Rh1BG078200

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1B
OG0000370
Physical Location & Seq
Forward (+)
12174260 .. 12177332
3073 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1BG078200.1

Sequence Viewer

Length: 804 bp
ATGGGCAAGCAAGATACTAGAACAGGTGGAGCTACTTCATCCACTACTGGGCTTCCACATGATGAGGAGGTGGCTAAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAACGGGGTCAATAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCCCCGAAATACGCGGGAAATCTTGATACTTCTTTTGAAGGGGTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGCGTATACTCTTACTGGAGCGGCTGGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGATGAATTGGAATGACTTTGAGCAGATATTTTTGGATAGGTACTTTCCTGAGGCTATAAGGCGAGCTAAATTAGAAGAATTTCTCAATTTGACACAGGGGGAAATGACAGTTTTTCAGTACGATTCTAAGTTCATTGAATTATCATGGCATGCACCTAATATTCTGACTTCGGATAAAGACAGGGCATTGCAGTTTTTACGCGGGTTGAGGCCTTCCATTGGTAGGGTTATACCTGGTTTTATGCATAATACTTATCAAGAGGCGGTGGAAGCAGCACTGATGGGAGAACAAATTGAAAATATCAACTGTCAGAGTGTGCAAGAGTCTGAGGGAGCTTCTGGTAGAGGGGAAAAAAGGCAAAGGAAGCAGTACACTTGCCACAACTGTGGTGAGCCTGGTCATATTCGGCCTCATTGCCCATACTATCCGTCATCTTCCTAA
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

267

Amino Acids

30.38

Weight (kDa)

6.11

Isoelectric Point (pI)

56.8

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 93 - 221 1.8e-09 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 97 - 192 4.1e-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) 314
AccI GTMKAC 1 cut(s) 299
AccII CGCG 2 cut(s) 191, 564
AciI CCGC 4 cut(s) 191, 314, 564, 626
AcsI RAATTY 2 cut(s) 149, 440
AfaI GTAC 4 cut(s) 267, 404, 482, 734
AfiI CCNNNNNNNGG 3 cut(s) 48, 581, 585
AgsI TTSAA 5 cut(s) 86, 157, 215, 500, 659
AjnI CCWGG 3 cut(s) 268, 595, 757
AleI CACNNNNGTG 1 cut(s) 747
AluBI AGCT 4 cut(s) 32, 115, 428, 698
AluI AGCT 4 cut(s) 32, 115, 428, 698
Alw26I GTCTC 1 cut(s) 267
Ama87I CYCGRG 1 cut(s) 110
AoxI GGCC 2 cut(s) 572, 770
ApeKI GCWGC 2 cut(s) 293, 635
ApoI RAATTY 2 cut(s) 149, 440
Asp700I GAANNNNTTC 3 cut(s) 103, 161, 441
AspS9I GGNCC 1 cut(s) 345
AsuHPI GGTGA 2 cut(s) 168, 764
AvaI CYCGRG 1 cut(s) 110
AvaII GGWCC 1 cut(s) 345
AxyI CCTNAGG 1 cut(s) 411
BaeGI GKGCMC 1 cut(s) 125
BbvI GCAGC 2 cut(s) 305, 647
BccI CCATC 1 cut(s) 637
BciT130I CCWGG 3 cut(s) 270, 597, 759
BcoDI GTCTC 1 cut(s) 267
BfaI CTAG 1 cut(s) 18
BisI GCNGC 3 cut(s) 294, 315, 636
BlsI GCNGC 3 cut(s) 295, 316, 637
Bme1390I CCNGG 3 cut(s) 270, 597, 759
Bme18I GGWCC 1 cut(s) 345
BmeT110I CYCGRG 1 cut(s) 110
BmgT120I GGNCC 1 cut(s) 345
BmrFI CCNGG 3 cut(s) 270, 597, 759
BmrI ACTGGG 1 cut(s) 57
BmuI ACTGGG 1 cut(s) 57
BpmI CTGGAG 2 cut(s) 291, 330
BpuEI CTTGAG 1 cut(s) 137
Bsa29I ATCGAT 1 cut(s) 362
BsaI GGTCTC 1 cut(s) 267
Bsc4I CCNNNNNNNGG 3 cut(s) 48, 581, 585
Bse1I ACTGG 3 cut(s) 52, 313, 329
Bse21I CCTNAGG 1 cut(s) 411
Bse3DI GCAATG 3 cut(s) 251, 548, 775
BseBI CCWGG 3 cut(s) 270, 597, 759
BseCI ATCGAT 1 cut(s) 362
BseGI GGATG 1 cut(s) 38
BseLI CCNNNNNNNGG 3 cut(s) 48, 581, 585
BseMI GCAATG 3 cut(s) 251, 548, 775
BseMII CTCAG 2 cut(s) 402, 681
BseNI ACTGG 3 cut(s) 52, 313, 329
BseRI GAGGAG 1 cut(s) 80
BseSI GKGCMC 1 cut(s) 125
BseXI GCAGC 2 cut(s) 305, 647
Bsh1236I CGCG 2 cut(s) 191, 564
BshFI GGCC 2 cut(s) 574, 772
BshVI ATCGAT 1 cut(s) 362
BsiHKCI CYCGRG 1 cut(s) 110
BslI CCNNNNNNNGG 3 cut(s) 48, 581, 585
BsmAI GTCTC 1 cut(s) 267
BsnI GGCC 2 cut(s) 574, 772
Bso31I GGTCTC 1 cut(s) 267
BsoBI CYCGRG 1 cut(s) 110
Bsp1286I GDGCHC 1 cut(s) 125
BspACI CCGC 4 cut(s) 191, 314, 564, 626
BspANI GGCC 2 cut(s) 574, 772
BspCNI CTCAG 2 cut(s) 403, 682
BspDI ATCGAT 1 cut(s) 362
BspFNI CGCG 2 cut(s) 191, 564
BspTNI GGTCTC 1 cut(s) 267
BsrBI CCGCTC 1 cut(s) 314
BsrDI GCAATG 3 cut(s) 251, 548, 775
BsrI ACTGG 3 cut(s) 52, 313, 329
BssNAI GTATAC 1 cut(s) 300
Bst1107I GTATAC 1 cut(s) 300
Bst2UI CCWGG 3 cut(s) 270, 597, 759
Bst4CI ACNGT 3 cut(s) 472, 671, 749
BstC8I GCNNGC 4 cut(s) 8, 319, 426, 513
BstDEI CTNAG 5 cut(s) 75, 278, 411, 489, 690
BstF5I GGATG 1 cut(s) 38
BstFNI CGCG 2 cut(s) 191, 564
BstMAI GTCTC 1 cut(s) 267
BstMWI GCNNNNNNNGC 2 cut(s) 632, 727
BstNI CCWGG 3 cut(s) 270, 597, 759
BstNSI RCATGY 1 cut(s) 515
BstSCI CCNGG 3 cut(s) 268, 595, 757
BstSLI GKGCMC 1 cut(s) 125
BstUI CGCG 2 cut(s) 191, 564
BstV1I GCAGC 2 cut(s) 305, 647
BstXI CCANNNNNNTGG 1 cut(s) 749
BstZ17I GTATAC 1 cut(s) 300
Bsu15I ATCGAT 1 cut(s) 362
Bsu36I CCTNAGG 1 cut(s) 411
BsuRI GGCC 2 cut(s) 574, 772
BsuTUI ATCGAT 1 cut(s) 362
BtsCI GGATG 1 cut(s) 38
BtsIMutI CAGTG 1 cut(s) 638
Cac8I GCNNGC 4 cut(s) 8, 319, 426, 513
Cfr13I GGNCC 1 cut(s) 345
ClaI ATCGAT 1 cut(s) 362
CsiI ACCWGGT 1 cut(s) 595
Csp6I GTAC 4 cut(s) 266, 403, 481, 733
CviAII CATG 3 cut(s) 59, 507, 512
CviQI GTAC 4 cut(s) 266, 403, 481, 733
DdeI CTNAG 5 cut(s) 75, 278, 411, 489, 690
Eco147I AGGCCT 1 cut(s) 574
Eco31I GGTCTC 1 cut(s) 267
Eco47I GGWCC 1 cut(s) 345
Eco81I CCTNAGG 1 cut(s) 411
Eco88I CYCGRG 1 cut(s) 110
EcoO109I RGGNCCY 1 cut(s) 345
EcoRII CCWGG 3 cut(s) 268, 595, 757
EcoT22I ATGCAT 1 cut(s) 609
FaeI CATG 3 cut(s) 62, 510, 515
FatI CATG 3 cut(s) 58, 506, 511
FauI CCCGC 2 cut(s) 184, 557
FblI GTMKAC 1 cut(s) 299
Fnu4HI GCNGC 3 cut(s) 294, 315, 636
FokI GGATG 1 cut(s) 25
Fsp4HI GCNGC 3 cut(s) 294, 315, 636
FspBI CTAG 1 cut(s) 18
GluI GCNGC 3 cut(s) 294, 315, 636
GsuI CTGGAG 2 cut(s) 291, 330
HaeIII GGCC 2 cut(s) 574, 772
Hin1II CATG 3 cut(s) 62, 510, 515
HinfI GANTC 3 cut(s) 359, 485, 686
HphI GGTGA 2 cut(s) 168, 764
Hpy166II GTNNAC 2 cut(s) 300, 735
Hpy188I TCNGA 4 cut(s) 528, 535, 675, 691
Hpy188III TCNNGA 4 cut(s) 200, 260, 410, 620
Hpy8I GTNNAC 2 cut(s) 300, 735
HpyAV CCTTC 3 cut(s) 209, 228, 585
HpyCH4III ACNGT 3 cut(s) 472, 671, 749
HpyCH4V TGCA 5 cut(s) 293, 515, 553, 607, 682
HpyF10VI GCNNNNNNNGC 2 cut(s) 632, 727
HpyF3I CTNAG 5 cut(s) 75, 278, 411, 489, 690
Hsp92II CATG 3 cut(s) 62, 510, 515
LmnI GCTCC 3 cut(s) 29, 311, 695
Lsp1109I GCAGC 2 cut(s) 305, 647
MabI ACCWGGT 1 cut(s) 595
MaeI CTAG 1 cut(s) 18
MaeIII GTNAC 2 cut(s) 174, 228
MbiI CCGCTC 1 cut(s) 314
MboII GAAGA 3 cut(s) 169, 449, 789
MhlI GDGCHC 1 cut(s) 125
MluCI AATT 7 cut(s) 149, 367, 431, 440, 448, 500, 654
MlyI GAGTC 1 cut(s) 695
Mph1103I ATGCAT 1 cut(s) 609
MroXI GAANNNNTTC 3 cut(s) 103, 161, 441
MseI TTAA 1 cut(s) 339
MslI CAYNNNNRTG 1 cut(s) 747
MspR9I CCNGG 3 cut(s) 270, 597, 759
MvaI CCWGG 3 cut(s) 270, 597, 759
MvnI CGCG 2 cut(s) 191, 564
MwoI GCNNNNNNNGC 2 cut(s) 632, 727
NlaIII CATG 3 cut(s) 62, 510, 515
NmuCI GTSAC 1 cut(s) 174
NsiI ATGCAT 1 cut(s) 609
NspI RCATGY 1 cut(s) 515
OliI CACNNNNGTG 1 cut(s) 747
PaeI GCATGC 1 cut(s) 515
PaeR7I CTCGAG 1 cut(s) 110
PceI AGGCCT 1 cut(s) 574
PdmI GAANNNNTTC 3 cut(s) 103, 161, 441
PfeI GAWTC 2 cut(s) 359, 485
PkrI GCNGC 3 cut(s) 295, 316, 637
PleI GAGTC 1 cut(s) 694
PpsI GAGTC 1 cut(s) 694
PpuMI RGGWCCY 1 cut(s) 345
Psp5II RGGWCCY 1 cut(s) 345
Psp6I CCWGG 3 cut(s) 268, 595, 757
PspGI CCWGG 3 cut(s) 268, 595, 757
PspPI GGNCC 1 cut(s) 345
PspPPI RGGWCCY 1 cut(s) 345
PspXI VCTCGAGB 1 cut(s) 110
RsaI GTAC 4 cut(s) 267, 404, 482, 734
RsaNI GTAC 4 cut(s) 266, 403, 481, 733
RseI CAYNNNNRTG 1 cut(s) 747
SaqAI TTAA 1 cut(s) 339
SatI GCNGC 3 cut(s) 294, 315, 636
Sau96I GGNCC 1 cut(s) 345
SchI GAGTC 1 cut(s) 695
ScrFI CCNGG 3 cut(s) 270, 597, 759
SduI GDGCHC 1 cut(s) 125
SexAI ACCWGGT 1 cut(s) 595
Sfr274I CTCGAG 1 cut(s) 110
SinI GGWCC 1 cut(s) 345
SlaI CTCGAG 1 cut(s) 110
SmiMI CAYNNNNRTG 1 cut(s) 747
SmlI CTYRAG 2 cut(s) 110, 116
SmoI CTYRAG 2 cut(s) 110, 116
SphI GCATGC 1 cut(s) 515
Sse9I AATT 7 cut(s) 149, 367, 431, 440, 448, 500, 654
SseBI AGGCCT 1 cut(s) 574
SsiI CCGC 4 cut(s) 191, 314, 564, 626
SspI AATATT 1 cut(s) 523
SspMI CTAG 1 cut(s) 18
StuI AGGCCT 1 cut(s) 574
StyD4I CCNGG 3 cut(s) 268, 595, 757
TaaI ACNGT 3 cut(s) 472, 671, 749
TaqI TCGA 2 cut(s) 111, 362
TasI AATT 7 cut(s) 149, 367, 431, 440, 448, 500, 654
TatI WGTACW 1 cut(s) 732
TauI GCSGC 1 cut(s) 317
TfiI GAWTC 2 cut(s) 359, 485
Tru1I TTAA 1 cut(s) 339
Tru9I TTAA 1 cut(s) 339
TscAI CASTG 1 cut(s) 645
TseFI GTSAC 1 cut(s) 174
TseI GCWGC 2 cut(s) 293, 635
Tsp45I GTSAC 1 cut(s) 174
TspDTI ATGAA 4 cut(s) 27, 154, 380, 484
TspGWI ACGGA 1 cut(s) 780
TspRI CASTG 1 cut(s) 645
VpaK11BI GGWCC 1 cut(s) 345
XapI RAATTY 2 cut(s) 149, 440
XceI RCATGY 1 cut(s) 515
XhoI CTCGAG 1 cut(s) 110
XmiI GTMKAC 1 cut(s) 299
XmnI GAANNNNTTC 3 cut(s) 103, 161, 441
XspI CTAG 1 cut(s) 18
Zsp2I ATGCAT 1 cut(s) 609
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.