Rroxscaffold_3G00233350

repressing transcription factor binding

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000518
Physical Location & Seq
Reverse (-)
19290885 .. 19295336
4452 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00233350.1

Sequence Viewer

Length: 591 bp
ATGAAGCGGAAGCGAGCCTCTGCTATGGCTTCCTCCTCATCGTTTGCAGTGAAACCCTCGCGCTTCCTTGAAGAAGATTCAGTCCGGTGTTGGGAGAGCGAAACGGCGTCGTCAAACATGACCCGACCCCAAATCCAATCCAGATCAAGAAAAGGATCGAAAACAAGAAACATCAATGATGTATTAAAAGATGAGAGATCCAAGATTTCTGGGATCAACCGGATTTTGGGGACACCCATTCCCGTGAGCAATAACCTGACATGGAGGCTTTTGAAATCTCACATGCGAATTGAATCTTATTACGGCATCAAGCTCCACTCGGCTCTCAATGCCATCCACGAGTGTTTCGAGCCTTCCAAAGACCCTTACACCAACAGAGACATTGCTGAGGACATTGTCTTCGACTTGGAATCCGATTCCGAGTTGAATTTGAGAGGCTTTTACACCGTGGTTCTGGAGAGGAGAGATGATGATGATGGTCATGAGGAGATGATCGGTGCCGCCACGGTGAGGATCAATAAGGGAGTGGCTGAAGTGCCACTTGTGGCGACTAGGCCTCGCTTAGGAGACTTGGGATGTGCAGGATTTTGA
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

196

Amino Acids

22.06

Weight (kDa)

8.44

Isoelectric Point (pI)

55.69

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
IDM1_C PF23209 116 - 188 7.1e-12 Increased DNA methylation 1, 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)
AccB1I GGYRCC 1 cut(s) 497
AccII CGCG 1 cut(s) 61
AciI CCGC 2 cut(s) 7, 501
AclWI GGATC 4 cut(s) 163, 192, 221, 521
AcsI RAATTY 1 cut(s) 427
AcuI CTGAAG 1 cut(s) 552
AcyI GRCGYC 1 cut(s) 107
AfiI CCNNNNNNNGG 4 cut(s) 91, 226, 510, 563
AgsI TTSAA 4 cut(s) 71, 274, 293, 427
AluBI AGCT 1 cut(s) 313
AluI AGCT 1 cut(s) 313
Alw26I GTCTC 2 cut(s) 372, 561
AlwI GGATC 4 cut(s) 163, 192, 221, 521
AoxI GGCC 1 cut(s) 554
ApoI RAATTY 1 cut(s) 427
ArsI GACNNNNNNTTYG 2 cut(s) 383, 415
AspLEI GCGC 1 cut(s) 63
AsuHPI GGTGA 1 cut(s) 520
BanI GGYRCC 1 cut(s) 497
BauI CACGAG 1 cut(s) 338
BbsI GAAGAC 1 cut(s) 391
BbvCI CCTCAGC 1 cut(s) 387
BccI CCATC 2 cut(s) 341, 470
BceAI ACGGC 2 cut(s) 120, 319
BcoDI GTCTC 2 cut(s) 372, 561
BfaI CTAG 1 cut(s) 552
BisI GCNGC 1 cut(s) 501
BlsI GCNGC 1 cut(s) 502
BmiI GGNNCC 1 cut(s) 499
BmsI GCATC 1 cut(s) 315
BpiI GAAGAC 1 cut(s) 391
BpmI CTGGAG 1 cut(s) 476
Bpu10I CCTNAGC 2 cut(s) 387, 562
BsaHI GRCGYC 1 cut(s) 107
BsaJI CCNNGG 2 cut(s) 447, 504
BsaWI WCCGGW 2 cut(s) 84, 219
Bsc4I CCNNNNNNNGG 4 cut(s) 91, 226, 510, 563
Bse3DI GCAATG 1 cut(s) 381
BseDI CCNNGG 2 cut(s) 447, 504
BseGI GGATG 2 cut(s) 333, 581
BseLI CCNNNNNNNGG 4 cut(s) 91, 226, 510, 563
BseMI GCAATG 1 cut(s) 381
BseMII CTCAG 1 cut(s) 378
BseRI GAGGAG 3 cut(s) 25, 475, 500
Bsh1236I CGCG 1 cut(s) 61
BshFI GGCC 1 cut(s) 556
BshNI GGYRCC 1 cut(s) 497
BsiSI CCGG 2 cut(s) 85, 220
BslFI GGGAC 1 cut(s) 244
BslI CCNNNNNNNGG 4 cut(s) 91, 226, 510, 563
BsmAI GTCTC 2 cut(s) 372, 561
BsmFI GGGAC 1 cut(s) 244
BsnI GGCC 1 cut(s) 556
Bsp143I GATC 6 cut(s) 143, 155, 197, 213, 492, 513
BspACI CCGC 2 cut(s) 7, 501
BspANI GGCC 1 cut(s) 556
BspCNI CTCAG 1 cut(s) 379
BspFNI CGCG 1 cut(s) 61
BspHI TCATGA 1 cut(s) 481
BspLI GGNNCC 1 cut(s) 499
BspPI GGATC 4 cut(s) 163, 192, 221, 521
BspT107I GGYRCC 1 cut(s) 497
BsrDI GCAATG 1 cut(s) 381
BssECI CCNNGG 2 cut(s) 447, 504
BssMI GATC 6 cut(s) 143, 155, 197, 213, 492, 513
BssNI GRCGYC 1 cut(s) 107
BssSI CACGAG 1 cut(s) 338
Bst2BI CACGAG 1 cut(s) 338
Bst4CI ACNGT 2 cut(s) 448, 508
BstACI GRCGYC 1 cut(s) 107
BstC8I GCNNGC 1 cut(s) 15
BstDEI CTNAG 2 cut(s) 387, 562
BstDSI CCRYGG 2 cut(s) 447, 504
BstENI CCTNNNNNAGG 1 cut(s) 561
BstF5I GGATG 2 cut(s) 333, 581
BstFNI CGCG 1 cut(s) 61
BstHHI GCGC 1 cut(s) 63
BstKTI GATC 6 cut(s) 146, 158, 200, 216, 495, 516
BstMAI GTCTC 2 cut(s) 372, 561
BstMBI GATC 6 cut(s) 143, 155, 197, 213, 492, 513
BstMWI GCNNNNNNNGC 1 cut(s) 329
BstNSI RCATGY 1 cut(s) 286
BstUI CGCG 1 cut(s) 61
BstV2I GAAGAC 1 cut(s) 391
BstX2I RGATCY 1 cut(s) 197
BstYI RGATCY 1 cut(s) 197
BsuRI GGCC 1 cut(s) 556
BtgI CCRYGG 2 cut(s) 447, 504
BtsCI GGATG 2 cut(s) 333, 581
BtsI GCAGTG 1 cut(s) 54
BtsIMutI CAGTG 1 cut(s) 54
Cac8I GCNNGC 1 cut(s) 15
CciI TCATGA 1 cut(s) 481
CfoI GCGC 1 cut(s) 63
CseI GACGC 1 cut(s) 96
CviAII CATG 4 cut(s) 118, 261, 283, 482
CviJI RGCY 9 cut(s) 17, 29, 268, 313, 323, 352, 438, 530, 556
CviKI_1 RGCY 9 cut(s) 17, 29, 268, 313, 323, 352, 438, 530, 556
DdeI CTNAG 2 cut(s) 387, 562
DpnI GATC 6 cut(s) 145, 157, 199, 215, 494, 515
DpnII GATC 6 cut(s) 143, 155, 197, 213, 492, 513
Eco147I AGGCCT 1 cut(s) 556
Eco57I CTGAAG 1 cut(s) 552
EcoNI CCTNNNNNAGG 1 cut(s) 561
FaeI CATG 4 cut(s) 121, 264, 286, 485
FaiI YATR 5 cut(s) 26, 119, 262, 284, 483
FalI AAGNNNNNCTT 2 cut(s) 525, 557
FaqI GGGAC 1 cut(s) 244
FatI CATG 4 cut(s) 117, 260, 282, 481
Fnu4HI GCNGC 1 cut(s) 501
FokI GGATG 1 cut(s) 320
Fsp4HI GCNGC 1 cut(s) 501
FspBI CTAG 1 cut(s) 552
GlaI GCGC 1 cut(s) 62
GluI GCNGC 1 cut(s) 501
GsuI CTGGAG 1 cut(s) 476
HaeIII GGCC 1 cut(s) 556
HapII CCGG 2 cut(s) 85, 220
HgaI GACGC 1 cut(s) 96
HhaI GCGC 1 cut(s) 63
Hin1I GRCGYC 1 cut(s) 107
Hin1II CATG 4 cut(s) 121, 264, 286, 485
Hin6I GCGC 1 cut(s) 61
HinP1I GCGC 1 cut(s) 61
HinfI GANTC 4 cut(s) 77, 293, 410, 416
HpaII CCGG 2 cut(s) 85, 220
HphI GGTGA 1 cut(s) 520
Hpy188I TCNGA 2 cut(s) 415, 421
Hpy188III TCNNGA 4 cut(s) 141, 147, 455, 482
Hpy99I CGWCG 1 cut(s) 112
HpyAV CCTTC 1 cut(s) 363
HpyCH4III ACNGT 2 cut(s) 448, 508
HpyCH4V TGCA 2 cut(s) 47, 581
HpyF10VI GCNNNNNNNGC 1 cut(s) 329
HpyF3I CTNAG 2 cut(s) 387, 562
Hsp92I GRCGYC 1 cut(s) 107
Hsp92II CATG 4 cut(s) 121, 264, 286, 485
HspAI GCGC 1 cut(s) 61
Kzo9I GATC 6 cut(s) 143, 155, 197, 213, 492, 513
LmnI GCTCC 1 cut(s) 318
LpnPI CCDG 7 cut(s) 98, 154, 195, 233, 269, 440, 567
LweI GCATC 1 cut(s) 315
MaeI CTAG 1 cut(s) 552
MalI GATC 6 cut(s) 145, 157, 199, 215, 494, 515
MboI GATC 6 cut(s) 143, 155, 197, 213, 492, 513
MboII GAAGA 3 cut(s) 83, 86, 391
MflI RGATCY 1 cut(s) 197
MluCI AATT 2 cut(s) 288, 427
MseI TTAA 1 cut(s) 185
MslI CAYNNNNRTG 1 cut(s) 242
MspI CCGG 2 cut(s) 85, 220
MvnI CGCG 1 cut(s) 61
MwoI GCNNNNNNNGC 1 cut(s) 329
NdeII GATC 6 cut(s) 143, 155, 197, 213, 492, 513
NlaIII CATG 4 cut(s) 121, 264, 286, 485
NlaIV GGNNCC 1 cut(s) 499
NmeAIII GCCGAG 1 cut(s) 299
NspI RCATGY 1 cut(s) 286
PagI TCATGA 1 cut(s) 481
PceI AGGCCT 1 cut(s) 556
PcsI WCGNNNNNNNCGW 1 cut(s) 345
PfeI GAWTC 4 cut(s) 77, 293, 410, 416
PflFI GACNNNGTC 1 cut(s) 395
PkrI GCNGC 1 cut(s) 502
PspN4I GGNNCC 1 cut(s) 499
PsuI RGATCY 1 cut(s) 197
PsyI GACNNNGTC 1 cut(s) 395
RseI CAYNNNNRTG 1 cut(s) 242
SaqAI TTAA 1 cut(s) 185
SatI GCNGC 1 cut(s) 501
Sau3AI GATC 6 cut(s) 143, 155, 197, 213, 492, 513
SetI ASST 2 cut(s) 258, 315
SfaNI GCATC 1 cut(s) 315
SmiMI CAYNNNNRTG 1 cut(s) 242
Sse9I AATT 2 cut(s) 288, 427
SseBI AGGCCT 1 cut(s) 556
SsiI CCGC 2 cut(s) 7, 501
SspMI CTAG 1 cut(s) 552
StuI AGGCCT 1 cut(s) 556
TaaI ACNGT 2 cut(s) 448, 508
TaqI TCGA 3 cut(s) 158, 348, 402
TasI AATT 2 cut(s) 288, 427
TauI GCSGC 1 cut(s) 503
TfiI GAWTC 4 cut(s) 77, 293, 410, 416
Tru1I TTAA 1 cut(s) 185
Tru9I TTAA 1 cut(s) 185
TscAI CASTG 1 cut(s) 54
TspDTI ATGAA 1 cut(s) 17
TspRI CASTG 1 cut(s) 54
Tth111I GACNNNGTC 1 cut(s) 395
XagI CCTNNNNNAGG 1 cut(s) 561
XapI RAATTY 1 cut(s) 427
XceI RCATGY 1 cut(s) 286
XspI CTAG 1 cut(s) 552
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.