY 1 cut(s) 504
AseI ATTAAT 1 cut(s) 599
AspS9I GGNCC 3 cut(s) 254, 668, 684
AsuC2I CCSGG 1 cut(s) 120
AsuHPI GGTGA 3 cut(s) 80, 375, 569
AvaII GGWCC 2 cut(s) 668, 684
BaeI ACNNNNGTAYC 2 cut(s) 261, 294
BbsI GAAGAC 1 cut(s) 147
Bbv12I GWGCWC 1 cut(s) 771
BbvCI CCTCAGC 1 cut(s) 129
BbvI GCAGC 3 cut(s) 461, 464, 877
BccI CCATC 3 cut(s) 259, 385, 507
BceAI ACGGC 1 cut(s) 790
BciT130I CCWGG 1 cut(s) 218
BciVI GTATCC 1 cut(s) 262
BcnI CCSGG 1 cut(s) 120
BcoDI GTCTC 1 cut(s) 293
BfmI CTRYAG 1 cut(s) 591
BfuI GTATCC 1 cut(s) 262
BisI GCNGC 3 cut(s) 450, 453, 866
BlsI GCNGC 3 cut(s) 451, 454, 867
Bme1390I CCNGG 2 cut(s) 120, 218
Bme18I GGWCC 2 cut(s) 668, 684
BmgT120I GGNCC 3 cut(s) 254, 668, 684
BmiI GGNNCC 3 cut(s) 39, 685, 702
BmrFI CCNGG 2 cut(s) 120, 218
BmrI ACTGGG 2 cut(s) 304, 738
BmsI GCATC 1 cut(s) 745
BmuI ACTGGG 2 cut(s) 304, 738
BpiI GAAGAC 1 cut(s) 147
BpmI CTGGAG 1 cut(s) 303
Bpu10I CCTNAGC 2 cut(s) 107, 129
BpuEI CTTGAG 1 cut(s) 854
BpuMI CCSGG 1 cut(s) 120
BsaJI CCNNGG 4 cut(s) 162, 217, 687, 772
BsaXI ACNNNNNCTCC 4 cut(s) 125, 128, 155, 158
Bse1I ACTGG 5 cut(s) 299, 320, 575, 580, 733
BseBI CCWGG 1 cut(s) 218
BseDI CCNNGG 4 cut(s) 162, 217, 687, 772
BseGI GGATG 2 cut(s) 79, 518
BseMII CTCAG 3 cut(s) 120, 121, 803
BseNI ACTGG 5 cut(s) 299, 320, 575, 580, 733
BseRI GAGGAG 4 cut(s) 26, 42, 146, 149
BseXI GCAGC 3 cut(s) 461, 464, 877
BseYI CCCAGC 1 cut(s) 230
BshFI GGCC 2 cut(s) 256, 777
BsiHKAI GWGCWC 1 cut(s) 771
BsiSI CCGG 2 cut(s) 41, 120
BslFI GGGAC 2 cut(s) 102, 107
BsmAI GTCTC 1 cut(s) 293
BsmFI GGGAC 2 cut(s) 102, 107
BsnI GGCC 2 cut(s) 256, 777
Bsp1286I GDGCHC 1 cut(s) 771
Bsp143I GATC 4 cut(s) 22, 48, 551, 732
BspACI CCGC 1 cut(s) 66
BspANI GGCC 2 cut(s) 256, 777
BspCNI CTCAG 3 cut(s) 120, 121, 802
BspLI GGNNCC 3 cut(s) 39, 685, 702
BspPI GGATC 1 cut(s) 740
BsrI ACTGG 5 cut(s) 299, 320, 575, 580, 733
BssECI CCNNGG 4 cut(s) 162, 217, 687, 772
BssMI GATC 4 cut(s) 22, 48, 551, 732
BssT1I CCWWGG 2 cut(s) 162, 687
Bst2UI CCWGG 1 cut(s) 218
Bst4CI ACNGT 4 cut(s) 641, 805, 850, 900
Bst6I CTCTTC 1 cut(s) 497
BstC8I GCNNGC 2 cut(s) 327, 559
BstDEI CTNAG 4 cut(s) 107, 129, 548, 789
BstDSI CCRYGG 1 cut(s) 772
BstF5I GGATG 2 cut(s) 79, 518
BstKTI GATC 4 cut(s) 25, 51, 554, 735
BstMAI GTCTC 1 cut(s) 293
BstMBI GATC 4 cut(s) 22, 48, 551, 732
BstMWI GCNNNNNNNGC 2 cut(s) 350, 901
BstNI CCWGG 1 cut(s) 218
BstSCI CCNGG 2 cut(s) 118, 216
BstSFI CTRYAG 1 cut(s) 591
BstV1I GCAGC 3 cut(s) 461, 464, 877
BstV2I GAAGAC 1 cut(s) 147
BstX2I RGATCY 1 cut(s) 732
BstYI RGATCY 1 cut(s) 732
BsuI GTATCC 1 cut(s) 262
BsuRI GGCC 2 cut(s) 256, 777
BtgI CCRYGG 1 cut(s) 772
BtsCI GGATG 2 cut(s) 79, 518
BtsIMutI CAGTG 5 cut(s) 327, 726, 801, 855, 896
Cac8I GCNNGC 2 cut(s) 327, 559
Cfr13I GGNCC 3 cut(s) 254, 668, 684
Csp6I GTAC 1 cut(s) 673
CviAII CATG 2 cut(s) 211, 764
CviQI GTAC 1 cut(s) 673
DdeI CTNAG 4 cut(s) 107, 129, 548, 789
DpnI GATC 4 cut(s) 24, 50, 553, 734
DpnII GATC 4 cut(s) 22, 48, 551, 732
Eam1104I CTCTTC 1 cut(s) 497
EarI CTCTTC 1 cut(s) 497
Eco130I CCWWGG 2 cut(s) 162, 687
Eco47I GGWCC 2 cut(s) 668, 684
EcoO109I RGGNCCY 1 cut(s) 684
EcoRII CCWGG 1 cut(s) 216
EcoT14I CCWWGG 2 cut(s) 162, 687
ErhI CCWWGG 2 cut(s) 162, 687
FaeI CATG 2 cut(s) 214, 767
FaqI GGGAC 2 cut(s) 102, 107
FatI CATG 2 cut(s) 210, 763
Fnu4HI GCNGC 3 cut(s) 450, 453, 866
FokI GGATG 2 cut(s) 86, 525
Fsp4HI GCNGC 3 cut(s) 450, 453, 866
GluI GCNGC 3 cut(s) 450, 453, 866
GsaI CCCAGC 1 cut(s) 234
GsuI CTGGAG 1 cut(s) 303
HaeIII GGCC 2 cut(s) 256, 777
HapII CCGG 2 cut(s) 41, 120
Hin1II CATG 2 cut(s) 214, 767
HinfI GANTC 1 cut(s) 137
HpaII CCGG 2 cut(s) 41, 120
HphI GGTGA 3 cut(s) 80, 375, 569
Hpy188I TCNGA 2 cut(s) 264, 792
Hpy188III TCNNGA 2 cut(s) 604, 704
Hpy99I CGWCG 4 cut(s) 145, 148, 151, 154
HpyAV CCTTC 4 cut(s) 76, 396, 557, 877
HpyCH4III ACNGT 4 cut(s) 641, 805, 850, 900
HpyCH4V TGCA 3 cut(s) 857, 880, 904
HpyF10VI GCNNNNNNNGC 2 cut(s) 350, 901
HpyF3I CTNAG 4 cut(s) 107, 129, 548, 789
Hsp92II CATG 2 cut(s) 214, 767
Kzo9I GATC 4 cut(s) 22, 48, 551, 732
LmnI GCTCC 2 cut(s) 37, 43
Lsp1109I GCAGC 3 cut(s) 461, 464, 877
LweI GCATC 1 cut(s) 745
MalI GATC 4 cut(s) 24, 50, 553, 734
MboI GATC 4 cut(s) 22, 48, 551, 732
MboII GAAGA 7 cut(s) 147, 372, 425, 484, 790, 835, 899
MflI RGATCY 1 cut(s) 732
MhlI GDGCHC 1 cut(s) 771
MluCI AATT 5 cut(s) 57, 285, 504, 837, 875
MlyI GAGTC 1 cut(s) 146
MseI TTAA 3 cut(s) 291, 599, 737
MspA1I CMGCKG 1 cut(s) 557
MspI CCGG 2 cut(s) 41, 120
MspR9I CCNGG 2 cut(s) 120, 218
MvaI CCWGG 1 cut(s) 218
MwoI GCNNNNNNNGC 2 cut(s) 350, 901
NciI CCSGG 1 cut(s) 120
NdeII GATC 4 cut(s) 22, 48, 551, 732
NlaIII CATG 2 cut(s) 214, 767
NlaIV GGNNCC 3 cut(s) 39, 685, 702
PcsI WCGNNNNNNNCGW 2 cut(s) 146, 149
PkrI GCNGC 3 cut(s) 451, 454, 867
PleI GAGTC 1 cut(s) 145
PpsI GAGTC 1 cut(s) 145
PpuMI RGGWCCY 1 cut(s) 684
PshBI ATTAAT 1 cut(s) 599
Psp5II RGGWCCY 1 cut(s) 684
Psp6I CCWGG 1 cut(s) 216
PspFI CCCAGC 1 cut(s) 230
PspGI CCWGG 1 cut(s) 216
PspN4I GGNNCC 3 cut(s) 39, 685, 702
PspPI GGNCC 3 cut(s) 254, 668, 684
PspPPI RGGWCCY 1 cut(s) 684
PsuI RGATCY 1 cut(s) 732
PvuII CAGCTG 1 cut(s) 557
RsaI GTAC 1 cut(s) 674
RsaNI GTAC 1 cut(s) 673
SaqAI TTAA 3 cut(s) 291, 599, 737
SatI GCNGC 3 cut(s) 450, 453, 866
Sau3AI GATC 4 cut(s) 22, 48, 551, 732
Sau96I GGNCC 3 cut(s) 254, 668, 684
SchI GAGTC 1 cut(s) 146
ScrFI CCNGG 2 cut(s) 120, 218
SduI GDGCHC 1 cut(s) 771
SfaNI GCATC 1 cut(s) 745
SfcI CTRYAG 1 cut(s) 591
SinI GGWCC 2 cut(s) 668, 684
SmlI CTYRAG 1 cut(s) 869
SmoI CTYRAG 1 cut(s) 869
Sse9I AATT 5 cut(s) 57, 285, 504, 837, 875
SsiI CCGC 1 cut(s) 66
StyD4I CCNGG 2 cut(s) 118, 216
StyI CCWWGG 2 cut(s) 162, 687
TaaI ACNGT 4 cut(s) 641, 805, 850, 900
TaqI TCGA 2 cut(s) 25, 586
TasI AATT 5 cut(s) 57, 285, 504, 837, 875
Tru1I TTAA 3 cut(s) 291, 599, 737
Tru9I TTAA 3 cut(s) 291, 599, 737
TscAI CASTG 5 cut(s) 327, 733, 808, 855, 903
TseI GCWGC 3 cut(s) 449, 452, 865
TspDTI ATGAA 2 cut(s) 199, 469
TspGWI ACGGA 3 cut(s) 287, 660, 757
TspRI CASTG 5 cut(s) 327, 733, 808, 855, 903
VpaK11BI GGWCC 2 cut(s) 668, 684
VspI ATTAAT 1 cut(s) 599
XapI RAATTY 1 cut(s) 504
XcmI CCANNNNNNNNNTGG 1 cut(s) 291
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.