Rorug07G0233000

repressing transcription factor binding

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000007
OG0000518
Physical Location & Seq
Forward (+)
21377260 .. 21382114
4855 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug07G0233000.1

Sequence Viewer

Length: 621 bp
ATGGCTCTATCAGAAGATGAAATCACGAGGCTTTACAGAATTCGAAGAACGGTGTTGGAAATGCTGAAAGATCGGGATTACTTAGTTACAGAAGCTGAGATCAACATGACAAAAGAACAATTCAAGAGCACATATGGAGAGAACATGAAAAGGGAAGATCTTGACATCAATAAAGAAAAGCGGAGTAACAGCTCTGATCAGATATATGTCTTCTTCCCTAATGAGGCAAAGGTTGGGGTAAATACAATGAGGGACTACACCAAGCGCATGCAATCGCAGAATGTGTTCAGAGCAATCTTGGTGTCTCAAACAAAGCTGACTCCTTTTGCAAATAGATGTATAAGTGAGATGTCTACAAGGTTCCGCATGGAGGTTTTCCAGGAGGAAGAACTGTTGGTGAATATTAAAGAGCATGTTCTAGTTCCCGCGCATCAGGTGCTTACAAATGAGGAAAAGAAGAGTTTGCTGCAGAGGTATACCGTGAAAGAAACACAGCTTCCTCGGATGCAGGTGGTTGATCCAGTTGCAAGGTATTACGGGCTTTCACGTGGACAAGTTGTGAAGATAATCAGGCCAAGTGAGACTGCCGGAAGATACGTCACCTACCGTTATGTTGTGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000118 GO:0000228 GO:0000785 GO:0000790 GO:0001085 GO:0001103 GO:0003674 GO:0003676 GO:0003677 GO:0003678 GO:0003824 GO:0004003 GO:0004386 GO:0004407 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005813 GO:0005815 GO:0005856 GO:0006325 GO:0006355 GO:0006357 GO:0006464 GO:0006476 GO:0006807 GO:0006996 GO:0008026 GO:0008094 GO:0008134 GO:0008150 GO:0008152 GO:0008270 GO:0009889 GO:0009987 GO:0010468 GO:0010556 GO:0015630 GO:0016043 GO:0016462 GO:0016569 GO:0016570 GO:0016575 GO:0016581 GO:0016787 GO:0016810 GO:0016811 GO:0016817 GO:0016818 GO:0016887 GO:0017053 GO:0017111 GO:0019213 GO:0019219 GO:0019222 GO:0019538 GO:0019899 GO:0031323 GO:0031326 GO:0031974 GO:0031981 GO:0032392 GO:0032508 GO:0032991 GO:0033558 GO:0035601 GO:0036211 GO:0042623 GO:0042826 GO:0043167 GO:0043169 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043412 GO:0044237 GO:0044238 GO:0044260 GO:0044267 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044430 GO:0044446 GO:0044451 GO:0044454 GO:0044464 GO:0046872 GO:0046914 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0051276 GO:0060255 GO:0065007 GO:0070013 GO:0070035 GO:0070491 GO:0070603 GO:0071103 GO:0071704 GO:0071840 GO:0080090 GO:0090545 GO:0090568 GO:0097159 GO:0098732 GO:0140096 GO:0140097 GO:1901363 GO:1901564 GO:1902494 GO:1903506 GO:1904949 GO:2000112 GO:2001141
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Acetyltransf_1 Acetyltransf_10 Agenet Jas PHD

Protein Analysis

206

Amino Acids

24.39

Weight (kDa)

9.32

Isoelectric Point (pI)

39.9

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_N PF03871 5 - 90 2.7e-32 RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C PF01191 133 - 205 5.7e-35 RNA polymerase Rpb5, C-terminal domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000518)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g21681 FvH4_3g29252 FvH4_3g38950 FvH4_3g44310 FvH4_5g29400
malus_domestica MD03G1066300.v1.1
rosa_chinensis RchiOBHm_Chr2g0087341 RchiOBHm_Chr7g0225691 RchiOBHm_Chr7g0225721 RchiOBHm_Chr7g0225751 RchiOBHm_Chr7g0225781 RchiOBHm_Chr7g0225811 RchiOBHm_Chr7g0225821 RchiOBHm_Chr7g0225841 RchiOBHm_Chr7g0225941
rosa_laevigata RLG00000001777 RLG00000001779 RLG00000001787 RLG00000001796 RLG00000015858 RLG00000018399 RLG00000030202
rosa_multiflora Rmu_co7995100.1_g000001 Rmu_sc0003367.1_g000025 Rmu_sc0004082.1_g000018 Rmu_sc0006064.1_g000002 Rmu_sc0011806.1_g000001 Rmu_sc0014642.1_g000005 Rmu_sc0014767.1_g000003 Rmu_sc0015723.1_g000001 Rmu_sc0030795.1_g000001 Rmu_sc0033647.1_g000001
rosa_roxburghii Rroxscaffold_1G00028220 Rroxscaffold_2G00089180 Rroxscaffold_2G00125860 Rroxscaffold_3G00233350 Rroxscaffold_3G00239570 Rroxscaffold_4G00325690 Rroxscaffold_5G00348560 Rroxscaffold_7G00198070
rosa_rugosa Rorug01G0045600 Rorug01G0474300.1 Rorug07G0220000 Rorug07G0220100 Rorug07G0220200 Rorug07G0220300 Rorug07G0232800 Rorug07G0233000 Rorug07G0233100 Rorug07G0233100 Rorug07G0233200 Rorug07G0233300.1
rosa_samantha Rh1AG061100 Rh1BG052200 Rh1CG063300 Rh1CG063600 Rh1DG067700 Rh2AG027900 Rh2BG027400 Rh2CG028200 Rh2DG028000 Rh7AG369700 Rh7AG370100 Rh7AG371200 Rh7AG387800 Rh7BG366500 Rh7BG366800 Rh7BG367000 Rh7BG367600 Rh7CG388600 Rh7CG389000 Rh7CG389800 Rh7CG407400 Rh7DG377400 Rh7DG377500 Rh7DG377900 Rh7DG378600 Rh7DG378700 Rh7DG378800
rosa_wichuraiana Rw0G020970 Rw0G020980 Rw1G005200 Rw2G002210 Rw7G031830 Rw7G031860 Rw7G031900

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 499
Acc36I ACCTGC 1 cut(s) 499
AccI GTMKAC 2 cut(s) 353, 476
AccII CGCG 1 cut(s) 428
AciI CCGC 3 cut(s) 181, 364, 426
AclWI GGATC 1 cut(s) 512
AcsI RAATTY 1 cut(s) 39
AcvI CACGTG 1 cut(s) 548
AfiI CCNNNNNNNGG 2 cut(s) 223, 370
AgsI TTSAA 1 cut(s) 124
AjnI CCWGG 1 cut(s) 378
AluBI AGCT 4 cut(s) 95, 192, 316, 496
AluI AGCT 4 cut(s) 95, 192, 316, 496
Alw21I GWGCWC 1 cut(s) 131
Alw26I GTCTC 2 cut(s) 309, 575
AlwI GGATC 1 cut(s) 512
AlwNI CAGNNNCTG 1 cut(s) 95
AoxI GGCC 1 cut(s) 572
ApeKI GCWGC 1 cut(s) 466
ApoI RAATTY 1 cut(s) 39
Asp700I GAANNNNTTC 1 cut(s) 284
AspLEI GCGC 2 cut(s) 267, 430
AsuHPI GGTGA 2 cut(s) 409, 592
AsuII TTCGAA 1 cut(s) 43
BauI CACGAG 1 cut(s) 25
BbrPI CACGTG 1 cut(s) 548
BbsI GAAGAC 1 cut(s) 202
Bbv12I GWGCWC 1 cut(s) 131
BbvI GCAGC 1 cut(s) 453
BciT130I CCWGG 1 cut(s) 380
BclI TGATCA 1 cut(s) 196
BcoDI GTCTC 2 cut(s) 309, 575
BfaI CTAG 1 cut(s) 419
BfmI CTRYAG 1 cut(s) 467
BfuAI ACCTGC 1 cut(s) 499
BglII AGATCT 1 cut(s) 157
BisI GCNGC 1 cut(s) 467
BlsI GCNGC 1 cut(s) 468
Bme1390I CCNGG 1 cut(s) 380
BmiI GGNNCC 1 cut(s) 362
BmrFI CCNGG 1 cut(s) 380
BmsI GCATC 2 cut(s) 439, 495
BpiI GAAGAC 1 cut(s) 202
Bpu14I TTCGAA 1 cut(s) 43
BsaAI YACGTR 1 cut(s) 548
BsaJI CCNNGG 1 cut(s) 500
Bsc4I CCNNNNNNNGG 2 cut(s) 223, 370
Bse1I ACTGG 1 cut(s) 521
BseBI CCWGG 1 cut(s) 380
BseDI CCNNGG 1 cut(s) 500
BseGI GGATG 1 cut(s) 510
BseLI CCNNNNNNNGG 2 cut(s) 223, 370
BseMII CTCAG 1 cut(s) 87
BseNI ACTGG 1 cut(s) 521
BseXI GCAGC 1 cut(s) 453
Bsh1236I CGCG 1 cut(s) 428
BshFI GGCC 1 cut(s) 574
BsiHKAI GWGCWC 1 cut(s) 131
BsiSI CCGG 1 cut(s) 588
BslFI GGGAC 1 cut(s) 266
BslI CCNNNNNNNGG 2 cut(s) 223, 370
BsmAI GTCTC 2 cut(s) 309, 575
BsmFI GGGAC 1 cut(s) 266
BsnI GGCC 1 cut(s) 574
Bsp119I TTCGAA 1 cut(s) 43
Bsp1286I GDGCHC 1 cut(s) 131
Bsp143I GATC 5 cut(s) 70, 99, 157, 196, 517
BspACI CCGC 3 cut(s) 181, 364, 426
BspANI GGCC 1 cut(s) 574
BspCNI CTCAG 1 cut(s) 88
BspFNI CGCG 1 cut(s) 428
BspLI GGNNCC 1 cut(s) 362
BspMAI CTGCAG 1 cut(s) 471
BspMI ACCTGC 1 cut(s) 499
BspPI GGATC 1 cut(s) 512
BspT104I TTCGAA 1 cut(s) 43
BsrI ACTGG 1 cut(s) 521
BssECI CCNNGG 1 cut(s) 500
BssMI GATC 5 cut(s) 70, 99, 157, 196, 517
BssNAI GTATAC 1 cut(s) 477
BssSI CACGAG 1 cut(s) 25
Bst1107I GTATAC 1 cut(s) 477
Bst2BI CACGAG 1 cut(s) 25
Bst2UI CCWGG 1 cut(s) 380
Bst4CI ACNGT 4 cut(s) 52, 393, 481, 608
Bst6I CTCTTC 1 cut(s) 452
BstAPI GCANNNNNTGC 1 cut(s) 436
BstBAI YACGTR 1 cut(s) 548
BstBI TTCGAA 1 cut(s) 43
BstC8I GCNNGC 1 cut(s) 269
BstDEI CTNAG 2 cut(s) 82, 96
BstF5I GGATG 1 cut(s) 510
BstFNI CGCG 1 cut(s) 428
BstHHI GCGC 2 cut(s) 267, 430
BstKTI GATC 5 cut(s) 73, 102, 160, 199, 520
BstMAI GTCTC 2 cut(s) 309, 575
BstMBI GATC 5 cut(s) 70, 99, 157, 196, 517
BstMWI GCNNNNNNNGC 1 cut(s) 436
BstNI CCWGG 1 cut(s) 380
BstNSI RCATGY 2 cut(s) 271, 416
BstSCI CCNGG 1 cut(s) 378
BstSFI CTRYAG 1 cut(s) 467
BstUI CGCG 1 cut(s) 428
BstV1I GCAGC 1 cut(s) 453
BstV2I GAAGAC 1 cut(s) 202
BstX2I RGATCY 1 cut(s) 157
BstYI RGATCY 1 cut(s) 157
BstZ17I GTATAC 1 cut(s) 477
BsuRI GGCC 1 cut(s) 574
BtsCI GGATG 1 cut(s) 510
BveI ACCTGC 1 cut(s) 499
Cac8I GCNNGC 1 cut(s) 269
CaiI CAGNNNCTG 1 cut(s) 95
CfoI GCGC 2 cut(s) 267, 430
CviAII CATG 5 cut(s) 106, 145, 268, 367, 413
CviJI RGCY 8 cut(s) 5, 31, 95, 192, 316, 496, 541, 574
CviKI_1 RGCY 8 cut(s) 5, 31, 95, 192, 316, 496, 541, 574
DdeI CTNAG 2 cut(s) 82, 96
DpnI GATC 5 cut(s) 72, 101, 159, 198, 519
DpnII GATC 5 cut(s) 70, 99, 157, 196, 517
Eam1104I CTCTTC 1 cut(s) 452
EarI CTCTTC 1 cut(s) 452
Eco72I CACGTG 1 cut(s) 548
EcoRI GAATTC 1 cut(s) 39
EcoRII CCWGG 1 cut(s) 378
FaeI CATG 5 cut(s) 109, 148, 271, 370, 416
FaqI GGGAC 1 cut(s) 266
FatI CATG 5 cut(s) 105, 144, 267, 366, 412
FauI CCCGC 1 cut(s) 433
FauNDI CATATG 1 cut(s) 133
FbaI TGATCA 1 cut(s) 196
FblI GTMKAC 2 cut(s) 353, 476
Fnu4HI GCNGC 1 cut(s) 467
FokI GGATG 1 cut(s) 517
Fsp4HI GCNGC 1 cut(s) 467
FspBI CTAG 1 cut(s) 419
GlaI GCGC 2 cut(s) 266, 429
GluI GCNGC 1 cut(s) 467
HaeIII GGCC 1 cut(s) 574
HapII CCGG 1 cut(s) 588
HhaI GCGC 2 cut(s) 267, 430
Hin1II CATG 5 cut(s) 109, 148, 271, 370, 416
Hin6I GCGC 2 cut(s) 265, 428
HinP1I GCGC 2 cut(s) 265, 428
HinfI GANTC 1 cut(s) 319
HpaII CCGG 1 cut(s) 588
HphI GGTGA 2 cut(s) 409, 592
Hpy166II GTNNAC 3 cut(s) 354, 477, 551
Hpy188I TCNGA 5 cut(s) 13, 196, 201, 290, 504
Hpy188III TCNNGA 4 cut(s) 25, 74, 124, 161
Hpy8I GTNNAC 3 cut(s) 354, 477, 551
HpyCH4III ACNGT 4 cut(s) 52, 393, 481, 608
HpyCH4IV ACGT 2 cut(s) 547, 597
HpyCH4V TGCA 5 cut(s) 271, 329, 469, 508, 527
HpyF10VI GCNNNNNNNGC 1 cut(s) 436
HpyF3I CTNAG 2 cut(s) 82, 96
HpySE526I ACGT 2 cut(s) 547, 597
Hsp92II CATG 5 cut(s) 109, 148, 271, 370, 416
HspAI GCGC 2 cut(s) 265, 428
Ksp22I TGATCA 1 cut(s) 196
Kzo9I GATC 5 cut(s) 70, 99, 157, 196, 517
LpnPI CCDG 7 cut(s) 365, 392, 419, 494, 534, 556, 601
Lsp1109I GCAGC 1 cut(s) 453
LweI GCATC 2 cut(s) 439, 495
MaeI CTAG 1 cut(s) 419
MaeII ACGT 2 cut(s) 547, 597
MaeIII GTNAC 3 cut(s) 85, 185, 598
MalI GATC 5 cut(s) 72, 101, 159, 198, 519
MboI GATC 5 cut(s) 70, 99, 157, 196, 517
MboII GAAGA 9 cut(s) 26, 57, 167, 202, 205, 398, 469, 574, 603
MflI RGATCY 1 cut(s) 157
MhlI GDGCHC 1 cut(s) 131
MluCI AATT 2 cut(s) 39, 119
MlyI GAGTC 1 cut(s) 313
MmeI TCCRAC 1 cut(s) 36
MnlI CCTC 8 cut(s) 21, 217, 243, 364, 376, 442, 465, 510
MroXI GAANNNNTTC 1 cut(s) 284
MseI TTAA 1 cut(s) 405
MspI CCGG 1 cut(s) 588
MspR9I CCNGG 1 cut(s) 380
MvaI CCWGG 1 cut(s) 380
MvnI CGCG 1 cut(s) 428
MwoI GCNNNNNNNGC 1 cut(s) 436
NdeI CATATG 1 cut(s) 133
NdeII GATC 5 cut(s) 70, 99, 157, 196, 517
NlaIII CATG 5 cut(s) 109, 148, 271, 370, 416
NlaIV GGNNCC 1 cut(s) 362
NmuCI GTSAC 1 cut(s) 598
NspI RCATGY 2 cut(s) 271, 416
NspV TTCGAA 1 cut(s) 43
PaeI GCATGC 1 cut(s) 271
PaqCI CACCTGC 1 cut(s) 499
PdmI GAANNNNTTC 1 cut(s) 284
PfoI TCCNGGA 1 cut(s) 378
PkrI GCNGC 1 cut(s) 468
PleI GAGTC 1 cut(s) 313
PmaCI CACGTG 1 cut(s) 548
PmlI CACGTG 1 cut(s) 548
PpsI GAGTC 1 cut(s) 313
Ppu21I YACGTR 1 cut(s) 548
Psp6I CCWGG 1 cut(s) 378
PspCI CACGTG 1 cut(s) 548
PspGI CCWGG 1 cut(s) 378
PspN4I GGNNCC 1 cut(s) 362
PstI CTGCAG 1 cut(s) 471
PstNI CAGNNNCTG 1 cut(s) 95
PsuI RGATCY 1 cut(s) 157
SaqAI TTAA 1 cut(s) 405
SatI GCNGC 1 cut(s) 467
Sau3AI GATC 5 cut(s) 70, 99, 157, 196, 517
SchI GAGTC 1 cut(s) 313
ScrFI CCNGG 1 cut(s) 380
SduI GDGCHC 1 cut(s) 131
SfaNI GCATC 2 cut(s) 439, 495
SfcI CTRYAG 1 cut(s) 467
SfuI TTCGAA 1 cut(s) 43
SphI GCATGC 1 cut(s) 271
Sse9I AATT 2 cut(s) 39, 119
SsiI CCGC 3 cut(s) 181, 364, 426
SspI AATATT 1 cut(s) 403
SspMI CTAG 1 cut(s) 419
StyD4I CCNGG 1 cut(s) 378
TaaI ACNGT 4 cut(s) 52, 393, 481, 608
TaiI ACGT 2 cut(s) 550, 600
TaqI TCGA 1 cut(s) 43
TasI AATT 2 cut(s) 39, 119
Tru1I TTAA 1 cut(s) 405
Tru9I TTAA 1 cut(s) 405
TseFI GTSAC 1 cut(s) 598
TseI GCWGC 1 cut(s) 466
Tsp45I GTSAC 1 cut(s) 598
TspDTI ATGAA 2 cut(s) 33, 161
XapI RAATTY 1 cut(s) 39
XceI RCATGY 2 cut(s) 271, 416
XmiI GTMKAC 2 cut(s) 353, 476
XmnI GAANNNNTTC 1 cut(s) 284
XspI CTAG 1 cut(s) 419
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.