Rh1CG094900

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1C
OG0000370
Physical Location & Seq
Forward (+)
20271907 .. 20288071
16165 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1CG094900.1

Sequence Viewer

Length: 750 bp
ATGGGCAAGGAAAGTGCTATCTCTAGTAGTACTGGTGTAATGTATCGTGTAAATGTGCCGTTTAGGATACTAGAACAGGTGGAGCTACTTCATCCACTACTGGGCTTCCACATAAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAAAGGGGTTCAACAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCCCCGGAGTACGCGGAAAATCTTGATACTTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGTCTATACTCTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGATGAATTGGGATGACTTTGAGCAGATATTTTTGAATAAGTACTTTCCTGAGACTATAAGGCGAGCTAAAGTAGAAGAATTTCTCAATTTGACACGGGGGGGAATGACAGTTTTTCAGTACGATTCTAAGTTCATTGAATTATCATGGCATGCACCTAATCTTCTGACTTCGGATAAAGATAGGGCAGGGAAGTTTTTACGCGGGTTGAGGCCTTCCATCCGTATGTCTTTACGTAGTTTTATGTATAATACATATAATGAGGCGGTGGCAGCAGCACTGAAGATAGAACAAATTGAAAATATCAGTCACTCGAATATCAAAGTCAACATACTCCATTTTGGGCAATAA
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

249

Amino Acids

28.96

Weight (kDa)

8.6

Isoelectric Point (pI)

57.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 107 - 234 6.1e-09 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 110 - 205 1.4e-16 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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 353
AccII CGCG 2 cut(s) 230, 603
AciI CCGC 4 cut(s) 230, 353, 603, 665
AcsI RAATTY 2 cut(s) 188, 479
AcuI CTGAAG 1 cut(s) 701
AfaI GTAC 5 cut(s) 31, 227, 306, 443, 521
AfiI CCNNNNNNNGG 1 cut(s) 101
AgsI TTSAA 6 cut(s) 124, 175, 196, 436, 539, 698
AjnI CCWGG 1 cut(s) 307
AluBI AGCT 4 cut(s) 85, 153, 360, 467
AluI AGCT 4 cut(s) 85, 153, 360, 467
Alw26I GTCTC 2 cut(s) 306, 446
Ama87I CYCGRG 1 cut(s) 148
AoxI GGCC 1 cut(s) 611
ApeKI GCWGC 2 cut(s) 671, 674
ApoI RAATTY 2 cut(s) 188, 479
Asp700I GAANNNNTTC 3 cut(s) 141, 200, 480
AspS9I GGNCC 1 cut(s) 384
AsuC2I CCSGG 1 cut(s) 221
AsuHPI GGTGA 1 cut(s) 207
AsuNHI GCTAGC 1 cut(s) 356
AvaI CYCGRG 1 cut(s) 148
AvaII GGWCC 1 cut(s) 384
BaeGI GKGCMC 1 cut(s) 163
BbvI GCAGC 2 cut(s) 683, 686
BccI CCATC 1 cut(s) 626
BceAI ACGGC 1 cut(s) 43
BciT130I CCWGG 1 cut(s) 309
BciVI GTATCC 1 cut(s) 60
BcnI CCSGG 1 cut(s) 221
BcoDI GTCTC 2 cut(s) 306, 446
BfaI CTAG 3 cut(s) 24, 71, 357
BfuI GTATCC 1 cut(s) 60
BisI GCNGC 3 cut(s) 354, 672, 675
BlsI GCNGC 3 cut(s) 355, 673, 676
BmcAI AGTACT 2 cut(s) 31, 443
Bme1390I CCNGG 2 cut(s) 221, 309
Bme18I GGWCC 1 cut(s) 384
BmeT110I CYCGRG 1 cut(s) 148
BmgT120I GGNCC 1 cut(s) 384
BmrFI CCNGG 2 cut(s) 221, 309
BmrI ACTGGG 1 cut(s) 110
BmtI GCTAGC 1 cut(s) 360
BmuI ACTGGG 1 cut(s) 110
BpmI CTGGAG 3 cut(s) 281, 330, 369
BpuEI CTTGAG 1 cut(s) 175
BpuMI CCSGG 1 cut(s) 221
Bsa29I ATCGAT 1 cut(s) 401
BsaAI YACGTR 1 cut(s) 635
BsaI GGTCTC 1 cut(s) 306
BsaJI CCNNGG 1 cut(s) 219
Bsc4I CCNNNNNNNGG 1 cut(s) 101
Bse1I ACTGG 4 cut(s) 37, 105, 352, 368
Bse3DI GCAATG 1 cut(s) 290
BseBI CCWGG 1 cut(s) 309
BseCI ATCGAT 1 cut(s) 401
BseDI CCNNGG 1 cut(s) 219
BseGI GGATG 3 cut(s) 91, 418, 618
BseLI CCNNNNNNNGG 1 cut(s) 101
BseMI GCAATG 1 cut(s) 290
BseMII CTCAG 1 cut(s) 441
BseNI ACTGG 4 cut(s) 37, 105, 352, 368
BseSI GKGCMC 1 cut(s) 163
BseXI GCAGC 2 cut(s) 683, 686
Bsh1236I CGCG 2 cut(s) 230, 603
BshFI GGCC 1 cut(s) 613
BshVI ATCGAT 1 cut(s) 401
BsiHKCI CYCGRG 1 cut(s) 148
BsiSI CCGG 1 cut(s) 221
BslI CCNNNNNNNGG 1 cut(s) 101
BsmAI GTCTC 2 cut(s) 306, 446
BsnI GGCC 1 cut(s) 613
Bso31I GGTCTC 1 cut(s) 306
BsoBI CYCGRG 1 cut(s) 148
Bsp1286I GDGCHC 1 cut(s) 163
BspACI CCGC 4 cut(s) 230, 353, 603, 665
BspANI GGCC 1 cut(s) 613
BspCNI CTCAG 1 cut(s) 442
BspDI ATCGAT 1 cut(s) 401
BspFNI CGCG 2 cut(s) 230, 603
BspOI GCTAGC 1 cut(s) 360
BspTNI GGTCTC 1 cut(s) 306
BsrBI CCGCTC 1 cut(s) 353
BsrDI GCAATG 1 cut(s) 290
BsrI ACTGG 4 cut(s) 37, 105, 352, 368
BssECI CCNNGG 1 cut(s) 219
Bst2UI CCWGG 1 cut(s) 309
Bst4CI ACNGT 1 cut(s) 511
BstBAI YACGTR 1 cut(s) 635
BstC8I GCNNGC 3 cut(s) 358, 465, 552
BstDEI CTNAG 3 cut(s) 317, 450, 528
BstF5I GGATG 3 cut(s) 91, 418, 618
BstFNI CGCG 2 cut(s) 230, 603
BstMAI GTCTC 2 cut(s) 306, 446
BstMWI GCNNNNNNNGC 1 cut(s) 671
BstNI CCWGG 1 cut(s) 309
BstNSI RCATGY 1 cut(s) 554
BstSCI CCNGG 2 cut(s) 219, 307
BstSLI GKGCMC 1 cut(s) 163
BstSNI TACGTA 1 cut(s) 635
BstUI CGCG 2 cut(s) 230, 603
BstV1I GCAGC 2 cut(s) 683, 686
Bsu15I ATCGAT 1 cut(s) 401
BsuI GTATCC 1 cut(s) 60
BsuRI GGCC 1 cut(s) 613
BsuTUI ATCGAT 1 cut(s) 401
BtsCI GGATG 3 cut(s) 91, 418, 618
BtsIMutI CAGTG 1 cut(s) 677
Cac8I GCNNGC 3 cut(s) 358, 465, 552
Cfr13I GGNCC 1 cut(s) 384
ClaI ATCGAT 1 cut(s) 401
Csp6I GTAC 5 cut(s) 30, 226, 305, 442, 520
CspCI CAANNNNNGTGG 2 cut(s) 98, 133
CviAII CATG 2 cut(s) 546, 551
CviQI GTAC 5 cut(s) 30, 226, 305, 442, 520
DdeI CTNAG 3 cut(s) 317, 450, 528
Eco105I TACGTA 1 cut(s) 635
Eco147I AGGCCT 1 cut(s) 613
Eco31I GGTCTC 1 cut(s) 306
Eco47I GGWCC 1 cut(s) 384
Eco57I CTGAAG 1 cut(s) 701
Eco88I CYCGRG 1 cut(s) 148
EcoO109I RGGNCCY 1 cut(s) 384
EcoRII CCWGG 1 cut(s) 307
FaeI CATG 2 cut(s) 549, 554
FatI CATG 2 cut(s) 545, 550
FauI CCCGC 1 cut(s) 596
Fnu4HI GCNGC 3 cut(s) 354, 672, 675
FokI GGATG 3 cut(s) 78, 425, 605
Fsp4HI GCNGC 3 cut(s) 354, 672, 675
FspBI CTAG 3 cut(s) 24, 71, 357
GluI GCNGC 3 cut(s) 354, 672, 675
GsuI CTGGAG 3 cut(s) 281, 330, 369
HaeIII GGCC 1 cut(s) 613
HapII CCGG 1 cut(s) 221
Hin1II CATG 2 cut(s) 549, 554
HincII GTYRAC 1 cut(s) 727
HindII GTYRAC 1 cut(s) 727
HinfI GANTC 2 cut(s) 398, 524
HpaII CCGG 1 cut(s) 221
HphI GGTGA 1 cut(s) 207
Hpy166II GTNNAC 1 cut(s) 727
Hpy188I TCNGA 2 cut(s) 567, 574
Hpy188III TCNNGA 3 cut(s) 239, 299, 449
Hpy8I GTNNAC 1 cut(s) 727
HpyAV CCTTC 3 cut(s) 248, 267, 624
HpyCH4III ACNGT 1 cut(s) 511
HpyCH4IV ACGT 1 cut(s) 634
HpyCH4V TGCA 2 cut(s) 332, 554
HpyF10VI GCNNNNNNNGC 1 cut(s) 671
HpyF3I CTNAG 3 cut(s) 317, 450, 528
HpySE526I ACGT 1 cut(s) 634
Hsp92II CATG 2 cut(s) 549, 554
LmnI GCTCC 2 cut(s) 82, 350
Lsp1109I GCAGC 2 cut(s) 683, 686
MaeI CTAG 3 cut(s) 24, 71, 357
MaeII ACGT 1 cut(s) 634
MaeIII GTNAC 3 cut(s) 213, 267, 707
MbiI CCGCTC 1 cut(s) 353
MboII GAAGA 4 cut(s) 208, 488, 554, 694
MhlI GDGCHC 1 cut(s) 163
MluCI AATT 6 cut(s) 188, 406, 479, 487, 539, 693
MnlI CCTC 5 cut(s) 150, 157, 174, 603, 655
MroXI GAANNNNTTC 3 cut(s) 141, 200, 480
MseI TTAA 1 cut(s) 378
MslI CAYNNNNRTG 1 cut(s) 623
MspI CCGG 1 cut(s) 221
MspR9I CCNGG 2 cut(s) 221, 309
MvaI CCWGG 1 cut(s) 309
MvnI CGCG 2 cut(s) 230, 603
MwoI GCNNNNNNNGC 1 cut(s) 671
NciI CCSGG 1 cut(s) 221
NheI GCTAGC 1 cut(s) 356
NlaIII CATG 2 cut(s) 549, 554
NmuCI GTSAC 2 cut(s) 213, 707
NspI RCATGY 1 cut(s) 554
PaeI GCATGC 1 cut(s) 554
PaeR7I CTCGAG 1 cut(s) 148
PceI AGGCCT 1 cut(s) 613
PdmI GAANNNNTTC 3 cut(s) 141, 200, 480
PfeI GAWTC 2 cut(s) 398, 524
PkrI GCNGC 3 cut(s) 355, 673, 676
Ppu21I YACGTR 1 cut(s) 635
PpuMI RGGWCCY 1 cut(s) 384
Psp5II RGGWCCY 1 cut(s) 384
Psp6I CCWGG 1 cut(s) 307
PspGI CCWGG 1 cut(s) 307
PspPI GGNCC 1 cut(s) 384
PspPPI RGGWCCY 1 cut(s) 384
PspXI VCTCGAGB 1 cut(s) 148
RsaI GTAC 5 cut(s) 31, 227, 306, 443, 521
RsaNI GTAC 5 cut(s) 30, 226, 305, 442, 520
RseI CAYNNNNRTG 1 cut(s) 623
SaqAI TTAA 1 cut(s) 378
SatI GCNGC 3 cut(s) 354, 672, 675
Sau96I GGNCC 1 cut(s) 384
ScaI AGTACT 2 cut(s) 31, 443
ScrFI CCNGG 2 cut(s) 221, 309
SduI GDGCHC 1 cut(s) 163
Sfr274I CTCGAG 1 cut(s) 148
SinI GGWCC 1 cut(s) 384
SlaI CTCGAG 1 cut(s) 148
SmiMI CAYNNNNRTG 1 cut(s) 623
SmlI CTYRAG 2 cut(s) 148, 154
SmoI CTYRAG 2 cut(s) 148, 154
SnaBI TACGTA 1 cut(s) 635
SphI GCATGC 1 cut(s) 554
Sse9I AATT 6 cut(s) 188, 406, 479, 487, 539, 693
SseBI AGGCCT 1 cut(s) 613
SsiI CCGC 4 cut(s) 230, 353, 603, 665
SspMI CTAG 3 cut(s) 24, 71, 357
StuI AGGCCT 1 cut(s) 613
StyD4I CCNGG 2 cut(s) 219, 307
TaaI ACNGT 1 cut(s) 511
TaiI ACGT 1 cut(s) 637
TaqI TCGA 3 cut(s) 149, 401, 713
TasI AATT 6 cut(s) 188, 406, 479, 487, 539, 693
TatI WGTACW 2 cut(s) 29, 441
TauI GCSGC 1 cut(s) 356
TfiI GAWTC 2 cut(s) 398, 524
Tru1I TTAA 1 cut(s) 378
Tru9I TTAA 1 cut(s) 378
TscAI CASTG 1 cut(s) 684
TseFI GTSAC 2 cut(s) 213, 707
TseI GCWGC 2 cut(s) 671, 674
Tsp45I GTSAC 2 cut(s) 213, 707
TspDTI ATGAA 4 cut(s) 80, 193, 419, 523
TspGWI ACGGA 1 cut(s) 611
TspRI CASTG 1 cut(s) 684
VpaK11BI GGWCC 1 cut(s) 384
XapI RAATTY 2 cut(s) 188, 479
XceI RCATGY 1 cut(s) 554
XhoI CTCGAG 1 cut(s) 148
XmnI GAANNNNTTC 3 cut(s) 141, 200, 480
XspI CTAG 3 cut(s) 24, 71, 357
ZrmI AGTACT 2 cut(s) 31, 443
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.