Rorug02G0044500

RNA polymerase-associated protein CTR9 homolog

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000002
OG0016235
Physical Location & Seq
Reverse (-)
3512160 .. 3512645
486 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug02G0044500.1

Sequence Viewer

Length: 486 bp
ATGCAAGATAAGTTTTACAATGATTATCCATGTATAATCATCACCGGAATGGGAATGCCTGAGGTGGCGACCAGAAGATTTTTAAAGCTATTGTCGGACAATTTTGGACTTCCAGTGTATGGCCTTTTCGACTGTGATCCAGAAGGCATCAAAATGTTTACAATTTATACTGTTGGATCATATGAGGAGGCCTTCGATAGTGTAAACTTAACTTGGCCGTATATGACGTGGTTGGGTGTTTGGCCGAGTGACCTATGTGCGCTTGATATACCCTGCAAGGATTTGAGTCCGAGTGAGATTGCATTGGTAGATTATCTTTTGAGAGAAGATTTTGTGAAAGAGAATCCGAGGTTGGTTGAGGAGCTGGAACATATGAAAATAACGGAGAAAAAAGCGAATCTTGAAGCTTTGAAGGAATTTGGGCCCACTTGTTTGTCCAAGTACTATTTACCATATAAGTTGAATTATCTTTTGACCGCACCGTGA
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

161

Amino Acids

18.61

Weight (kDa)

4.59

Isoelectric Point (pI)

39.19

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TOP6A-Spo11_Toprim PF21180 2 - 154 7.6e-42 Topoisomerase 6 subunit A/Spo11, Toprim 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: OG0016235)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g08430 FvH4_1g08430
malus_domestica MD02G1088500.v1.1
prunus_persica Prupe.7G201100_v2.0.a1 Prupe.7G201100_v2.0.a1
pyrus_communis pycom02g07110
rosa_chinensis RchiOBHm_Chr2g0094531
rosa_laevigata RLG00000016499
rosa_multiflora Rmu_sc0004359.1_g000042
rosa_roxburghii Rroxscaffold_2G00147090
rosa_rugosa Rorug02G0044500
rosa_samantha Rh2AG092800 Rh2BG093000 Rh2CG095500 Rh2DG091900

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 119
AciI CCGC 1 cut(s) 477
AclWI GGATC 2 cut(s) 131, 184
AcoI YGGCCR 2 cut(s) 215, 242
AcsI RAATTY 1 cut(s) 416
AfaI GTAC 1 cut(s) 443
AfiI CCNNNNNNNGG 1 cut(s) 119
AgsI TTSAA 3 cut(s) 404, 412, 463
AjiI CACGTC 1 cut(s) 228
AjuI GAANNNNNNNTTGG 2 cut(s) 335, 367
AluBI AGCT 3 cut(s) 88, 364, 407
AluI AGCT 3 cut(s) 88, 364, 407
AlwI GGATC 2 cut(s) 131, 184
AoxI GGCC 5 cut(s) 121, 189, 215, 242, 422
ApaI GGGCCC 1 cut(s) 426
ApoI RAATTY 1 cut(s) 416
AspLEI GCGC 1 cut(s) 262
AspS9I GGNCC 2 cut(s) 422, 423
AsuHPI GGTGA 1 cut(s) 34
AxyI CCTNAGG 1 cut(s) 60
BaeGI GKGCMC 1 cut(s) 426
BanII GRGCYC 1 cut(s) 426
BceAI ACGGC 1 cut(s) 202
BmcAI AGTACT 1 cut(s) 443
BmgBI CACGTC 1 cut(s) 228
BmgT120I GGNCC 2 cut(s) 422, 423
BmiI GGNNCC 1 cut(s) 424
BmsI GCATC 1 cut(s) 156
BsaJI CCNNGG 1 cut(s) 347
BsaWI WCCGGW 1 cut(s) 44
Bsc4I CCNNNNNNNGG 1 cut(s) 119
Bse1I ACTGG 1 cut(s) 113
Bse21I CCTNAGG 1 cut(s) 60
BseDI CCNNGG 1 cut(s) 347
BseLI CCNNNNNNNGG 1 cut(s) 119
BseMII CTCAG 1 cut(s) 51
BseNI ACTGG 1 cut(s) 113
BseRI GAGGAG 2 cut(s) 200, 374
BseSI GKGCMC 1 cut(s) 426
BshFI GGCC 5 cut(s) 123, 191, 217, 244, 424
BsiSI CCGG 1 cut(s) 45
BslI CCNNNNNNNGG 1 cut(s) 119
BsmI GAATGC 1 cut(s) 60
BsnI GGCC 5 cut(s) 123, 191, 217, 244, 424
Bsp120I GGGCCC 1 cut(s) 422
Bsp1286I GDGCHC 1 cut(s) 426
Bsp143I GATC 2 cut(s) 136, 176
BspACI CCGC 1 cut(s) 477
BspANI GGCC 5 cut(s) 123, 191, 217, 244, 424
BspCNI CTCAG 1 cut(s) 52
BspLI GGNNCC 1 cut(s) 424
BspPI GGATC 2 cut(s) 131, 184
BsrI ACTGG 1 cut(s) 113
BssECI CCNNGG 1 cut(s) 347
BssMI GATC 2 cut(s) 136, 176
Bst4CI ACNGT 3 cut(s) 134, 172, 483
BstDEI CTNAG 1 cut(s) 60
BstHHI GCGC 1 cut(s) 262
BstKTI GATC 2 cut(s) 139, 179
BstMBI GATC 2 cut(s) 136, 176
BstSLI GKGCMC 1 cut(s) 426
Bsu36I CCTNAGG 1 cut(s) 60
BsuRI GGCC 5 cut(s) 123, 191, 217, 244, 424
BtrI CACGTC 1 cut(s) 228
BtsIMutI CAGTG 1 cut(s) 120
CfoI GCGC 1 cut(s) 262
Cfr13I GGNCC 2 cut(s) 422, 423
Csp6I GTAC 1 cut(s) 442
CviAII CATG 1 cut(s) 30
CviJI RGCY 8 cut(s) 88, 123, 191, 217, 244, 364, 407, 424
CviKI_1 RGCY 8 cut(s) 88, 123, 191, 217, 244, 364, 407, 424
CviQI GTAC 1 cut(s) 442
DdeI CTNAG 1 cut(s) 60
DpnI GATC 2 cut(s) 138, 178
DpnII GATC 2 cut(s) 136, 176
DraI TTTAAA 1 cut(s) 84
EaeI YGGCCR 2 cut(s) 215, 242
Eco147I AGGCCT 1 cut(s) 191
Eco24I GRGCYC 1 cut(s) 426
Eco81I CCTNAGG 1 cut(s) 60
EcoT38I GRGCYC 1 cut(s) 426
FaeI CATG 1 cut(s) 33
FalI AAGNNNNNCTT 2 cut(s) 384, 416
FatI CATG 1 cut(s) 29
FauNDI CATATG 2 cut(s) 181, 372
FriOI GRGCYC 1 cut(s) 426
GlaI GCGC 1 cut(s) 261
HaeIII GGCC 5 cut(s) 123, 191, 217, 244, 424
HapII CCGG 1 cut(s) 45
HhaI GCGC 1 cut(s) 262
Hin1II CATG 1 cut(s) 33
Hin6I GCGC 1 cut(s) 260
HinP1I GCGC 1 cut(s) 260
HindIII AAGCTT 1 cut(s) 405
HinfI GANTC 3 cut(s) 286, 343, 397
HpaII CCGG 1 cut(s) 45
HphI GGTGA 1 cut(s) 34
Hpy166II GTNNAC 2 cut(s) 159, 205
Hpy188I TCNGA 3 cut(s) 97, 291, 348
Hpy188III TCNNGA 2 cut(s) 140, 401
Hpy8I GTNNAC 2 cut(s) 159, 205
HpyAV CCTTC 3 cut(s) 137, 202, 406
HpyCH4III ACNGT 3 cut(s) 134, 172, 483
HpyCH4IV ACGT 1 cut(s) 227
HpyCH4V TGCA 3 cut(s) 4, 276, 302
HpyF3I CTNAG 1 cut(s) 60
HpySE526I ACGT 1 cut(s) 227
Hsp92II CATG 1 cut(s) 33
HspAI GCGC 1 cut(s) 260
Kzo9I GATC 2 cut(s) 136, 176
LmnI GCTCC 1 cut(s) 361
LpnPI CCDG 7 cut(s) 58, 72, 85, 126, 153, 286, 350
LweI GCATC 1 cut(s) 156
MaeII ACGT 1 cut(s) 227
MaeIII GTNAC 1 cut(s) 248
MalI GATC 2 cut(s) 138, 178
MboI GATC 2 cut(s) 136, 176
MboII GAAGA 2 cut(s) 87, 338
MhlI GDGCHC 1 cut(s) 426
MluCI AATT 4 cut(s) 100, 162, 416, 463
MlyI GAGTC 1 cut(s) 295
MmeI TCCRAC 2 cut(s) 75, 154
MnlI CCTC 5 cut(s) 55, 178, 181, 342, 352
MseI TTAA 2 cut(s) 83, 209
MslI CAYNNNNRTG 2 cut(s) 47, 152
MspI CCGG 1 cut(s) 45
Mva1269I GAATGC 1 cut(s) 60
NdeI CATATG 2 cut(s) 181, 372
NdeII GATC 2 cut(s) 136, 176
NlaIII CATG 1 cut(s) 33
NlaIV GGNNCC 1 cut(s) 424
NmeAIII GCCGAG 1 cut(s) 270
NmuCI GTSAC 1 cut(s) 248
PceI AGGCCT 1 cut(s) 191
PctI GAATGC 1 cut(s) 60
PfeI GAWTC 2 cut(s) 343, 397
PflMI CCANNNNNTGG 1 cut(s) 119
PleI GAGTC 1 cut(s) 294
PpsI GAGTC 1 cut(s) 294
PspN4I GGNNCC 1 cut(s) 424
PspOMI GGGCCC 1 cut(s) 422
PspPI GGNCC 2 cut(s) 422, 423
RsaI GTAC 1 cut(s) 443
RsaNI GTAC 1 cut(s) 442
RseI CAYNNNNRTG 2 cut(s) 47, 152
SaqAI TTAA 2 cut(s) 83, 209
Sau3AI GATC 2 cut(s) 136, 176
Sau96I GGNCC 2 cut(s) 422, 423
ScaI AGTACT 1 cut(s) 443
SchI GAGTC 1 cut(s) 295
SduI GDGCHC 1 cut(s) 426
SetI ASST 7 cut(s) 66, 90, 230, 255, 353, 366, 409
SfaNI GCATC 1 cut(s) 156
SmiMI CAYNNNNRTG 2 cut(s) 47, 152
Sse9I AATT 4 cut(s) 100, 162, 416, 463
SseBI AGGCCT 1 cut(s) 191
SsiI CCGC 1 cut(s) 477
StuI AGGCCT 1 cut(s) 191
TaaI ACNGT 3 cut(s) 134, 172, 483
TaiI ACGT 1 cut(s) 230
TaqI TCGA 2 cut(s) 129, 195
TasI AATT 4 cut(s) 100, 162, 416, 463
TatI WGTACW 1 cut(s) 441
TfiI GAWTC 2 cut(s) 343, 397
Tru1I TTAA 2 cut(s) 83, 209
Tru9I TTAA 2 cut(s) 83, 209
TscAI CASTG 1 cut(s) 120
TseFI GTSAC 1 cut(s) 248
Tsp45I GTSAC 1 cut(s) 248
TspDTI ATGAA 1 cut(s) 389
TspGWI ACGGA 1 cut(s) 398
TspRI CASTG 1 cut(s) 120
Van91I CCANNNNNTGG 1 cut(s) 119
XapI RAATTY 1 cut(s) 416
ZrmI AGTACT 1 cut(s) 443
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.