Rh3BG359700

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3B
OG0000414
Physical Location & Seq
Reverse (-)
43196352 .. 43196798
447 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3BG359700.1

Sequence Viewer

Length: 447 bp
ATGGCAGCAGTGCTAAGGGCATTCGAAGCCCTAGGCAATGCCCCGGAACAGACCCCAGAGGAACTTGAAAGATATAGGGTGACGCAATGCTTGGACCAGTTCACCAAGCTTAAACCACCCCAGTTCAACAAAACCGGTGAAGCCTGCAAGGCCGAAAACTGGTTAAAGCAAATCTTGAAGATCTTGGATATCATACAAACACCGGAGCAGTACCATGTGTCCCTCGCTGTACACCAGCTTTTCGGGGAGGCTGACAACTGGTGGGATACCGTCCGTAGCCTACGGACTGTCGCTGACCTAACTTGGGTAGAGTTCGAGCAACATTTCCTGGAGCTGTTCTTTCCACCCGTCCTCAAGGCACAAAAGATCAGTGAATTCTTTGCTCTAACCCAAGGAAACAAGACCACTCACGAGTATGTTGTGGCCTTCACACGACTACTTAAGTAA
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
Retrotrans_gag zf-CCHC

Protein Analysis

148

Amino Acids

17.24

Weight (kDa)

5.81

Isoelectric Point (pI)

29.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 29 - 148 5e-07 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 75 - 147 8.1e-15 Retrotransposon gag 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: OG0000414)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g15941 FvH4_1g22181 FvH4_3g31442 FvH4_4g06832 FvH4_5g15722 FvH4_6g30661 FvH4_7g13761
rosa_chinensis RchiOBHm_Chr3g0478271 RchiOBHm_Chr4g0421141
rosa_laevigata RLG00000002038 RLG00000016047 RLG00000021902 RLG00000024696 RLG00000027779 RLG00000033727 RLG00000035621
rosa_multiflora Rmu_sc0000125.1_g000007 Rmu_sc0000221.1_g000019 Rmu_sc0000221.1_g000020 Rmu_sc0000338.1_g000006 Rmu_sc0000429.1_g000059 Rmu_sc0000429.1_g000060 Rmu_sc0000429.1_g000061 Rmu_sc0000543.1_g000046 Rmu_sc0000689.1_g000008 Rmu_sc0000689.1_g000009 Rmu_sc0001436.1_g000002 Rmu_sc0001634.1_g000004 Rmu_sc0001782.1_g000025 Rmu_sc0002206.1_g000012 Rmu_sc0002985.1_g000008 Rmu_sc0002985.1_g000009 Rmu_sc0003044.1_g000040 Rmu_sc0003044.1_g000041 Rmu_sc0003044.1_g000042 Rmu_sc0003275.1_g000010 Rmu_sc0003561.1_g000002 Rmu_sc0003850.1_g000001 Rmu_sc0003850.1_g000002 Rmu_sc0004092.1_g000039 Rmu_sc0004311.1_g000003 Rmu_sc0004443.1_g000016 Rmu_sc0004542.1_g000002 Rmu_sc0004873.1_g000001 Rmu_sc0005757.1_g000002 Rmu_sc0005964.1_g000004 Rmu_sc0006598.1_g000014 Rmu_sc0006598.1_g000015 Rmu_sc0006889.1_g000023 Rmu_sc0007059.1_g000007 Rmu_sc0007390.1_g000014 Rmu_sc0008085.1_g000015 Rmu_sc0009948.1_g000001 Rmu_sc0010235.1_g000005 Rmu_sc0010665.1_g000022 Rmu_sc0011183.1_g000001 Rmu_sc0021637.1_g000001 Rmu_ssc0000242.1_g000016 Rmu_ssc0000317.1_g000003 Rmu_ssc0000317.1_g000004 Rmu_ssc0000432.1_g000093 Rmu_ssc0000432.1_g000095
rosa_roxburghii Rroxscaffold_1G00024670 Rroxscaffold_1G00047120 Rroxscaffold_4G00283230 Rroxscaffold_5G00365300 Rroxscaffold_7G00192220
rosa_rugosa Rorug03G0325200 Rorug06G0093800 Rorug07G0209800
rosa_samantha Rh1AG084000 Rh1AG202300 Rh1AG294200 Rh1BG259000 Rh2AG357500 Rh2AG389500 Rh2CG376700 Rh2CG468700 Rh2DG441200 Rh2DG504700 Rh2DG505700 Rh3BG359700 Rh3DG120200 Rh4BG161300 Rh4CG087000 Rh5BG550100 Rh5CG573000 Rh6AG284900 Rh6AG426700 Rh7DG285400
rosa_wichuraiana Rw1G030090 Rw2G030600 Rw3G018220 Rw3G027930 Rw4G000900 Rw6G003680 Rw6G036920 Rw6G043190 Rw7G020880

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AcsI RAATTY 1 cut(s) 374
AfaI GTAC 2 cut(s) 212, 231
AfiI CCNNNNNNNGG 2 cut(s) 159, 304
AflII CTTAAG 1 cut(s) 440
AgeI ACCGGT 1 cut(s) 134
AgsI TTSAA 3 cut(s) 68, 127, 178
AjnI CCWGG 1 cut(s) 327
AluBI AGCT 3 cut(s) 109, 238, 334
AluI AGCT 3 cut(s) 109, 238, 334
AoxI GGCC 2 cut(s) 150, 423
ApeKI GCWGC 1 cut(s) 5
ApoI RAATTY 1 cut(s) 374
AsiGI ACCGGT 1 cut(s) 134
AspA2I CCTAGG 1 cut(s) 31
AspS9I GGNCC 1 cut(s) 94
AsuC2I CCSGG 1 cut(s) 44
AsuHPI GGTGA 3 cut(s) 91, 94, 149
AsuII TTCGAA 1 cut(s) 24
AvaII GGWCC 1 cut(s) 94
AvrII CCTAGG 1 cut(s) 31
BauI CACGAG 1 cut(s) 410
BbvI GCAGC 1 cut(s) 17
BciT130I CCWGG 1 cut(s) 329
BciVI GTATCC 1 cut(s) 259
BcnI CCSGG 1 cut(s) 44
BfaI CTAG 1 cut(s) 32
BfrI CTTAAG 1 cut(s) 440
BfuI GTATCC 1 cut(s) 259
BglI GCCNNNNNGGC 1 cut(s) 149
BglII AGATCT 1 cut(s) 180
BisI GCNGC 1 cut(s) 6
BlnI CCTAGG 1 cut(s) 31
BlsI GCNGC 1 cut(s) 7
Bme1390I CCNGG 2 cut(s) 44, 329
Bme18I GGWCC 1 cut(s) 94
BmgT120I GGNCC 1 cut(s) 94
BmrFI CCNGG 2 cut(s) 44, 329
BmrI ACTGGG 1 cut(s) 115
BmuI ACTGGG 1 cut(s) 115
BpmI CTGGAG 1 cut(s) 350
Bpu10I CCTNAGC 1 cut(s) 14
Bpu14I TTCGAA 1 cut(s) 24
BpuEI CTTGAG 1 cut(s) 338
BpuMI CCSGG 1 cut(s) 44
BsaJI CCNNGG 3 cut(s) 31, 42, 391
BsaWI WCCGGW 2 cut(s) 134, 202
Bsc4I CCNNNNNNNGG 2 cut(s) 159, 304
Bse118I RCCGGY 1 cut(s) 134
Bse1I ACTGG 4 cut(s) 97, 121, 164, 263
Bse3DI GCAATG 2 cut(s) 43, 92
BseBI CCWGG 1 cut(s) 329
BseDI CCNNGG 3 cut(s) 31, 42, 391
BseLI CCNNNNNNNGG 2 cut(s) 159, 304
BseMI GCAATG 2 cut(s) 43, 92
BseNI ACTGG 4 cut(s) 97, 121, 164, 263
BseXI GCAGC 1 cut(s) 17
BshFI GGCC 2 cut(s) 152, 425
BshTI ACCGGT 1 cut(s) 134
BsiSI CCGG 3 cut(s) 44, 135, 203
BslFI GGGAC 1 cut(s) 205
BslI CCNNNNNNNGG 2 cut(s) 159, 304
BsmFI GGGAC 1 cut(s) 205
BsmI GAATGC 1 cut(s) 20
BsnI GGCC 2 cut(s) 152, 425
Bsp119I TTCGAA 1 cut(s) 24
Bsp1407I TGTACA 1 cut(s) 229
Bsp143I GATC 2 cut(s) 180, 366
BspANI GGCC 2 cut(s) 152, 425
BspT104I TTCGAA 1 cut(s) 24
BspTI CTTAAG 1 cut(s) 440
BsrDI GCAATG 2 cut(s) 43, 92
BsrFI RCCGGY 1 cut(s) 134
BsrGI TGTACA 1 cut(s) 229
BsrI ACTGG 4 cut(s) 97, 121, 164, 263
BssAI RCCGGY 1 cut(s) 134
BssECI CCNNGG 3 cut(s) 31, 42, 391
BssMI GATC 2 cut(s) 180, 366
BssSI CACGAG 1 cut(s) 410
BssT1I CCWWGG 2 cut(s) 31, 391
Bst2BI CACGAG 1 cut(s) 410
Bst2UI CCWGG 1 cut(s) 329
Bst4CI ACNGT 2 cut(s) 271, 289
BstAFI CTTAAG 1 cut(s) 440
BstAUI TGTACA 1 cut(s) 229
BstBI TTCGAA 1 cut(s) 24
BstC8I GCNNGC 1 cut(s) 145
BstDEI CTNAG 1 cut(s) 14
BstKTI GATC 2 cut(s) 183, 369
BstMBI GATC 2 cut(s) 180, 366
BstMWI GCNNNNNNNGC 2 cut(s) 26, 149
BstNI CCWGG 1 cut(s) 329
BstSCI CCNGG 2 cut(s) 42, 327
BstV1I GCAGC 1 cut(s) 17
BstX2I RGATCY 1 cut(s) 180
BstYI RGATCY 1 cut(s) 180
BsuI GTATCC 1 cut(s) 259
BsuRI GGCC 2 cut(s) 152, 425
BtsI GCAGTG 1 cut(s) 15
BtsIMutI CAGTG 2 cut(s) 15, 376
Cac8I GCNNGC 1 cut(s) 145
Cfr10I RCCGGY 1 cut(s) 134
Cfr13I GGNCC 1 cut(s) 94
CseI GACGC 1 cut(s) 91
Csp6I GTAC 2 cut(s) 211, 230
CspAI ACCGGT 1 cut(s) 134
CviAII CATG 1 cut(s) 215
CviJI RGCY 9 cut(s) 29, 109, 143, 152, 238, 251, 279, 334, 425
CviKI_1 RGCY 9 cut(s) 29, 109, 143, 152, 238, 251, 279, 334, 425
CviQI GTAC 2 cut(s) 211, 230
DdeI CTNAG 1 cut(s) 14
DpnI GATC 2 cut(s) 182, 368
DpnII GATC 2 cut(s) 180, 366
Eco130I CCWWGG 2 cut(s) 31, 391
Eco32I GATATC 1 cut(s) 190
Eco47I GGWCC 1 cut(s) 94
EcoRI GAATTC 1 cut(s) 374
EcoRII CCWGG 1 cut(s) 327
EcoRV GATATC 1 cut(s) 190
EcoT14I CCWWGG 2 cut(s) 31, 391
ErhI CCWWGG 2 cut(s) 31, 391
FaeI CATG 1 cut(s) 218
FaiI YATR 4 cut(s) 75, 194, 216, 417
FalI AAGNNNNNCTT 2 cut(s) 158, 190
FaqI GGGAC 1 cut(s) 205
FatI CATG 1 cut(s) 214
Fnu4HI GCNGC 1 cut(s) 6
Fsp4HI GCNGC 1 cut(s) 6
FspBI CTAG 1 cut(s) 32
GluI GCNGC 1 cut(s) 6
GsuI CTGGAG 1 cut(s) 350
HaeIII GGCC 2 cut(s) 152, 425
HapII CCGG 3 cut(s) 44, 135, 203
HgaI GACGC 1 cut(s) 91
Hin1II CATG 1 cut(s) 218
HindIII AAGCTT 1 cut(s) 107
HpaII CCGG 3 cut(s) 44, 135, 203
HphI GGTGA 3 cut(s) 91, 94, 149
Hpy166II GTNNAC 2 cut(s) 102, 232
Hpy188III TCNNGA 2 cut(s) 175, 410
Hpy8I GTNNAC 2 cut(s) 102, 232
HpyAV CCTTC 1 cut(s) 436
HpyCH4III ACNGT 2 cut(s) 271, 289
HpyCH4V TGCA 1 cut(s) 147
HpyF10VI GCNNNNNNNGC 2 cut(s) 26, 149
HpyF3I CTNAG 1 cut(s) 14
Hsp92II CATG 1 cut(s) 218
Kzo9I GATC 2 cut(s) 180, 366
LmnI GCTCC 2 cut(s) 205, 331
Lsp1109I GCAGC 1 cut(s) 17
MaeI CTAG 1 cut(s) 32
MaeIII GTNAC 1 cut(s) 79
MalI GATC 2 cut(s) 182, 368
MboI GATC 2 cut(s) 180, 366
MboII GAAGA 1 cut(s) 190
MflI RGATCY 1 cut(s) 180
MluCI AATT 1 cut(s) 374
MnlI CCTC 4 cut(s) 52, 233, 241, 362
MseI TTAA 3 cut(s) 111, 164, 441
MslI CAYNNNNRTG 1 cut(s) 414
MspCI CTTAAG 1 cut(s) 440
MspI CCGG 3 cut(s) 44, 135, 203
MspR9I CCNGG 2 cut(s) 44, 329
Mva1269I GAATGC 1 cut(s) 20
MvaI CCWGG 1 cut(s) 329
MwoI GCNNNNNNNGC 2 cut(s) 26, 149
NciI CCSGG 1 cut(s) 44
NdeII GATC 2 cut(s) 180, 366
NlaIII CATG 1 cut(s) 218
NmuCI GTSAC 1 cut(s) 79
NspV TTCGAA 1 cut(s) 24
PctI GAATGC 1 cut(s) 20
PfoI TCCNGGA 1 cut(s) 327
PinAI ACCGGT 1 cut(s) 134
PkrI GCNGC 1 cut(s) 7
Psp6I CCWGG 1 cut(s) 327
PspGI CCWGG 1 cut(s) 327
PspPI GGNCC 1 cut(s) 94
PsuI RGATCY 1 cut(s) 180
RsaI GTAC 2 cut(s) 212, 231
RsaNI GTAC 2 cut(s) 211, 230
RseI CAYNNNNRTG 1 cut(s) 414
SaqAI TTAA 3 cut(s) 111, 164, 441
SatI GCNGC 1 cut(s) 6
Sau3AI GATC 2 cut(s) 180, 366
Sau96I GGNCC 1 cut(s) 94
ScrFI CCNGG 2 cut(s) 44, 329
SetI ASST 4 cut(s) 111, 240, 300, 336
SfuI TTCGAA 1 cut(s) 24
SinI GGWCC 1 cut(s) 94
SmiMI CAYNNNNRTG 1 cut(s) 414
SmlI CTYRAG 2 cut(s) 353, 440
SmoI CTYRAG 2 cut(s) 353, 440
Sse9I AATT 1 cut(s) 374
SspMI CTAG 1 cut(s) 32
StyD4I CCNGG 2 cut(s) 42, 327
StyI CCWWGG 2 cut(s) 31, 391
TaaI ACNGT 2 cut(s) 271, 289
TaqI TCGA 2 cut(s) 24, 315
TasI AATT 1 cut(s) 374
TatI WGTACW 1 cut(s) 229
Tru1I TTAA 3 cut(s) 111, 164, 441
Tru9I TTAA 3 cut(s) 111, 164, 441
TscAI CASTG 2 cut(s) 15, 376
TseFI GTSAC 1 cut(s) 79
TseI GCWGC 1 cut(s) 5
Tsp45I GTSAC 1 cut(s) 79
TspGWI ACGGA 2 cut(s) 263, 298
TspRI CASTG 2 cut(s) 15, 376
Vha464I CTTAAG 1 cut(s) 440
VpaK11BI GGWCC 1 cut(s) 94
XapI RAATTY 1 cut(s) 374
XmaJI CCTAGG 1 cut(s) 31
XspI CTAG 1 cut(s) 32
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.