Rroxscaffold_5G00348560

repressing transcription factor binding

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000518
Physical Location & Seq
Forward (+)
20867356 .. 20872698
5343 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00348560.1

Sequence Viewer

Length: 636 bp
ATGCCATCCACGAGTGTTTCGAGCCTTCCAAAGACCCTTACACCAACGAGAGACATTGCCGAGGACATTGTCTTCAACTTGGAATCCGATTCCGAGTTGAATTTGAGAGGCTTTTACACCGTGGTTCTGGAGAGGAGAGATGATGATGATGGTCATGAGGAGATGATTGGTGCCGCCACGGTGAGGATCAATAAGGGAGTGGCTGAAGTGCCACTCGTGGCGACTAGGCCTCGGTTTAGGAGACTTGGGATGTGCATGATTTTGATGAAAGAGCTCGAAAATCGGCTCATGGAATTCGGCATTGAGAGGTTAGTGTTGCCTTCGGCACAAAGTGCACTCAATACATGGACTAGTAGTTCAATTGGGTTTTCTATGATGACCGAAAAAATTATTCGTCCACACAAAAACTACATATTGACCGGCCCAAGACCAGTCGACGACGATGGTGACTCTCTCCCAAGAAATCAAAGAAAAATGGCTTCTTCTTCTTCTTCTTCAACCTCACTCTTCTTCTTTTTCTCTCTCCTCTCCTTCTCCTCCTCCCAAACCATCACTAACGTCGCCGAGATCCTCTCCAATTCTTGCTACAAATCCATCTCCCTCGTACTCCTGTGGATTAACGACGATGTTACATGA
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

211

Amino Acids

23.59

Weight (kDa)

5.29

Isoelectric Point (pI)

54.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
IDM1_C PF23209 16 - 136 2.3e-28 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) 170
AccI GTMKAC 1 cut(s) 435
AciI CCGC 1 cut(s) 174
AclWI GGATC 2 cut(s) 194, 562
AcsI RAATTY 2 cut(s) 100, 293
AcuI CTGAAG 1 cut(s) 225
AdeI CACNNNGTG 1 cut(s) 332
AfaI GTAC 1 cut(s) 606
AfiI CCNNNNNNNGG 1 cut(s) 183
AgsI TTSAA 4 cut(s) 76, 100, 360, 498
AhlI ACTAGT 1 cut(s) 350
AloI GAACNNNNNNTCC 2 cut(s) 340, 372
AluBI AGCT 1 cut(s) 274
AluI AGCT 1 cut(s) 274
Alw21I GWGCWC 2 cut(s) 276, 337
Alw26I GTCTC 2 cut(s) 45, 235
Alw44I GTGCAC 1 cut(s) 333
AlwI GGATC 2 cut(s) 194, 562
AoxI GGCC 2 cut(s) 227, 421
ApaLI GTGCAC 1 cut(s) 333
ApoI RAATTY 2 cut(s) 100, 293
AspS9I GGNCC 1 cut(s) 422
AsuHPI GGTGA 2 cut(s) 193, 458
BaeGI GKGCMC 1 cut(s) 337
BanI GGYRCC 1 cut(s) 170
BanII GRGCYC 1 cut(s) 276
BauI CACGAG 2 cut(s) 10, 215
BbsI GAAGAC 1 cut(s) 64
Bbv12I GWGCWC 2 cut(s) 276, 337
BccI CCATC 5 cut(s) 13, 143, 437, 557, 602
BcoDI GTCTC 2 cut(s) 45, 235
BcuI ACTAGT 1 cut(s) 350
BfaI CTAG 2 cut(s) 225, 351
BisI GCNGC 1 cut(s) 174
BlsI GCNGC 1 cut(s) 175
BmgT120I GGNCC 1 cut(s) 422
BmiI GGNNCC 1 cut(s) 172
BpiI GAAGAC 1 cut(s) 64
BplI GAGNNNNNCTC 2 cut(s) 557, 589
BpmI CTGGAG 1 cut(s) 149
BsaJI CCNNGG 4 cut(s) 60, 120, 177, 230
Bsc4I CCNNNNNNNGG 1 cut(s) 183
Bse118I RCCGGY 1 cut(s) 419
Bse1I ACTGG 1 cut(s) 431
Bse3DI GCAATG 1 cut(s) 54
BseDI CCNNGG 4 cut(s) 60, 120, 177, 230
BseGI GGATG 2 cut(s) 5, 255
BseLI CCNNNNNNNGG 1 cut(s) 183
BseMI GCAATG 1 cut(s) 54
BseNI ACTGG 1 cut(s) 431
BseRI GAGGAG 5 cut(s) 148, 173, 515, 526, 529
BseSI GKGCMC 1 cut(s) 337
BshFI GGCC 2 cut(s) 229, 423
BshNI GGYRCC 1 cut(s) 170
BsiHKAI GWGCWC 2 cut(s) 276, 337
BsiSI CCGG 1 cut(s) 420
BslI CCNNNNNNNGG 1 cut(s) 183
BsmAI GTCTC 2 cut(s) 45, 235
BsnI GGCC 2 cut(s) 229, 423
Bsp1286I GDGCHC 2 cut(s) 276, 337
Bsp143I GATC 2 cut(s) 186, 567
BspACI CCGC 1 cut(s) 174
BspANI GGCC 2 cut(s) 229, 423
BspHI TCATGA 1 cut(s) 154
BspLI GGNNCC 1 cut(s) 172
BspPI GGATC 2 cut(s) 194, 562
BspT107I GGYRCC 1 cut(s) 170
BsrDI GCAATG 1 cut(s) 54
BsrFI RCCGGY 1 cut(s) 419
BsrI ACTGG 1 cut(s) 431
BssAI RCCGGY 1 cut(s) 419
BssECI CCNNGG 4 cut(s) 60, 120, 177, 230
BssMI GATC 2 cut(s) 186, 567
BssSI CACGAG 2 cut(s) 10, 215
Bst2BI CACGAG 2 cut(s) 10, 215
Bst4CI ACNGT 2 cut(s) 121, 181
Bst6I CTCTTC 1 cut(s) 512
BstAPI GCANNNNNTGC 1 cut(s) 332
BstDSI CCRYGG 2 cut(s) 120, 177
BstF5I GGATG 2 cut(s) 5, 255
BstKTI GATC 2 cut(s) 189, 570
BstMAI GTCTC 2 cut(s) 45, 235
BstMBI GATC 2 cut(s) 186, 567
BstMWI GCNNNNNNNGC 1 cut(s) 332
BstSLI GKGCMC 1 cut(s) 337
BstV2I GAAGAC 1 cut(s) 64
BstX2I RGATCY 1 cut(s) 567
BstYI RGATCY 1 cut(s) 567
BsuRI GGCC 2 cut(s) 229, 423
BtgI CCRYGG 2 cut(s) 120, 177
BtsCI GGATG 2 cut(s) 5, 255
CciI TCATGA 1 cut(s) 154
Cfr10I RCCGGY 1 cut(s) 419
Cfr13I GGNCC 1 cut(s) 422
Csp6I GTAC 1 cut(s) 605
CviAII CATG 5 cut(s) 155, 256, 289, 345, 633
CviJI RGCY 8 cut(s) 24, 111, 203, 229, 274, 286, 423, 479
CviKI_1 RGCY 8 cut(s) 24, 111, 203, 229, 274, 286, 423, 479
CviQI GTAC 1 cut(s) 605
DpnI GATC 2 cut(s) 188, 569
DpnII GATC 2 cut(s) 186, 567
DraIII CACNNNGTG 1 cut(s) 332
Eam1104I CTCTTC 1 cut(s) 512
EarI CTCTTC 1 cut(s) 512
Ecl136II GAGCTC 1 cut(s) 274
Eco147I AGGCCT 1 cut(s) 229
Eco24I GRGCYC 1 cut(s) 276
Eco53kI GAGCTC 1 cut(s) 274
Eco57I CTGAAG 1 cut(s) 225
EcoICRI GAGCTC 1 cut(s) 274
EcoRI GAATTC 1 cut(s) 293
EcoT38I GRGCYC 1 cut(s) 276
FaeI CATG 5 cut(s) 158, 259, 292, 348, 636
FaiI YATR 7 cut(s) 156, 257, 290, 346, 374, 413, 634
FatI CATG 5 cut(s) 154, 255, 288, 344, 632
FblI GTMKAC 1 cut(s) 435
Fnu4HI GCNGC 1 cut(s) 174
FokI GGATG 1 cut(s) 262
FriOI GRGCYC 1 cut(s) 276
Fsp4HI GCNGC 1 cut(s) 174
FspBI CTAG 2 cut(s) 225, 351
GluI GCNGC 1 cut(s) 174
GsuI CTGGAG 1 cut(s) 149
HaeIII GGCC 2 cut(s) 229, 423
HapII CCGG 1 cut(s) 420
Hin1II CATG 5 cut(s) 158, 259, 292, 348, 636
HincII GTYRAC 1 cut(s) 436
HindII GTYRAC 1 cut(s) 436
HinfI GANTC 3 cut(s) 83, 89, 449
HpaII CCGG 1 cut(s) 420
HphI GGTGA 2 cut(s) 193, 458
Hpy166II GTNNAC 3 cut(s) 335, 398, 436
Hpy188I TCNGA 2 cut(s) 88, 94
Hpy188III TCNNGA 2 cut(s) 128, 155
Hpy8I GTNNAC 3 cut(s) 335, 398, 436
Hpy99I CGWCG 4 cut(s) 440, 443, 563, 626
HpyAV CCTTC 3 cut(s) 35, 330, 541
HpyCH4III ACNGT 2 cut(s) 121, 181
HpyCH4IV ACGT 1 cut(s) 558
HpyCH4V TGCA 2 cut(s) 255, 335
HpyF10VI GCNNNNNNNGC 1 cut(s) 332
HpySE526I ACGT 1 cut(s) 558
Hsp92II CATG 5 cut(s) 158, 259, 292, 348, 636
Kzo9I GATC 2 cut(s) 186, 567
LpnPI CCDG 4 cut(s) 113, 433, 444, 623
MaeI CTAG 2 cut(s) 225, 351
MaeII ACGT 1 cut(s) 558
MaeIII GTNAC 2 cut(s) 446, 628
MalI GATC 2 cut(s) 188, 569
MboI GATC 2 cut(s) 186, 567
MboII GAAGA 8 cut(s) 64, 474, 477, 480, 483, 486, 499, 502
MfeI CAATTG 1 cut(s) 360
MflI RGATCY 1 cut(s) 567
MhlI GDGCHC 2 cut(s) 276, 337
MluCI AATT 5 cut(s) 100, 293, 360, 387, 577
MlyI GAGTC 1 cut(s) 443
MseI TTAA 1 cut(s) 618
MspI CCGG 1 cut(s) 420
MunI CAATTG 1 cut(s) 360
MwoI GCNNNNNNNGC 1 cut(s) 332
NdeII GATC 2 cut(s) 186, 567
NlaIII CATG 5 cut(s) 158, 259, 292, 348, 636
NlaIV GGNNCC 1 cut(s) 172
NmeAIII GCCGAG 2 cut(s) 85, 589
NmuCI GTSAC 1 cut(s) 446
PagI TCATGA 1 cut(s) 154
PceI AGGCCT 1 cut(s) 229
PcsI WCGNNNNNNNCGW 1 cut(s) 17
PfeI GAWTC 2 cut(s) 83, 89
PflFI GACNNNGTC 1 cut(s) 68
PkrI GCNGC 1 cut(s) 175
PleI GAGTC 1 cut(s) 443
PpsI GAGTC 1 cut(s) 443
Psp124BI GAGCTC 1 cut(s) 276
PspN4I GGNNCC 1 cut(s) 172
PspPI GGNCC 1 cut(s) 422
PsuI RGATCY 1 cut(s) 567
PsyI GACNNNGTC 1 cut(s) 68
RsaI GTAC 1 cut(s) 606
RsaNI GTAC 1 cut(s) 605
SacI GAGCTC 1 cut(s) 276
SalI GTCGAC 1 cut(s) 434
SaqAI TTAA 1 cut(s) 618
SatI GCNGC 1 cut(s) 174
Sau3AI GATC 2 cut(s) 186, 567
Sau96I GGNCC 1 cut(s) 422
SchI GAGTC 1 cut(s) 443
SduI GDGCHC 2 cut(s) 276, 337
SetI ASST 4 cut(s) 276, 311, 503, 561
SpeI ACTAGT 1 cut(s) 350
Sse9I AATT 5 cut(s) 100, 293, 360, 387, 577
SseBI AGGCCT 1 cut(s) 229
SsiI CCGC 1 cut(s) 174
SspMI CTAG 2 cut(s) 225, 351
SstI GAGCTC 1 cut(s) 276
StuI AGGCCT 1 cut(s) 229
TaaI ACNGT 2 cut(s) 121, 181
TaiI ACGT 1 cut(s) 561
TaqI TCGA 3 cut(s) 20, 276, 435
TaqII GACCGA 1 cut(s) 395
TasI AATT 5 cut(s) 100, 293, 360, 387, 577
TauI GCSGC 1 cut(s) 176
TfiI GAWTC 2 cut(s) 83, 89
Tru1I TTAA 1 cut(s) 618
Tru9I TTAA 1 cut(s) 618
TseFI GTSAC 1 cut(s) 446
Tsp45I GTSAC 1 cut(s) 446
TspDTI ATGAA 1 cut(s) 281
Tth111I GACNNNGTC 1 cut(s) 68
VneI GTGCAC 1 cut(s) 333
XapI RAATTY 2 cut(s) 100, 293
XmiI GTMKAC 1 cut(s) 435
XspI CTAG 2 cut(s) 225, 351
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.