Rroxscaffold_2G00123930

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0000437
Physical Location & Seq
Forward (+)
57882391 .. 57886360
3970 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00123930.1

Sequence Viewer

Length: 498 bp
ATGTCTTCCTTGTCTAAGGAACATGTGAATTCTATGGGGCAACAAAGGCCTAAATATGGCCCTTATTCGAACATGTACAATCCGGGATGGAAGGATCACCCCAACTTCCTTTGGAGCGGTAATGACAACGTGGTTCAACTCACCCAAGGCATCTACAATGGACCACCTGGACTCCAACAAGAGGCTAAGCAGCAAGTCTATCAACAAACTCCCCTCAACAATCCTCAAGCAAGTCCTTGGAAGAACTCGGTGAAGGAGATGGCTATGAACACCGCATCATTCCACAAAGAGACCACATCCTTCCAAAAGGATATCGCAACCTTCATACAAAAGGCAAGATCTCAACTCAAGGAGCATGGCCAATCTATCAAGAATTTGGAAAGGCAAGTTGGGCAACTTGTAACAGAGATCCATACTAGACTTCCGGCACTCTCCCTAGCACAACCATTCAAAATCCCAAGGATGAGAGAATGGCTGAACTTAATGCAATCACTTTAA
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 RVT_1 Retrotrans_gag rve

Protein Analysis

165

Amino Acids

18.92

Weight (kDa)

9.73

Isoelectric Point (pI)

40.03

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: OG0000437)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G06105
fragaria_vesca FvH4_1g09709 FvH4_4g02101 FvH4_4g08975 FvH4_6g23372 FvH4_6g39851 FvH4_c1g00300
malus_domestica MD01G1176100.v1.1 MD09G1284900.v1.1 MD15G1306600.v1.1
prunus_persica Prupe.1G227700_v2.0.a1
pyrus_communis pycom01g00630 pycom01g01020 pycom01g01690 pycom01g01760 pycom01g04190 pycom01g04400 pycom02g18130 pycom03g10160 pycom05g06370 pycom05g08930 pycom06g05590 pycom10g06320 pycom11g14330 pycom11g15320 pycom11g16240 pycom12416g00050 pycom12420g00010 pycom12420g00120 pycom12426g00180 pycom12426g00710 pycom12531g00010 pycom1256g00020 pycom1256g00050 pycom1341g00030 pycom1353g00030 pycom13g23070 pycom13g23210 pycom13g26260 pycom13g26370 pycom13g26470 pycom13g26980 pycom14g08550 pycom14g08850 pycom1534g00040 pycom15g28760 pycom15g31230 pycom1604g00040 pycom16g21900 pycom16g26030 pycom1739g00020 pycom1739g00050 pycom17g12970 pycom17g17960 pycom17g18300 pycom17g18650 pycom2172g00020 pycom2438g00020 pycom436g00370 pycom436g00390 pycom576g00050 pycom76g00020
rosa_chinensis RchiOBHm_Chr1g0320811 RchiOBHm_Chr2g0135321 RchiOBHm_Chr3g0485721 RchiOBHm_Chr7g0236571
rosa_multiflora Rmu_sc0000185.1_g000007 Rmu_sc0002094.1_g000030 Rmu_sc0002764.1_g000007 Rmu_sc0002809.1_g000014 Rmu_sc0003005.1_g000007 Rmu_sc0003798.1_g000005 Rmu_sc0004646.1_g000027 Rmu_sc0004665.1_g000009 Rmu_sc0004818.1_g000001 Rmu_sc0004988.1_g000031 Rmu_sc0006373.1_g000007 Rmu_sc0007142.1_g000015 Rmu_sc0009930.1_g000001 Rmu_sc0011451.1_g000001 Rmu_sc0020424.1_g000001 Rmu_sc0036944.1_g000001 Rmu_ssc0000062.1_g000010
rosa_roxburghii Rroxscaffold_2G00123930 Rroxscaffold_3G00231480 Rroxscaffold_6G00413880
rosa_rugosa Rorug04G0084800
rosa_samantha Rh3BG150500 Rh6DG232400
rosa_wichuraiana Rw2G018400 Rw3G027860 Rw4G021220 Rw6G020670 Rw6G037970

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 117
AciI CCGC 2 cut(s) 117, 273
AclWI GGATC 2 cut(s) 102, 403
AcoI YGGCCR 1 cut(s) 358
AcsI RAATTY 2 cut(s) 28, 373
AfaI GTAC 1 cut(s) 77
AfiI CCNNNNNNNGG 2 cut(s) 56, 181
AflIII ACRYGT 2 cut(s) 22, 72
AgsI TTSAA 2 cut(s) 137, 451
AjnI CCWGG 1 cut(s) 166
AjuI GAANNNNNNNTTGG 2 cut(s) 372, 404
Alw26I GTCTC 1 cut(s) 284
AlwI GGATC 2 cut(s) 102, 403
AoxI GGCC 3 cut(s) 47, 58, 358
ApeKI GCWGC 1 cut(s) 190
ApoI RAATTY 2 cut(s) 28, 373
AspS9I GGNCC 2 cut(s) 59, 161
AsuC2I CCSGG 1 cut(s) 84
AsuHPI GGTGA 3 cut(s) 89, 133, 262
AsuII TTCGAA 1 cut(s) 68
AvaII GGWCC 1 cut(s) 161
BalI TGGCCA 1 cut(s) 360
BbvI GCAGC 1 cut(s) 202
BccI CCATC 2 cut(s) 81, 253
BciT130I CCWGG 1 cut(s) 168
BcnI CCSGG 1 cut(s) 84
BcoDI GTCTC 1 cut(s) 284
BfaI CTAG 2 cut(s) 417, 437
BglII AGATCT 1 cut(s) 338
BisI GCNGC 1 cut(s) 191
BlpI GCTNAGC 1 cut(s) 186
BlsI GCNGC 1 cut(s) 192
Bme1390I CCNGG 2 cut(s) 84, 168
Bme18I GGWCC 1 cut(s) 161
BmgT120I GGNCC 2 cut(s) 59, 161
BmrFI CCNGG 2 cut(s) 84, 168
BmsI GCATC 2 cut(s) 159, 284
Bpu1102I GCTNAGC 1 cut(s) 186
Bpu14I TTCGAA 1 cut(s) 68
BpuEI CTTGAG 2 cut(s) 210, 332
BpuMI CCSGG 1 cut(s) 84
BsaI GGTCTC 1 cut(s) 284
BsaJI CCNNGG 3 cut(s) 145, 236, 458
BsaXI ACNNNNNCTCC 2 cut(s) 156, 186
Bsc4I CCNNNNNNNGG 2 cut(s) 56, 181
BseBI CCWGG 1 cut(s) 168
BseDI CCNNGG 3 cut(s) 145, 236, 458
BseGI GGATG 3 cut(s) 92, 296, 468
BseLI CCNNNNNNNGG 2 cut(s) 56, 181
BseXI GCAGC 1 cut(s) 202
BshFI GGCC 3 cut(s) 49, 60, 360
BsiSI CCGG 2 cut(s) 83, 425
BslI CCNNNNNNNGG 2 cut(s) 56, 181
BsmAI GTCTC 1 cut(s) 284
BsnI GGCC 3 cut(s) 49, 60, 360
Bso31I GGTCTC 1 cut(s) 284
Bsp119I TTCGAA 1 cut(s) 68
Bsp1407I TGTACA 1 cut(s) 75
Bsp143I GATC 3 cut(s) 94, 338, 408
Bsp1720I GCTNAGC 1 cut(s) 186
BspACI CCGC 2 cut(s) 117, 273
BspANI GGCC 3 cut(s) 49, 60, 360
BspPI GGATC 2 cut(s) 102, 403
BspT104I TTCGAA 1 cut(s) 68
BspTNI GGTCTC 1 cut(s) 284
BsrBI CCGCTC 1 cut(s) 117
BsrGI TGTACA 1 cut(s) 75
BssECI CCNNGG 3 cut(s) 145, 236, 458
BssMI GATC 3 cut(s) 94, 338, 408
BssT1I CCWWGG 3 cut(s) 145, 236, 458
Bst2UI CCWGG 1 cut(s) 168
BstAUI TGTACA 1 cut(s) 75
BstBI TTCGAA 1 cut(s) 68
BstDEI CTNAG 2 cut(s) 15, 186
BstF5I GGATG 3 cut(s) 92, 296, 468
BstKTI GATC 3 cut(s) 97, 341, 411
BstMAI GTCTC 1 cut(s) 284
BstMBI GATC 3 cut(s) 94, 338, 408
BstMWI GCNNNNNNNGC 2 cut(s) 46, 391
BstNI CCWGG 1 cut(s) 168
BstNSI RCATGY 2 cut(s) 26, 76
BstSCI CCNGG 2 cut(s) 82, 166
BstV1I GCAGC 1 cut(s) 202
BstX2I RGATCY 2 cut(s) 338, 408
BstYI RGATCY 2 cut(s) 338, 408
BsuRI GGCC 3 cut(s) 49, 60, 360
BtsCI GGATG 3 cut(s) 92, 296, 468
Cfr13I GGNCC 2 cut(s) 59, 161
Csp6I GTAC 1 cut(s) 76
CviAII CATG 3 cut(s) 23, 73, 356
CviJI RGCY 6 cut(s) 49, 60, 185, 263, 360, 475
CviKI_1 RGCY 6 cut(s) 49, 60, 185, 263, 360, 475
CviQI GTAC 1 cut(s) 76
DdeI CTNAG 2 cut(s) 15, 186
DpnI GATC 3 cut(s) 96, 340, 410
DpnII GATC 3 cut(s) 94, 338, 408
EaeI YGGCCR 1 cut(s) 358
Eco130I CCWWGG 3 cut(s) 145, 236, 458
Eco147I AGGCCT 1 cut(s) 49
Eco31I GGTCTC 1 cut(s) 284
Eco32I GATATC 1 cut(s) 313
Eco47I GGWCC 1 cut(s) 161
EcoRI GAATTC 1 cut(s) 28
EcoRII CCWGG 1 cut(s) 166
EcoRV GATATC 1 cut(s) 313
EcoT14I CCWWGG 3 cut(s) 145, 236, 458
ErhI CCWWGG 3 cut(s) 145, 236, 458
FaeI CATG 3 cut(s) 26, 76, 359
FaiI YATR 8 cut(s) 24, 35, 57, 74, 266, 326, 357, 414
FatI CATG 3 cut(s) 22, 72, 355
Fnu4HI GCNGC 1 cut(s) 191
FokI GGATG 3 cut(s) 99, 283, 475
Fsp4HI GCNGC 1 cut(s) 191
FspBI CTAG 2 cut(s) 417, 437
GluI GCNGC 1 cut(s) 191
HaeIII GGCC 3 cut(s) 49, 60, 360
HapII CCGG 2 cut(s) 83, 425
Hin1II CATG 3 cut(s) 26, 76, 359
HinfI GANTC 1 cut(s) 171
HpaII CCGG 2 cut(s) 83, 425
HphI GGTGA 3 cut(s) 89, 133, 262
Hpy188III TCNNGA 1 cut(s) 370
HpyAV CCTTC 4 cut(s) 85, 247, 310, 331
HpyCH4IV ACGT 1 cut(s) 129
HpyCH4V TGCA 1 cut(s) 487
HpyF10VI GCNNNNNNNGC 2 cut(s) 46, 391
HpyF3I CTNAG 2 cut(s) 15, 186
HpySE526I ACGT 1 cut(s) 129
Hsp92II CATG 3 cut(s) 26, 76, 359
Kzo9I GATC 3 cut(s) 94, 338, 408
LmnI GCTCC 2 cut(s) 114, 352
LpnPI CCDG 4 cut(s) 96, 153, 180, 438
Lsp1109I GCAGC 1 cut(s) 202
LweI GCATC 2 cut(s) 159, 284
MaeI CTAG 2 cut(s) 417, 437
MaeII ACGT 1 cut(s) 129
MaeIII GTNAC 1 cut(s) 400
MalI GATC 3 cut(s) 96, 340, 410
MbiI CCGCTC 1 cut(s) 117
MboI GATC 3 cut(s) 94, 338, 408
MboII GAAGA 1 cut(s) 253
MflI RGATCY 2 cut(s) 338, 408
MlsI TGGCCA 1 cut(s) 360
MluCI AATT 2 cut(s) 28, 373
MluNI TGGCCA 1 cut(s) 360
MlyI GAGTC 1 cut(s) 165
MmeI TCCRAC 1 cut(s) 199
MnlI CCTC 3 cut(s) 175, 224, 234
Mox20I TGGCCA 1 cut(s) 360
MscI TGGCCA 1 cut(s) 360
MseI TTAA 2 cut(s) 482, 496
Msp20I TGGCCA 1 cut(s) 360
MspI CCGG 2 cut(s) 83, 425
MspR9I CCNGG 2 cut(s) 84, 168
MvaI CCWGG 1 cut(s) 168
MwoI GCNNNNNNNGC 2 cut(s) 46, 391
NciI CCSGG 1 cut(s) 84
NdeII GATC 3 cut(s) 94, 338, 408
NlaIII CATG 3 cut(s) 26, 76, 359
NspI RCATGY 2 cut(s) 26, 76
NspV TTCGAA 1 cut(s) 68
PceI AGGCCT 1 cut(s) 49
PciI ACATGT 2 cut(s) 22, 72
PfoI TCCNGGA 1 cut(s) 82
PkrI GCNGC 1 cut(s) 192
PleI GAGTC 1 cut(s) 165
PpsI GAGTC 1 cut(s) 165
PscI ACATGT 2 cut(s) 22, 72
Psp6I CCWGG 1 cut(s) 166
PspGI CCWGG 1 cut(s) 166
PspPI GGNCC 2 cut(s) 59, 161
PsuI RGATCY 2 cut(s) 338, 408
RsaI GTAC 1 cut(s) 77
RsaNI GTAC 1 cut(s) 76
SaqAI TTAA 2 cut(s) 482, 496
SatI GCNGC 1 cut(s) 191
Sau3AI GATC 3 cut(s) 94, 338, 408
Sau96I GGNCC 2 cut(s) 59, 161
SchI GAGTC 1 cut(s) 165
ScrFI CCNGG 2 cut(s) 84, 168
SetI ASST 3 cut(s) 132, 169, 323
SfaNI GCATC 2 cut(s) 159, 284
SfuI TTCGAA 1 cut(s) 68
SinI GGWCC 1 cut(s) 161
SmlI CTYRAG 2 cut(s) 225, 347
SmoI CTYRAG 2 cut(s) 225, 347
Sse9I AATT 2 cut(s) 28, 373
SseBI AGGCCT 1 cut(s) 49
SsiI CCGC 2 cut(s) 117, 273
SspMI CTAG 2 cut(s) 417, 437
StuI AGGCCT 1 cut(s) 49
StyD4I CCNGG 2 cut(s) 82, 166
StyI CCWWGG 3 cut(s) 145, 236, 458
TaiI ACGT 1 cut(s) 132
TaqI TCGA 1 cut(s) 68
TasI AATT 2 cut(s) 28, 373
TatI WGTACW 1 cut(s) 75
Tru1I TTAA 2 cut(s) 482, 496
Tru9I TTAA 2 cut(s) 482, 496
TseI GCWGC 1 cut(s) 190
TspDTI ATGAA 2 cut(s) 281, 313
VpaK11BI GGWCC 1 cut(s) 161
XapI RAATTY 2 cut(s) 28, 373
XceI RCATGY 2 cut(s) 26, 76
XspI CTAG 2 cut(s) 417, 437
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.