Rh1AG098800

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1A
OG0000370
Physical Location & Seq
Forward (+)
17255921 .. 17256415
495 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1AG098800.1

Sequence Viewer

Length: 495 bp
ATGGAAGCTAATGTTTCATTTGTTAAAATTCAGCAGGATACTAGAACAGGTGGAGCTACTTCATCGATGAGGAGGTGGCTAAGTTGTTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAAAGGGGTTCAACAGGAGGCTGAATTTTTTGAAGATGTTCATTAGTCTGTCACCCCTGGAGTACGCGGAAAATCTTGATACTTCTTTGGAAGGGCTGGAGTGGTTACGAAGGGTAAAGCAATGTTTTGATGTTCTTGATGTACCTGGAGACCTAAGAGTTGGGTTTGCAGGCTATACTCTTACTGGAGCGGCTAGCTACTGGTGGGATTTTGTTAAAAGGACCTGTGATGTGGAATCGATGAATTGGGATGACTTTGAGCAGATATTTTTGAATAAGTACTTTCCTGGGACTATAAGGCGAGCTAAAGTAGAAGAATTTCTCAATTTGACACGGGGGAATGACAGTTTTTCAGTACGATTCTAA
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

164

Amino Acids

19.19

Weight (kDa)

8.36

Isoelectric Point (pI)

46.9

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 100 - 160 1.8e-08 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
AccII CGCG 1 cut(s) 197
AciI CCGC 2 cut(s) 197, 320
AcsI RAATTY 3 cut(s) 27, 154, 446
AfaI GTAC 4 cut(s) 194, 273, 410, 486
AgsI TTSAA 4 cut(s) 91, 142, 163, 403
AjnI CCWGG 3 cut(s) 186, 274, 415
AluBI AGCT 5 cut(s) 8, 56, 120, 327, 434
AluI AGCT 5 cut(s) 8, 56, 120, 327, 434
Alw26I GTCTC 1 cut(s) 273
Ama87I CYCGRG 1 cut(s) 115
ApoI RAATTY 3 cut(s) 27, 154, 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
BciT130I CCWGG 3 cut(s) 188, 276, 417
BciVI GTATCC 1 cut(s) 31
BcoDI GTCTC 1 cut(s) 273
BfaI CTAG 2 cut(s) 42, 324
BfuI GTATCC 1 cut(s) 31
BisI GCNGC 1 cut(s) 321
BlsI GCNGC 1 cut(s) 322
BmcAI AGTACT 1 cut(s) 410
Bme1390I CCNGG 3 cut(s) 188, 276, 417
Bme18I GGWCC 1 cut(s) 351
BmeT110I CYCGRG 1 cut(s) 115
BmgT120I GGNCC 1 cut(s) 351
BmrFI CCNGG 3 cut(s) 188, 276, 417
BmtI GCTAGC 1 cut(s) 327
BpmI CTGGAG 4 cut(s) 209, 248, 297, 336
BpuEI CTTGAG 1 cut(s) 142
Bsa29I ATCGAT 2 cut(s) 65, 368
BsaI GGTCTC 1 cut(s) 273
BsaJI CCNNGG 2 cut(s) 186, 416
Bse1I ACTGG 2 cut(s) 319, 335
Bse3DI GCAATG 1 cut(s) 257
BseBI CCWGG 3 cut(s) 188, 276, 417
BseCI ATCGAT 2 cut(s) 65, 368
BseDI CCNNGG 2 cut(s) 186, 416
BseGI GGATG 1 cut(s) 385
BseMI GCAATG 1 cut(s) 257
BseNI ACTGG 2 cut(s) 319, 335
BseRI GAGGAG 1 cut(s) 85
BseSI GKGCMC 1 cut(s) 130
Bsh1236I CGCG 1 cut(s) 197
BshVI ATCGAT 2 cut(s) 65, 368
BsiHKCI CYCGRG 1 cut(s) 115
BslFI GGGAC 1 cut(s) 433
BsmAI GTCTC 1 cut(s) 273
BsmFI GGGAC 1 cut(s) 433
Bso31I GGTCTC 1 cut(s) 273
BsoBI CYCGRG 1 cut(s) 115
Bsp1286I GDGCHC 1 cut(s) 130
BspACI CCGC 2 cut(s) 197, 320
BspDI ATCGAT 2 cut(s) 65, 368
BspFNI CGCG 1 cut(s) 197
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 2 cut(s) 186, 416
Bst2UI CCWGG 3 cut(s) 188, 276, 417
Bst4CI ACNGT 1 cut(s) 476
BstC8I GCNNGC 3 cut(s) 301, 325, 432
BstDEI CTNAG 2 cut(s) 80, 284
BstF5I GGATG 1 cut(s) 385
BstFNI CGCG 1 cut(s) 197
BstMAI GTCTC 1 cut(s) 273
BstNI CCWGG 3 cut(s) 188, 276, 417
BstSCI CCNGG 3 cut(s) 186, 274, 415
BstSLI GKGCMC 1 cut(s) 130
BstUI CGCG 1 cut(s) 197
Bsu15I ATCGAT 2 cut(s) 65, 368
BsuI GTATCC 1 cut(s) 31
BsuTUI ATCGAT 2 cut(s) 65, 368
BtsCI GGATG 1 cut(s) 385
Cac8I GCNNGC 3 cut(s) 301, 325, 432
Cfr13I GGNCC 1 cut(s) 351
ClaI ATCGAT 2 cut(s) 65, 368
Csp6I GTAC 4 cut(s) 193, 272, 409, 485
CviQI GTAC 4 cut(s) 193, 272, 409, 485
DdeI CTNAG 2 cut(s) 80, 284
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 3 cut(s) 186, 274, 415
FaiI YATR 2 cut(s) 306, 425
FaqI GGGAC 1 cut(s) 433
Fnu4HI GCNGC 1 cut(s) 321
FokI GGATG 1 cut(s) 392
Fsp4HI GCNGC 1 cut(s) 321
FspBI CTAG 2 cut(s) 42, 324
GluI GCNGC 1 cut(s) 321
GsuI CTGGAG 4 cut(s) 209, 248, 297, 336
HinfI GANTC 2 cut(s) 365, 489
HphI GGTGA 1 cut(s) 174
Hpy188III TCNNGA 2 cut(s) 206, 266
HpyAV CCTTC 2 cut(s) 215, 234
HpyCH4III ACNGT 1 cut(s) 476
HpyCH4V TGCA 1 cut(s) 299
HpyF3I CTNAG 2 cut(s) 80, 284
LmnI GCTCC 2 cut(s) 53, 317
MaeI CTAG 2 cut(s) 42, 324
MaeIII GTNAC 2 cut(s) 180, 234
MbiI CCGCTC 1 cut(s) 320
MboII GAAGA 2 cut(s) 175, 455
MhlI GDGCHC 1 cut(s) 130
MluCI AATT 5 cut(s) 27, 154, 373, 446, 454
MnlI CCTC 5 cut(s) 63, 66, 117, 124, 141
MroXI GAANNNNTTC 3 cut(s) 108, 167, 447
MseI TTAA 2 cut(s) 24, 345
MspR9I CCNGG 3 cut(s) 188, 276, 417
MvaI CCWGG 3 cut(s) 188, 276, 417
MvnI CGCG 1 cut(s) 197
NheI GCTAGC 1 cut(s) 323
NmuCI GTSAC 1 cut(s) 180
PaeR7I CTCGAG 1 cut(s) 115
PdmI GAANNNNTTC 3 cut(s) 108, 167, 447
PfeI GAWTC 2 cut(s) 365, 489
PkrI GCNGC 1 cut(s) 322
PpuMI RGGWCCY 1 cut(s) 351
Psp5II RGGWCCY 1 cut(s) 351
Psp6I CCWGG 3 cut(s) 186, 274, 415
PspGI CCWGG 3 cut(s) 186, 274, 415
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, 486
RsaNI GTAC 4 cut(s) 193, 272, 409, 485
SaqAI TTAA 2 cut(s) 24, 345
SatI GCNGC 1 cut(s) 321
Sau96I GGNCC 1 cut(s) 351
ScaI AGTACT 1 cut(s) 410
ScrFI CCNGG 3 cut(s) 188, 276, 417
SduI GDGCHC 1 cut(s) 130
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
Sse9I AATT 5 cut(s) 27, 154, 373, 446, 454
SsiI CCGC 2 cut(s) 197, 320
SspMI CTAG 2 cut(s) 42, 324
StyD4I CCNGG 3 cut(s) 186, 274, 415
TaaI ACNGT 1 cut(s) 476
TaqI TCGA 3 cut(s) 65, 116, 368
TasI AATT 5 cut(s) 27, 154, 373, 446, 454
TatI WGTACW 1 cut(s) 408
TauI GCSGC 1 cut(s) 323
TfiI GAWTC 2 cut(s) 365, 489
Tru1I TTAA 2 cut(s) 24, 345
Tru9I TTAA 2 cut(s) 24, 345
TseFI GTSAC 1 cut(s) 180
Tsp45I GTSAC 1 cut(s) 180
TspDTI ATGAA 4 cut(s) 6, 51, 160, 386
VpaK11BI GGWCC 1 cut(s) 351
XapI RAATTY 3 cut(s) 27, 154, 446
XhoI CTCGAG 1 cut(s) 115
XmnI GAANNNNTTC 3 cut(s) 108, 167, 447
XspI CTAG 2 cut(s) 42, 324
ZrmI AGTACT 1 cut(s) 410
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.