Rroxscaffold_63G00444420

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000063
OG0000385
Physical Location & Seq
Forward (+)
17411 .. 90999
73589 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_63G00444420.1

Sequence Viewer

Length: 420 bp
ATGGAGGAAACCATGAAGGTGATGGATGCAGCTTACAAGGGGTACGTTGCAGAAGTCAATGTTCGGCTAACTTCCATATTGGAAGAGTTAGCTAGCCTGAAGGAGATGGTGATGGCAAATGACGACGAGACAAAGTCCAAGGTCCTAGACTTGGAGGAGGAGATCCAGGTTCTGAGGAGGACGAGGAGCAATGAGTGCTTGAATGTCTCTAAGGTCAAAGTGCCGGAACCAAAGGCATTTCATGGTGTTCGGAATGCGAAGGAGTTGGAAAACTTTCTATGGGACATGGAGCAATATTTCTGGAGCAAGTCTCCATTACCAGCATGTATCTTTCAGGAGATGCCAAACTATGGTGGCGGACTCGGGTGCAAGATGATGCTAAAATGGGGAGACCCAAGATCGAGGAGTGGGAAACCCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Asp_protease_2 Chromo RVT_1 Retrotrans_gag gag-asp_proteas rve

Protein Analysis

139

Amino Acids

15.94

Weight (kDa)

5.57

Isoelectric Point (pI)

58.38

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000385)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g23713 FvH4_1g25744 FvH4_2g00261 FvH4_2g00262 FvH4_2g15681 FvH4_2g17851 FvH4_2g35550 FvH4_3g05280 FvH4_3g10531 FvH4_3g25910 FvH4_3g28953 FvH4_3g33371 FvH4_3g33536 FvH4_3g36090 FvH4_4g03471 FvH4_4g03480 FvH4_4g06701 FvH4_4g19351 FvH4_4g34281 FvH4_5g00040 FvH4_5g03811 FvH4_5g03812 FvH4_5g11822 FvH4_5g30921 FvH4_5g31701 FvH4_6g12161 FvH4_6g15222 FvH4_6g15223 FvH4_6g17701 FvH4_6g17710 FvH4_6g19301 FvH4_6g33011 FvH4_6g34501 FvH4_6g50161 FvH4_7g04111 FvH4_7g04120 FvH4_7g04121 FvH4_7g04122 FvH4_7g04123 FvH4_7g28231 FvH4_c7g00010
malus_domestica MD12G1084200.v1.1
prunus_persica Prupe.1G206200_v2.0.a1 Prupe.8G085600_v2.0.a1
pyrus_communis pycom01g11080 pycom02g20500 pycom09g18370 pycom12555g00210 pycom13g23120 pycom14g10590 pycom16g17620 pycom16g22750
rosa_chinensis RchiOBHm_Chr2g0137481 RchiOBHm_Chr6g0251961 RchiOBHm_Chr7g0185821
rosa_laevigata RLG00000005585 RLG00000010281 RLG00000010912 RLG00000030342 RLG00000034281
rosa_multiflora Rmu_sc0000096.1_g000010 Rmu_sc0002481.1_g000045 Rmu_sc0003598.1_g000009 Rmu_sc0003863.1_g000019 Rmu_sc0003973.1_g000002 Rmu_sc0004823.1_g000050 Rmu_sc0005621.1_g000007 Rmu_sc0006537.1_g000030 Rmu_sc0006608.1_g000014 Rmu_sc0008506.1_g000007 Rmu_sc0014428.1_g000001 Rmu_sc0035437.1_g000001 Rmu_ssc0000396.1_g000022
rosa_roxburghii Rroxscaffold_175G00432300 Rroxscaffold_17G00435390 Rroxscaffold_27G00446590 Rroxscaffold_29G00441820 Rroxscaffold_31G00438110 Rroxscaffold_32G00442750 Rroxscaffold_33G00439810 Rroxscaffold_37G00445160 Rroxscaffold_4G00306500 Rroxscaffold_4G00327700 Rroxscaffold_4G00332630 Rroxscaffold_52G00439360 Rroxscaffold_63G00444420 Rroxscaffold_76G00448580 Rroxscaffold_7G00156270
rosa_rugosa Rorug03G0295200
rosa_samantha Rh1BG433700 Rh1CG115400 Rh2AG676300 Rh2CG341800 Rh2DG381400 Rh3BG370100 Rh3BG370200 Rh4AG441600 Rh4BG076500 Rh4BG107400 Rh5BG005600 Rh6BG010100 Rh7BG000200
rosa_wichuraiana Rw0G003820

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 350
AciI CCGC 1 cut(s) 357
AclWI GGATC 1 cut(s) 157
AcuI CTGAAG 1 cut(s) 119
AfaI GTAC 1 cut(s) 44
AfiI CCNNNNNNNGG 2 cut(s) 151, 350
AgsI TTSAA 1 cut(s) 202
AjnI CCWGG 1 cut(s) 165
AluBI AGCT 2 cut(s) 32, 92
AluI AGCT 2 cut(s) 32, 92
Alw26I GTCTC 4 cut(s) 122, 211, 315, 384
AlwI GGATC 1 cut(s) 157
AlwNI CAGNNNCTG 1 cut(s) 172
Ama87I CYCGRG 1 cut(s) 362
ApeKI GCWGC 1 cut(s) 29
Asp700I GAANNNNTTC 1 cut(s) 273
AspS9I GGNCC 1 cut(s) 142
AsuHPI GGTGA 2 cut(s) 31, 121
AsuNHI GCTAGC 1 cut(s) 92
AvaI CYCGRG 1 cut(s) 362
AvaII GGWCC 1 cut(s) 142
BbvI GCAGC 1 cut(s) 41
BccI CCATC 3 cut(s) 16, 100, 106
BciT130I CCWGG 1 cut(s) 167
BcoDI GTCTC 4 cut(s) 122, 211, 315, 384
BfaI CTAG 2 cut(s) 93, 146
BisI GCNGC 1 cut(s) 30
BlsI GCNGC 1 cut(s) 31
Bme1390I CCNGG 1 cut(s) 167
Bme18I GGWCC 1 cut(s) 142
BmeT110I CYCGRG 1 cut(s) 362
BmgT120I GGNCC 1 cut(s) 142
BmiI GGNNCC 1 cut(s) 228
BmrFI CCNGG 1 cut(s) 167
BmsI GCATC 3 cut(s) 16, 330, 366
BmtI GCTAGC 1 cut(s) 96
BplI GAGNNNNNCTC 2 cut(s) 295, 327
BpmI CTGGAG 1 cut(s) 322
BsaI GGTCTC 1 cut(s) 384
BsaJI CCNNGG 1 cut(s) 138
Bsc4I CCNNNNNNNGG 2 cut(s) 151, 350
Bse3DI GCAATG 1 cut(s) 196
BseBI CCWGG 1 cut(s) 167
BseDI CCNNGG 1 cut(s) 138
BseGI GGATG 1 cut(s) 31
BseLI CCNNNNNNNGG 2 cut(s) 151, 350
BseMI GCAATG 1 cut(s) 196
BseMII CTCAG 1 cut(s) 164
BseRI GAGGAG 5 cut(s) 170, 173, 190, 199, 418
BseXI GCAGC 1 cut(s) 41
BsiHKCI CYCGRG 1 cut(s) 362
BsiSI CCGG 1 cut(s) 224
BslFI GGGAC 1 cut(s) 296
BslI CCNNNNNNNGG 2 cut(s) 151, 350
BsmAI GTCTC 4 cut(s) 122, 211, 315, 384
BsmFI GGGAC 1 cut(s) 296
BsmI GAATGC 1 cut(s) 259
Bso31I GGTCTC 1 cut(s) 384
BsoBI CYCGRG 1 cut(s) 362
Bsp143I GATC 2 cut(s) 162, 398
BspACI CCGC 1 cut(s) 357
BspCNI CTCAG 1 cut(s) 165
BspLI GGNNCC 1 cut(s) 228
BspOI GCTAGC 1 cut(s) 96
BspPI GGATC 1 cut(s) 157
BspTNI GGTCTC 1 cut(s) 384
BsrDI GCAATG 1 cut(s) 196
BssECI CCNNGG 1 cut(s) 138
BssMI GATC 2 cut(s) 162, 398
BssT1I CCWWGG 1 cut(s) 138
Bst2UI CCWGG 1 cut(s) 167
Bst6I CTCTTC 1 cut(s) 78
BstAPI GCANNNNNTGC 1 cut(s) 195
BstC8I GCNNGC 1 cut(s) 94
BstDEI CTNAG 2 cut(s) 173, 210
BstF5I GGATG 1 cut(s) 31
BstKTI GATC 2 cut(s) 165, 401
BstMAI GTCTC 4 cut(s) 122, 211, 315, 384
BstMBI GATC 2 cut(s) 162, 398
BstMWI GCNNNNNNNGC 1 cut(s) 195
BstNI CCWGG 1 cut(s) 167
BstNSI RCATGY 1 cut(s) 327
BstSCI CCNGG 1 cut(s) 165
BstV1I GCAGC 1 cut(s) 41
BstX2I RGATCY 1 cut(s) 162
BstYI RGATCY 1 cut(s) 162
BtsCI GGATG 1 cut(s) 31
Cac8I GCNNGC 1 cut(s) 94
CaiI CAGNNNCTG 1 cut(s) 172
Cfr13I GGNCC 1 cut(s) 142
Csp6I GTAC 1 cut(s) 43
CviAII CATG 4 cut(s) 13, 242, 286, 324
CviJI RGCY 4 cut(s) 32, 67, 92, 96
CviKI_1 RGCY 4 cut(s) 32, 67, 92, 96
CviQI GTAC 1 cut(s) 43
DdeI CTNAG 2 cut(s) 173, 210
DpnI GATC 2 cut(s) 164, 400
DpnII GATC 2 cut(s) 162, 398
Eam1104I CTCTTC 1 cut(s) 78
EarI CTCTTC 1 cut(s) 78
EciI GGCGGA 1 cut(s) 372
Eco130I CCWWGG 1 cut(s) 138
Eco31I GGTCTC 1 cut(s) 384
Eco47I GGWCC 1 cut(s) 142
Eco57I CTGAAG 1 cut(s) 119
Eco88I CYCGRG 1 cut(s) 362
EcoO109I RGGNCCY 1 cut(s) 142
EcoRII CCWGG 1 cut(s) 165
EcoT14I CCWWGG 1 cut(s) 138
ErhI CCWWGG 1 cut(s) 138
FaeI CATG 4 cut(s) 16, 245, 289, 327
FaiI YATR 7 cut(s) 14, 77, 243, 280, 287, 325, 351
FaqI GGGAC 1 cut(s) 296
FatI CATG 4 cut(s) 12, 241, 285, 323
Fnu4HI GCNGC 1 cut(s) 30
FokI GGATG 1 cut(s) 38
Fsp4HI GCNGC 1 cut(s) 30
FspBI CTAG 2 cut(s) 93, 146
GluI GCNGC 1 cut(s) 30
GsuI CTGGAG 1 cut(s) 322
HapII CCGG 1 cut(s) 224
Hin1II CATG 4 cut(s) 16, 245, 289, 327
HinfI GANTC 1 cut(s) 360
HpaII CCGG 1 cut(s) 224
HphI GGTGA 2 cut(s) 31, 121
Hpy188I TCNGA 2 cut(s) 174, 252
Hpy188III TCNNGA 2 cut(s) 301, 335
Hpy99I CGWCG 1 cut(s) 128
HpyAV CCTTC 3 cut(s) 10, 94, 253
HpyCH4IV ACGT 1 cut(s) 45
HpyCH4V TGCA 3 cut(s) 29, 50, 369
HpyF10VI GCNNNNNNNGC 1 cut(s) 195
HpyF3I CTNAG 2 cut(s) 173, 210
HpySE526I ACGT 1 cut(s) 45
Hsp92II CATG 4 cut(s) 16, 245, 289, 327
Kzo9I GATC 2 cut(s) 162, 398
LmnI GCTCC 3 cut(s) 186, 289, 303
LpnPI CCDG 7 cut(s) 110, 152, 179, 237, 286, 320, 333
Lsp1109I GCAGC 1 cut(s) 41
LweI GCATC 3 cut(s) 16, 330, 366
MaeI CTAG 2 cut(s) 93, 146
MaeII ACGT 1 cut(s) 45
MalI GATC 2 cut(s) 164, 400
MboI GATC 2 cut(s) 162, 398
MboII GAAGA 1 cut(s) 95
MflI RGATCY 1 cut(s) 162
MlyI GAGTC 1 cut(s) 354
MmeI TCCRAC 1 cut(s) 246
MnlI CCTC 6 cut(s) 148, 151, 168, 171, 177, 396
MroXI GAANNNNTTC 1 cut(s) 273
MslI CAYNNNNRTG 1 cut(s) 17
MspI CCGG 1 cut(s) 224
MspR9I CCNGG 1 cut(s) 167
Mva1269I GAATGC 1 cut(s) 259
MvaI CCWGG 1 cut(s) 167
MwoI GCNNNNNNNGC 1 cut(s) 195
NdeII GATC 2 cut(s) 162, 398
NheI GCTAGC 1 cut(s) 92
NlaIII CATG 4 cut(s) 16, 245, 289, 327
NlaIV GGNNCC 1 cut(s) 228
NspI RCATGY 1 cut(s) 327
PctI GAATGC 1 cut(s) 259
PdmI GAANNNNTTC 1 cut(s) 273
PflFI GACNNNGTC 1 cut(s) 133
PflMI CCANNNNNTGG 1 cut(s) 350
PkrI GCNGC 1 cut(s) 31
PleI GAGTC 1 cut(s) 354
PpsI GAGTC 1 cut(s) 354
PpuMI RGGWCCY 1 cut(s) 142
Psp5II RGGWCCY 1 cut(s) 142
Psp6I CCWGG 1 cut(s) 165
PspGI CCWGG 1 cut(s) 165
PspN4I GGNNCC 1 cut(s) 228
PspPI GGNCC 1 cut(s) 142
PspPPI RGGWCCY 1 cut(s) 142
PstNI CAGNNNCTG 1 cut(s) 172
PsuI RGATCY 1 cut(s) 162
PsyI GACNNNGTC 1 cut(s) 133
RsaI GTAC 1 cut(s) 44
RsaNI GTAC 1 cut(s) 43
RseI CAYNNNNRTG 1 cut(s) 17
SatI GCNGC 1 cut(s) 30
Sau3AI GATC 2 cut(s) 162, 398
Sau96I GGNCC 1 cut(s) 142
SchI GAGTC 1 cut(s) 354
ScrFI CCNGG 1 cut(s) 167
SetI ASST 7 cut(s) 21, 34, 48, 94, 144, 171, 216
SfaNI GCATC 3 cut(s) 16, 330, 366
SinI GGWCC 1 cut(s) 142
SmiMI CAYNNNNRTG 1 cut(s) 17
SsiI CCGC 1 cut(s) 357
SspI AATATT 1 cut(s) 296
SspMI CTAG 2 cut(s) 93, 146
StyD4I CCNGG 1 cut(s) 165
StyI CCWWGG 1 cut(s) 138
TaiI ACGT 1 cut(s) 48
TaqI TCGA 1 cut(s) 401
TseI GCWGC 1 cut(s) 29
TspDTI ATGAA 2 cut(s) 29, 230
Tth111I GACNNNGTC 1 cut(s) 133
Van91I CCANNNNNTGG 1 cut(s) 350
VpaK11BI GGWCC 1 cut(s) 142
XceI RCATGY 1 cut(s) 327
XcmI CCANNNNNNNNNTGG 1 cut(s) 19
XmnI GAANNNNTTC 1 cut(s) 273
XspI CTAG 2 cut(s) 93, 146
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.