Rh1DG101700

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0000370
Physical Location & Seq
Forward (+)
18960252 .. 18977931
17680 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG101700.1

Sequence Viewer

Length: 432 bp
ATGCATGCGTGTATGTTACATTCCCAGAGAAGCATCCAAAGAAATCGTGCTGTTAAACAAGCTCTCAGAGCTAATATGGTCAAGGGCAAGCAAGATACTAGAACAGTTGGAGCTACTTCATCCACTACTGGGCTTCCACATGATGAGGAGGTGGCTAAGTTATTTCAAGCCTTACTGCGAATGGCTTCCCTCGAGCTTGAGGGCACAAACGGGTTCAATAGGAGGCTGAAATTTTTGAAGATGTTCATTAGTCTGTCACCTCCGGAGTACGCAGGAAATCTTGATAATTCTTTGGAAGGGCTGGAGTGGTTACGAAGGAACTACCAAACTTGGATCCATATGATTGATAACGTTCACGTAGAACATTCCTCTATGGTAGATGTTGTTTCTCCTACGATACCCAATTGTTCCACTTCGGATCAAATTCTTTAG
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

143

Amino Acids

16.18

Weight (kDa)

8.69

Isoelectric Point (pI)

51.46

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this 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
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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)
AccIII TCCGGA 1 cut(s) 262
AclI AACGTT 1 cut(s) 351
AclWI GGATC 3 cut(s) 328, 341, 426
AcsI RAATTY 2 cut(s) 230, 423
AfaI GTAC 1 cut(s) 269
AfiI CCNNNNNNNGG 1 cut(s) 129
AgsI TTSAA 3 cut(s) 167, 217, 238
AluBI AGCT 4 cut(s) 62, 71, 113, 196
AluI AGCT 4 cut(s) 62, 71, 113, 196
AlwI GGATC 3 cut(s) 328, 341, 426
Ama87I CYCGRG 1 cut(s) 191
Aor13HI TCCGGA 1 cut(s) 262
ApoI RAATTY 2 cut(s) 230, 423
Asp700I GAANNNNTTC 2 cut(s) 184, 242
AsuHPI GGTGA 1 cut(s) 249
AvaI CYCGRG 1 cut(s) 191
BaeGI GKGCMC 1 cut(s) 206
BamHI GGATCC 1 cut(s) 333
BfaI CTAG 1 cut(s) 99
BmeT110I CYCGRG 1 cut(s) 191
BmiI GGNNCC 1 cut(s) 335
BmrI ACTGGG 1 cut(s) 138
BmsI GCATC 1 cut(s) 42
BmuI ACTGGG 1 cut(s) 138
BpmI CTGGAG 1 cut(s) 323
BpuEI CTTGAG 1 cut(s) 218
BsaAI YACGTR 1 cut(s) 358
BsaWI WCCGGW 1 cut(s) 262
Bsc4I CCNNNNNNNGG 1 cut(s) 129
Bse1I ACTGG 1 cut(s) 133
BseAI TCCGGA 1 cut(s) 262
BseGI GGATG 2 cut(s) 33, 119
BseLI CCNNNNNNNGG 1 cut(s) 129
BseMII CTCAG 1 cut(s) 79
BseNI ACTGG 1 cut(s) 133
BseRI GAGGAG 1 cut(s) 161
BseSI GKGCMC 1 cut(s) 206
BsiHKCI CYCGRG 1 cut(s) 191
BsiSI CCGG 1 cut(s) 263
BslI CCNNNNNNNGG 1 cut(s) 129
BsoBI CYCGRG 1 cut(s) 191
Bsp1286I GDGCHC 1 cut(s) 206
Bsp13I TCCGGA 1 cut(s) 262
Bsp143I GATC 2 cut(s) 333, 418
BspCNI CTCAG 1 cut(s) 78
BspEI TCCGGA 1 cut(s) 262
BspLI GGNNCC 1 cut(s) 335
BspPI GGATC 3 cut(s) 328, 341, 426
BsrI ACTGG 1 cut(s) 133
BssMI GATC 2 cut(s) 333, 418
Bst4CI ACNGT 1 cut(s) 106
BstBAI YACGTR 1 cut(s) 358
BstC8I GCNNGC 2 cut(s) 6, 89
BstDEI CTNAG 2 cut(s) 65, 156
BstF5I GGATG 2 cut(s) 33, 119
BstKTI GATC 2 cut(s) 336, 421
BstMBI GATC 2 cut(s) 333, 418
BstMWI GCNNNNNNNGC 1 cut(s) 68
BstNSI RCATGY 1 cut(s) 8
BstSLI GKGCMC 1 cut(s) 206
BstX2I RGATCY 1 cut(s) 333
BstYI RGATCY 1 cut(s) 333
BtsCI GGATG 2 cut(s) 33, 119
Cac8I GCNNGC 2 cut(s) 6, 89
Csp6I GTAC 1 cut(s) 268
CviAII CATG 2 cut(s) 5, 140
CviQI GTAC 1 cut(s) 268
DdeI CTNAG 2 cut(s) 65, 156
DpnI GATC 2 cut(s) 335, 420
DpnII GATC 2 cut(s) 333, 418
Eco88I CYCGRG 1 cut(s) 191
EcoT22I ATGCAT 1 cut(s) 6
FaeI CATG 2 cut(s) 8, 143
FaiI YATR 7 cut(s) 6, 14, 77, 141, 339, 341, 374
FatI CATG 2 cut(s) 4, 139
FauNDI CATATG 1 cut(s) 339
FokI GGATG 2 cut(s) 20, 106
FspBI CTAG 1 cut(s) 99
GsuI CTGGAG 1 cut(s) 323
HapII CCGG 1 cut(s) 263
Hin1II CATG 2 cut(s) 8, 143
HpaII CCGG 1 cut(s) 263
HphI GGTGA 1 cut(s) 249
Hpy166II GTNNAC 1 cut(s) 355
Hpy188I TCNGA 2 cut(s) 68, 418
Hpy188III TCNNGA 2 cut(s) 263, 281
Hpy8I GTNNAC 1 cut(s) 355
HpyAV CCTTC 2 cut(s) 290, 309
HpyCH4III ACNGT 1 cut(s) 106
HpyCH4IV ACGT 2 cut(s) 351, 357
HpyCH4V TGCA 1 cut(s) 4
HpyF10VI GCNNNNNNNGC 1 cut(s) 68
HpyF3I CTNAG 2 cut(s) 65, 156
HpySE526I ACGT 2 cut(s) 351, 357
Hsp92II CATG 2 cut(s) 8, 143
Kpn2I TCCGGA 1 cut(s) 262
Kzo9I GATC 2 cut(s) 333, 418
LmnI GCTCC 1 cut(s) 110
LpnPI CCDG 5 cut(s) 38, 114, 258, 276, 287
LweI GCATC 1 cut(s) 42
MaeI CTAG 1 cut(s) 99
MaeII ACGT 2 cut(s) 351, 357
MaeIII GTNAC 3 cut(s) 15, 255, 309
MalI GATC 2 cut(s) 335, 420
MboI GATC 2 cut(s) 333, 418
MboII GAAGA 1 cut(s) 250
MfeI CAATTG 1 cut(s) 403
MflI RGATCY 1 cut(s) 333
MhlI GDGCHC 1 cut(s) 206
MluCI AATT 4 cut(s) 230, 286, 403, 423
MmeI TCCRAC 1 cut(s) 88
MnlI CCTC 7 cut(s) 139, 142, 193, 200, 216, 270, 379
Mph1103I ATGCAT 1 cut(s) 6
MroI TCCGGA 1 cut(s) 262
MroXI GAANNNNTTC 2 cut(s) 184, 242
MseI TTAA 1 cut(s) 54
MspI CCGG 1 cut(s) 263
MunI CAATTG 1 cut(s) 403
MwoI GCNNNNNNNGC 1 cut(s) 68
NdeI CATATG 1 cut(s) 339
NdeII GATC 2 cut(s) 333, 418
NlaIII CATG 2 cut(s) 8, 143
NlaIV GGNNCC 1 cut(s) 335
NmuCI GTSAC 1 cut(s) 255
NsiI ATGCAT 1 cut(s) 6
NspI RCATGY 1 cut(s) 8
PaeI GCATGC 1 cut(s) 8
PaeR7I CTCGAG 1 cut(s) 191
PdmI GAANNNNTTC 2 cut(s) 184, 242
Ppu21I YACGTR 1 cut(s) 358
Psp1406I AACGTT 1 cut(s) 351
PspN4I GGNNCC 1 cut(s) 335
PspXI VCTCGAGB 1 cut(s) 191
PsuI RGATCY 1 cut(s) 333
RsaI GTAC 1 cut(s) 269
RsaNI GTAC 1 cut(s) 268
SaqAI TTAA 1 cut(s) 54
Sau3AI GATC 2 cut(s) 333, 418
SduI GDGCHC 1 cut(s) 206
SetI ASST 8 cut(s) 64, 73, 115, 153, 198, 262, 354, 360
SfaNI GCATC 1 cut(s) 42
Sfr274I CTCGAG 1 cut(s) 191
SlaI CTCGAG 1 cut(s) 191
SmlI CTYRAG 2 cut(s) 191, 197
SmoI CTYRAG 2 cut(s) 191, 197
SphI GCATGC 1 cut(s) 8
Sse9I AATT 4 cut(s) 230, 286, 403, 423
SspMI CTAG 1 cut(s) 99
TaaI ACNGT 1 cut(s) 106
TaiI ACGT 2 cut(s) 354, 360
TaqI TCGA 1 cut(s) 192
TasI AATT 4 cut(s) 230, 286, 403, 423
Tru1I TTAA 1 cut(s) 54
Tru9I TTAA 1 cut(s) 54
TseFI GTSAC 1 cut(s) 255
Tsp45I GTSAC 1 cut(s) 255
TspDTI ATGAA 2 cut(s) 108, 235
XapI RAATTY 2 cut(s) 230, 423
XceI RCATGY 1 cut(s) 8
XhoI CTCGAG 1 cut(s) 191
XmnI GAANNNNTTC 2 cut(s) 184, 242
XspI CTAG 1 cut(s) 99
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.