Rh1BG078700

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1B
OG0000370
Physical Location & Seq
Forward (+)
12276744 .. 12277556
813 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1BG078700.1

Sequence Viewer

Length: 813 bp
ATGGAAGCTAATGTTTCATTTGTTAAAATTCAGCAGGATACTAGAACAGGTGGAGCTACTTCATCGATGAGGAGGTGGCTGAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAAAGGGGTTCAACAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCCCTGGAGTACGCGGAAAATCTTGATACTTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGTCTATACTCTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGAGGAATTGGGATGACTTTGAGCAGATATTTTTGAATAAGTACTTTCCTGAGACTATAAGGCGAGCTAAAGTAGAAGAATTTCTCAATTTGACACAGGGGGGAATGACAGTTTTTCAGTACGATTCTAAGTTCATTGAATTATCATGGCATGCACCTAATCTTCTGACTTCGGATAAAGATAGGGCAGTGAAGTTTTTACGCGGGTTGAGGCCTTCCATTGGTAGGGCTTTACCTGGTTTTATGCATAATACTTATCATGAGGCGGTGGCAGCAGCACTGATGGCAGAACAAATTGAAAATATCAAGTGTCAGAGTGTGCAAGAGTCATTTGAGGGAGATTCTGGTAGAGGGGAAAAAAGGCAAAGGAAGCAGTATACTTGCCACAACTGTTGTGAGCCTGGTCATATTTGGCCTTATTGCCCATATAATCCGTCATCTTCCTAA
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

270

Amino Acids

31.31

Weight (kDa)

8.32

Isoelectric Point (pI)

61.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 96 - 223 1.2e-07 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 99 - 194 7.9e-18 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) 320
AccI GTMKAC 1 cut(s) 743
AccII CGCG 2 cut(s) 197, 570
AciI CCGC 4 cut(s) 197, 320, 570, 632
AcsI RAATTY 3 cut(s) 27, 155, 446
AfaI GTAC 4 cut(s) 194, 273, 410, 488
AfiI CCNNNNNNNGG 2 cut(s) 587, 591
AgsI TTSAA 6 cut(s) 91, 142, 163, 403, 506, 665
AjnI CCWGG 4 cut(s) 186, 274, 601, 766
AluBI AGCT 5 cut(s) 8, 56, 120, 327, 434
AluI AGCT 5 cut(s) 8, 56, 120, 327, 434
Alw26I GTCTC 2 cut(s) 273, 413
Ama87I CYCGRG 1 cut(s) 115
AoxI GGCC 2 cut(s) 578, 779
ApeKI GCWGC 2 cut(s) 638, 641
ApoI RAATTY 3 cut(s) 27, 155, 446
Asp700I GAANNNNTTC 3 cut(s) 108, 167, 447
AspS9I GGNCC 1 cut(s) 351
AsuHPI GGTGA 1 cut(s) 174
AsuNHI GCTAGC 1 cut(s) 323
AvaI CYCGRG 1 cut(s) 115
AvaII GGWCC 1 cut(s) 351
BaeGI GKGCMC 1 cut(s) 130
BbvI GCAGC 2 cut(s) 650, 653
BccI CCATC 1 cut(s) 643
BciT130I CCWGG 4 cut(s) 188, 276, 603, 768
BciVI GTATCC 1 cut(s) 31
BcoDI GTCTC 2 cut(s) 273, 413
BfaI CTAG 2 cut(s) 42, 324
BfuI GTATCC 1 cut(s) 31
BisI GCNGC 3 cut(s) 321, 639, 642
BlsI GCNGC 3 cut(s) 322, 640, 643
BmcAI AGTACT 1 cut(s) 410
Bme1390I CCNGG 4 cut(s) 188, 276, 603, 768
Bme18I GGWCC 1 cut(s) 351
BmeT110I CYCGRG 1 cut(s) 115
BmgT120I GGNCC 1 cut(s) 351
BmrFI CCNGG 4 cut(s) 188, 276, 603, 768
BmtI GCTAGC 1 cut(s) 327
BpmI CTGGAG 4 cut(s) 209, 248, 297, 336
BpuEI CTTGAG 1 cut(s) 142
Bsa29I ATCGAT 1 cut(s) 65
BsaI GGTCTC 1 cut(s) 273
BsaJI CCNNGG 1 cut(s) 186
Bsc4I CCNNNNNNNGG 2 cut(s) 587, 591
Bse1I ACTGG 2 cut(s) 319, 335
Bse3DI GCAATG 1 cut(s) 257
BseBI CCWGG 4 cut(s) 188, 276, 603, 768
BseCI ATCGAT 1 cut(s) 65
BseDI CCNNGG 1 cut(s) 186
BseGI GGATG 1 cut(s) 385
BseLI CCNNNNNNNGG 2 cut(s) 587, 591
BseMI GCAATG 1 cut(s) 257
BseMII CTCAG 2 cut(s) 71, 408
BseNI ACTGG 2 cut(s) 319, 335
BseRI GAGGAG 1 cut(s) 85
BseSI GKGCMC 1 cut(s) 130
BseXI GCAGC 2 cut(s) 650, 653
Bsh1236I CGCG 2 cut(s) 197, 570
BshFI GGCC 2 cut(s) 580, 781
BshVI ATCGAT 1 cut(s) 65
BsiHKCI CYCGRG 1 cut(s) 115
BslI CCNNNNNNNGG 2 cut(s) 587, 591
BsmAI GTCTC 2 cut(s) 273, 413
BsnI GGCC 2 cut(s) 580, 781
Bso31I GGTCTC 1 cut(s) 273
BsoBI CYCGRG 1 cut(s) 115
Bsp1286I GDGCHC 1 cut(s) 130
BspACI CCGC 4 cut(s) 197, 320, 570, 632
BspANI GGCC 2 cut(s) 580, 781
BspCNI CTCAG 2 cut(s) 72, 409
BspDI ATCGAT 1 cut(s) 65
BspFNI CGCG 2 cut(s) 197, 570
BspHI TCATGA 1 cut(s) 625
BspOI GCTAGC 1 cut(s) 327
BspTNI GGTCTC 1 cut(s) 273
BsrBI CCGCTC 1 cut(s) 320
BsrDI GCAATG 1 cut(s) 257
BsrI ACTGG 2 cut(s) 319, 335
BssECI CCNNGG 1 cut(s) 186
BssNAI GTATAC 1 cut(s) 744
Bst1107I GTATAC 1 cut(s) 744
Bst2UI CCWGG 4 cut(s) 188, 276, 603, 768
Bst4CI ACNGT 2 cut(s) 478, 758
BstC8I GCNNGC 3 cut(s) 325, 432, 519
BstDEI CTNAG 4 cut(s) 80, 284, 417, 495
BstF5I GGATG 1 cut(s) 385
BstFNI CGCG 2 cut(s) 197, 570
BstMAI GTCTC 2 cut(s) 273, 413
BstMWI GCNNNNNNNGC 3 cut(s) 638, 650, 736
BstNI CCWGG 4 cut(s) 188, 276, 603, 768
BstNSI RCATGY 1 cut(s) 521
BstSCI CCNGG 4 cut(s) 186, 274, 601, 766
BstSLI GKGCMC 1 cut(s) 130
BstUI CGCG 2 cut(s) 197, 570
BstV1I GCAGC 2 cut(s) 650, 653
BstZ17I GTATAC 1 cut(s) 744
Bsu15I ATCGAT 1 cut(s) 65
BsuI GTATCC 1 cut(s) 31
BsuRI GGCC 2 cut(s) 580, 781
BsuTUI ATCGAT 1 cut(s) 65
BtsCI GGATG 1 cut(s) 385
BtsI GCAGTG 1 cut(s) 561
BtsIMutI CAGTG 2 cut(s) 561, 644
Cac8I GCNNGC 3 cut(s) 325, 432, 519
CciI TCATGA 1 cut(s) 625
Cfr13I GGNCC 1 cut(s) 351
ClaI ATCGAT 1 cut(s) 65
CsiI ACCWGGT 1 cut(s) 601
Csp6I GTAC 4 cut(s) 193, 272, 409, 487
CspCI CAANNNNNGTGG 2 cut(s) 740, 775
CviAII CATG 3 cut(s) 513, 518, 626
CviQI GTAC 4 cut(s) 193, 272, 409, 487
DdeI CTNAG 4 cut(s) 80, 284, 417, 495
Eco147I AGGCCT 1 cut(s) 580
Eco31I GGTCTC 1 cut(s) 273
Eco47I GGWCC 1 cut(s) 351
Eco88I CYCGRG 1 cut(s) 115
EcoO109I RGGNCCY 1 cut(s) 351
EcoRII CCWGG 4 cut(s) 186, 274, 601, 766
EcoT22I ATGCAT 1 cut(s) 615
FaeI CATG 3 cut(s) 516, 521, 629
FatI CATG 3 cut(s) 512, 517, 625
FauI CCCGC 1 cut(s) 563
FblI GTMKAC 1 cut(s) 743
Fnu4HI GCNGC 3 cut(s) 321, 639, 642
FokI GGATG 1 cut(s) 392
Fsp4HI GCNGC 3 cut(s) 321, 639, 642
FspBI CTAG 2 cut(s) 42, 324
GluI GCNGC 3 cut(s) 321, 639, 642
GsuI CTGGAG 4 cut(s) 209, 248, 297, 336
HaeIII GGCC 2 cut(s) 580, 781
Hin1II CATG 3 cut(s) 516, 521, 629
HinfI GANTC 4 cut(s) 365, 491, 692, 707
HphI GGTGA 1 cut(s) 174
Hpy166II GTNNAC 1 cut(s) 744
Hpy188I TCNGA 3 cut(s) 534, 541, 681
Hpy188III TCNNGA 4 cut(s) 206, 266, 416, 626
Hpy8I GTNNAC 1 cut(s) 744
HpyAV CCTTC 3 cut(s) 215, 234, 591
HpyCH4III ACNGT 2 cut(s) 478, 758
HpyCH4V TGCA 4 cut(s) 299, 521, 613, 688
HpyF10VI GCNNNNNNNGC 3 cut(s) 638, 650, 736
HpyF3I CTNAG 4 cut(s) 80, 284, 417, 495
Hsp92II CATG 3 cut(s) 516, 521, 629
LmnI GCTCC 2 cut(s) 53, 317
Lsp1109I GCAGC 2 cut(s) 650, 653
MabI ACCWGGT 1 cut(s) 601
MaeI CTAG 2 cut(s) 42, 324
MaeIII GTNAC 2 cut(s) 180, 234
MbiI CCGCTC 1 cut(s) 320
MboII GAAGA 4 cut(s) 175, 455, 521, 798
MhlI GDGCHC 1 cut(s) 130
MluCI AATT 7 cut(s) 27, 155, 373, 446, 454, 506, 660
MlyI GAGTC 1 cut(s) 701
Mph1103I ATGCAT 1 cut(s) 615
MroXI GAANNNNTTC 3 cut(s) 108, 167, 447
MseI TTAA 2 cut(s) 24, 345
MspR9I CCNGG 4 cut(s) 188, 276, 603, 768
MvaI CCWGG 4 cut(s) 188, 276, 603, 768
MvnI CGCG 2 cut(s) 197, 570
MwoI GCNNNNNNNGC 3 cut(s) 638, 650, 736
NheI GCTAGC 1 cut(s) 323
NlaIII CATG 3 cut(s) 516, 521, 629
NmuCI GTSAC 1 cut(s) 180
NsiI ATGCAT 1 cut(s) 615
NspI RCATGY 1 cut(s) 521
PaeI GCATGC 1 cut(s) 521
PaeR7I CTCGAG 1 cut(s) 115
PagI TCATGA 1 cut(s) 625
PceI AGGCCT 1 cut(s) 580
PdmI GAANNNNTTC 3 cut(s) 108, 167, 447
PfeI GAWTC 3 cut(s) 365, 491, 707
PkrI GCNGC 3 cut(s) 322, 640, 643
PleI GAGTC 1 cut(s) 700
PpsI GAGTC 1 cut(s) 700
PpuMI RGGWCCY 1 cut(s) 351
Psp5II RGGWCCY 1 cut(s) 351
Psp6I CCWGG 4 cut(s) 186, 274, 601, 766
PspGI CCWGG 4 cut(s) 186, 274, 601, 766
PspPI GGNCC 1 cut(s) 351
PspPPI RGGWCCY 1 cut(s) 351
PspXI VCTCGAGB 1 cut(s) 115
RsaI GTAC 4 cut(s) 194, 273, 410, 488
RsaNI GTAC 4 cut(s) 193, 272, 409, 487
SaqAI TTAA 2 cut(s) 24, 345
SatI GCNGC 3 cut(s) 321, 639, 642
Sau96I GGNCC 1 cut(s) 351
ScaI AGTACT 1 cut(s) 410
SchI GAGTC 1 cut(s) 701
ScrFI CCNGG 4 cut(s) 188, 276, 603, 768
SduI GDGCHC 1 cut(s) 130
SexAI ACCWGGT 1 cut(s) 601
Sfr274I CTCGAG 1 cut(s) 115
SinI GGWCC 1 cut(s) 351
SlaI CTCGAG 1 cut(s) 115
SmlI CTYRAG 2 cut(s) 115, 121
SmoI CTYRAG 2 cut(s) 115, 121
SphI GCATGC 1 cut(s) 521
Sse9I AATT 7 cut(s) 27, 155, 373, 446, 454, 506, 660
SseBI AGGCCT 1 cut(s) 580
SsiI CCGC 4 cut(s) 197, 320, 570, 632
SspMI CTAG 2 cut(s) 42, 324
StuI AGGCCT 1 cut(s) 580
StyD4I CCNGG 4 cut(s) 186, 274, 601, 766
TaaI ACNGT 2 cut(s) 478, 758
TaqI TCGA 3 cut(s) 65, 116, 368
TasI AATT 7 cut(s) 27, 155, 373, 446, 454, 506, 660
TatI WGTACW 1 cut(s) 408
TauI GCSGC 1 cut(s) 323
TfiI GAWTC 3 cut(s) 365, 491, 707
Tru1I TTAA 2 cut(s) 24, 345
Tru9I TTAA 2 cut(s) 24, 345
TscAI CASTG 2 cut(s) 561, 651
TseFI GTSAC 1 cut(s) 180
TseI GCWGC 2 cut(s) 638, 641
Tsp45I GTSAC 1 cut(s) 180
TspDTI ATGAA 4 cut(s) 6, 51, 160, 490
TspGWI ACGGA 1 cut(s) 789
TspRI CASTG 2 cut(s) 561, 651
VpaK11BI GGWCC 1 cut(s) 351
XapI RAATTY 3 cut(s) 27, 155, 446
XceI RCATGY 1 cut(s) 521
XhoI CTCGAG 1 cut(s) 115
XmiI GTMKAC 1 cut(s) 743
XmnI GAANNNNTTC 3 cut(s) 108, 167, 447
XspI CTAG 2 cut(s) 42, 324
ZrmI AGTACT 1 cut(s) 410
Zsp2I ATGCAT 1 cut(s) 615
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.