Rroxscaffold_4G00325690

repressing transcription factor binding

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000518
Physical Location & Seq
Forward (+)
57512265 .. 57513029
765 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00325690.1

Sequence Viewer

Length: 642 bp
ATGAAGCAGAAGAGAGTGTGTTCATCTCTCTCGGTTACACCCGCCTGTGGCCATGAAGCAGTCAGGTGTTGGAAGAATAAAACGTCGTCGTCAAGAGGATTGAAATTTAGAAAGATGGAGGATATATTGCGAGATAATAGGTCCAAGATTTCGGGAATCAATATCCTTCTTGGGATCCCTATTCCAGTACTGGGTGCCCAGAGCAATCTTACATGGAGATTGTTGAAACCTCACATGAGCGTTGAAAATTATTACGGCACCAAGCCCCATTCTGCTCTCAATGCCATTCACGAGTGTTTCGAGCCCTCTAAGGACCCATACACCAACAGAGACATTGCTGAGGATATTGGAAGTGGCCGAAGTGCCGCGCTTGTGGCTACTAGGCCTCAGTTTCGGAGACTTGGGATGTGCCGAATTCTGATGAATGAGCTTGAAAAGTGGCTCATGGAATTTGAAATTGAGAAGCTGGTTTTGCCTTCTGCGCAAAGTGCACTTGGTACATGGACCAGCAATTCAATAGGGTTTTCAAAGATGACTGAGGATGAGAGATCAAAATTTGCTACTTGTCATGATTTCTTGGATTTTAAGGACACTGCTACGTGCCATAAACAGCTCTTGAAGCAGCCAATAGAGTCATCATGA
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

213

Amino Acids

24.09

Weight (kDa)

9.2

Isoelectric Point (pI)

61.1

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
IDM1_C PF23209 123 - 204 2.4e-21 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)
Acc16I TGCGCA 1 cut(s) 483
AccB1I GGYRCC 2 cut(s) 194, 257
AccII CGCG 1 cut(s) 368
AciI CCGC 2 cut(s) 42, 366
AclWI GGATC 2 cut(s) 169, 182
AcoI YGGCCR 2 cut(s) 49, 355
AcsI RAATTY 4 cut(s) 104, 414, 449, 554
AfaI GTAC 2 cut(s) 189, 499
AfiI CCNNNNNNNGG 2 cut(s) 47, 191
AgsI TTSAA 8 cut(s) 103, 226, 245, 434, 455, 516, 528, 619
AluBI AGCT 3 cut(s) 430, 466, 613
AluI AGCT 3 cut(s) 430, 466, 613
Alw21I GWGCWC 1 cut(s) 493
Alw26I GTCTC 2 cut(s) 324, 391
Alw44I GTGCAC 1 cut(s) 489
AlwI GGATC 2 cut(s) 169, 182
AoxI GGCC 3 cut(s) 49, 355, 383
ApaLI GTGCAC 1 cut(s) 489
ApeKI GCWGC 1 cut(s) 622
ApoI RAATTY 4 cut(s) 104, 414, 449, 554
AspLEI GCGC 2 cut(s) 370, 484
AspS9I GGNCC 3 cut(s) 141, 313, 504
AvaII GGWCC 3 cut(s) 141, 313, 504
BaeGI GKGCMC 2 cut(s) 199, 493
BalI TGGCCA 1 cut(s) 51
BamHI GGATCC 1 cut(s) 174
BanI GGYRCC 2 cut(s) 194, 257
BanII GRGCYC 1 cut(s) 306
BauI CACGAG 1 cut(s) 290
Bbv12I GWGCWC 1 cut(s) 493
BbvCI CCTCAGC 1 cut(s) 339
BbvI GCAGC 1 cut(s) 634
BccI CCATC 1 cut(s) 109
BceAI ACGGC 1 cut(s) 271
BcoDI GTCTC 2 cut(s) 324, 391
BfaI CTAG 1 cut(s) 381
BisI GCNGC 2 cut(s) 366, 623
BlsI GCNGC 2 cut(s) 367, 624
BmcAI AGTACT 1 cut(s) 189
Bme18I GGWCC 3 cut(s) 141, 313, 504
BmgT120I GGNCC 3 cut(s) 141, 313, 504
BmiI GGNNCC 4 cut(s) 176, 196, 259, 315
BmrI ACTGGG 1 cut(s) 200
BmuI ACTGGG 1 cut(s) 200
Bpu10I CCTNAGC 1 cut(s) 339
BsaAI YACGTR 1 cut(s) 600
Bsc4I CCNNNNNNNGG 2 cut(s) 47, 191
Bse1I ACTGG 2 cut(s) 185, 195
Bse3DI GCAATG 1 cut(s) 333
BseGI GGATG 2 cut(s) 411, 547
BseLI CCNNNNNNNGG 2 cut(s) 47, 191
BseMI GCAATG 1 cut(s) 333
BseMII CTCAG 3 cut(s) 330, 401, 528
BseNI ACTGG 2 cut(s) 185, 195
BseSI GKGCMC 2 cut(s) 199, 493
BseXI GCAGC 1 cut(s) 634
Bsh1236I CGCG 1 cut(s) 368
BshFI GGCC 3 cut(s) 51, 357, 385
BshNI GGYRCC 2 cut(s) 194, 257
BsiHKAI GWGCWC 1 cut(s) 493
BslI CCNNNNNNNGG 2 cut(s) 47, 191
BsmAI GTCTC 2 cut(s) 324, 391
BsnI GGCC 3 cut(s) 51, 357, 385
Bsp1286I GDGCHC 3 cut(s) 199, 306, 493
Bsp143I GATC 2 cut(s) 174, 548
BspACI CCGC 2 cut(s) 42, 366
BspANI GGCC 3 cut(s) 51, 357, 385
BspCNI CTCAG 3 cut(s) 331, 400, 529
BspFNI CGCG 1 cut(s) 368
BspHI TCATGA 2 cut(s) 568, 638
BspLI GGNNCC 4 cut(s) 176, 196, 259, 315
BspPI GGATC 2 cut(s) 169, 182
BspT107I GGYRCC 2 cut(s) 194, 257
BsrDI GCAATG 1 cut(s) 333
BsrI ACTGG 2 cut(s) 185, 195
BssMI GATC 2 cut(s) 174, 548
BssSI CACGAG 1 cut(s) 290
Bst2BI CACGAG 1 cut(s) 290
Bst6I CTCTTC 1 cut(s) 5
BstBAI YACGTR 1 cut(s) 600
BstDEI CTNAG 4 cut(s) 309, 339, 387, 537
BstF5I GGATG 2 cut(s) 411, 547
BstFNI CGCG 1 cut(s) 368
BstHHI GCGC 2 cut(s) 370, 484
BstKTI GATC 2 cut(s) 177, 551
BstMAI GTCTC 2 cut(s) 324, 391
BstMBI GATC 2 cut(s) 174, 548
BstMWI GCNNNNNNNGC 6 cut(s) 281, 374, 472, 481, 488, 619
BstSLI GKGCMC 2 cut(s) 199, 493
BstUI CGCG 1 cut(s) 368
BstV1I GCAGC 1 cut(s) 634
BstX2I RGATCY 1 cut(s) 174
BstYI RGATCY 1 cut(s) 174
BsuRI GGCC 3 cut(s) 51, 357, 385
BtsCI GGATG 2 cut(s) 411, 547
BtsI GCAGTG 1 cut(s) 591
BtsIMutI CAGTG 1 cut(s) 591
CciI TCATGA 2 cut(s) 568, 638
CfoI GCGC 2 cut(s) 370, 484
Cfr13I GGNCC 3 cut(s) 141, 313, 504
Csp6I GTAC 2 cut(s) 188, 498
CviAII CATG 7 cut(s) 53, 213, 235, 445, 501, 569, 639
CviQI GTAC 2 cut(s) 188, 498
DdeI CTNAG 4 cut(s) 309, 339, 387, 537
DpnI GATC 2 cut(s) 176, 550
DpnII GATC 2 cut(s) 174, 548
EaeI YGGCCR 2 cut(s) 49, 355
Eam1104I CTCTTC 1 cut(s) 5
EarI CTCTTC 1 cut(s) 5
Eco147I AGGCCT 1 cut(s) 385
Eco24I GRGCYC 1 cut(s) 306
Eco47I GGWCC 3 cut(s) 141, 313, 504
EcoO109I RGGNCCY 1 cut(s) 313
EcoRI GAATTC 1 cut(s) 414
EcoT38I GRGCYC 1 cut(s) 306
FaeI CATG 7 cut(s) 56, 216, 238, 448, 504, 572, 642
FatI CATG 7 cut(s) 52, 212, 234, 444, 500, 568, 638
FauI CCCGC 1 cut(s) 49
Fnu4HI GCNGC 2 cut(s) 366, 623
FokI GGATG 2 cut(s) 418, 554
FriOI GRGCYC 1 cut(s) 306
Fsp4HI GCNGC 2 cut(s) 366, 623
FspBI CTAG 1 cut(s) 381
FspI TGCGCA 1 cut(s) 483
GlaI GCGC 2 cut(s) 369, 483
GluI GCNGC 2 cut(s) 366, 623
HaeIII GGCC 3 cut(s) 51, 357, 385
HhaI GCGC 2 cut(s) 370, 484
Hin1II CATG 7 cut(s) 56, 216, 238, 448, 504, 572, 642
Hin6I GCGC 2 cut(s) 368, 482
HinP1I GCGC 2 cut(s) 368, 482
HinfI GANTC 2 cut(s) 156, 632
Hpy166II GTNNAC 1 cut(s) 491
Hpy188I TCNGA 2 cut(s) 396, 420
Hpy188III TCNNGA 6 cut(s) 93, 153, 290, 569, 616, 639
Hpy8I GTNNAC 1 cut(s) 491
Hpy99I CGWCG 2 cut(s) 88, 91
HpyAV CCTTC 2 cut(s) 176, 486
HpyCH4IV ACGT 2 cut(s) 83, 599
HpyCH4V TGCA 1 cut(s) 491
HpyF10VI GCNNNNNNNGC 6 cut(s) 281, 374, 472, 481, 488, 619
HpyF3I CTNAG 4 cut(s) 309, 339, 387, 537
HpySE526I ACGT 2 cut(s) 83, 599
Hsp92II CATG 7 cut(s) 56, 216, 238, 448, 504, 572, 642
HspAI GCGC 2 cut(s) 368, 482
Kzo9I GATC 2 cut(s) 174, 548
LpnPI CCDG 7 cut(s) 49, 58, 176, 198, 212, 452, 520
Lsp1109I GCAGC 1 cut(s) 634
MaeI CTAG 1 cut(s) 381
MaeII ACGT 2 cut(s) 83, 599
MaeIII GTNAC 1 cut(s) 34
MalI GATC 2 cut(s) 176, 550
MboI GATC 2 cut(s) 174, 548
MboII GAAGA 2 cut(s) 22, 85
MflI RGATCY 1 cut(s) 174
MhlI GDGCHC 3 cut(s) 199, 306, 493
MlsI TGGCCA 1 cut(s) 51
MluCI AATT 7 cut(s) 104, 247, 414, 449, 456, 511, 554
MluNI TGGCCA 1 cut(s) 51
MlyI GAGTC 1 cut(s) 641
MmeI TCCRAC 1 cut(s) 50
MnlI CCTC 7 cut(s) 89, 112, 240, 316, 334, 396, 532
Mox20I TGGCCA 1 cut(s) 51
MscI TGGCCA 1 cut(s) 51
MseI TTAA 1 cut(s) 585
Msp20I TGGCCA 1 cut(s) 51
MvnI CGCG 1 cut(s) 368
MwoI GCNNNNNNNGC 6 cut(s) 281, 374, 472, 481, 488, 619
NdeII GATC 2 cut(s) 174, 548
NlaIII CATG 7 cut(s) 56, 216, 238, 448, 504, 572, 642
NlaIV GGNNCC 4 cut(s) 176, 196, 259, 315
NsbI TGCGCA 1 cut(s) 483
PagI TCATGA 2 cut(s) 568, 638
PceI AGGCCT 1 cut(s) 385
PcsI WCGNNNNNNNCGW 1 cut(s) 297
PfeI GAWTC 1 cut(s) 156
PkrI GCNGC 2 cut(s) 367, 624
PleI GAGTC 1 cut(s) 640
PpsI GAGTC 1 cut(s) 640
Ppu21I YACGTR 1 cut(s) 600
PpuMI RGGWCCY 1 cut(s) 313
Psp5II RGGWCCY 1 cut(s) 313
PspN4I GGNNCC 4 cut(s) 176, 196, 259, 315
PspPI GGNCC 3 cut(s) 141, 313, 504
PspPPI RGGWCCY 1 cut(s) 313
PsuI RGATCY 1 cut(s) 174
RsaI GTAC 2 cut(s) 189, 499
RsaNI GTAC 2 cut(s) 188, 498
SaqAI TTAA 1 cut(s) 585
SatI GCNGC 2 cut(s) 366, 623
Sau3AI GATC 2 cut(s) 174, 548
Sau96I GGNCC 3 cut(s) 141, 313, 504
ScaI AGTACT 1 cut(s) 189
SchI GAGTC 1 cut(s) 641
SduI GDGCHC 3 cut(s) 199, 306, 493
SetI ASST 8 cut(s) 68, 86, 143, 232, 432, 468, 602, 615
SinI GGWCC 3 cut(s) 141, 313, 504
Sse9I AATT 7 cut(s) 104, 247, 414, 449, 456, 511, 554
SseBI AGGCCT 1 cut(s) 385
SsiI CCGC 2 cut(s) 42, 366
SspMI CTAG 1 cut(s) 381
StuI AGGCCT 1 cut(s) 385
TaiI ACGT 2 cut(s) 86, 602
TaqI TCGA 1 cut(s) 300
TasI AATT 7 cut(s) 104, 247, 414, 449, 456, 511, 554
TatI WGTACW 1 cut(s) 187
TauI GCSGC 1 cut(s) 368
TfiI GAWTC 1 cut(s) 156
Tru1I TTAA 1 cut(s) 585
Tru9I TTAA 1 cut(s) 585
TscAI CASTG 1 cut(s) 598
TseI GCWGC 1 cut(s) 622
TspDTI ATGAA 4 cut(s) 12, 17, 69, 437
TspRI CASTG 1 cut(s) 598
VneI GTGCAC 1 cut(s) 489
VpaK11BI GGWCC 3 cut(s) 141, 313, 504
XapI RAATTY 4 cut(s) 104, 414, 449, 554
XspI CTAG 1 cut(s) 381
ZrmI AGTACT 1 cut(s) 189
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.