RchiOBHm_Chr2g0117261

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
2
OG0000146
Physical Location & Seq
Reverse (-)
29524102 .. 29524494
393 bp
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UTR
Exon/CDS
Intron
PRQ49022

Sequence Viewer

Length: 393 bp
ATGGAAGACGACGCTGCCACCCTTGCACTCCATAACATGCCTCCAATCATCAACCATTATCATACCACCGCTCAAAATAATTCAACGTTTCCTATGGGTGTTGCCTTGAGTGAATCCAACTACACCATATGGGCACCTCTTATGAAGATGAGGATTGGAGCACGAGAAAAGGTCGGCTACCTTACTGGAGCCAAAGCTGCACCAAATAAGAACTCTCCTGAATTTGAAGTTTGGGCCACAAACAATGAAAAAGTGAAGAGTTGGGTCACTGATTCTATGGAGCCATCACTCATGAATCAGTATATCCGCCTCCTAACAGCCAAAGATTTTTGGGAAGCGGTTGAGAAGACTTTTTATGATGATTCTAATGAAACCAAGATTTTTTCTAACTAA
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
Retrotran_gag_2

Protein Analysis

130

Amino Acids

14.78

Weight (kDa)

5.31

Isoelectric Point (pI)

36.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 48 - 128 3.9e-07 gag-polypeptide of LTR copia-type
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: OG0000146)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g19561 FvH4_1g25371 FvH4_1g25961 FvH4_2g00352 FvH4_2g00861 FvH4_2g04952 FvH4_2g05413 FvH4_2g07531 FvH4_2g08961 FvH4_2g25141 FvH4_2g27292 FvH4_3g18164 FvH4_3g19921 FvH4_3g43870 FvH4_4g14441 FvH4_4g15581 FvH4_4g15582 FvH4_4g16890 FvH4_4g19782 FvH4_4g33444 FvH4_4g33921 FvH4_5g22281 FvH4_5g22282 FvH4_5g32571 FvH4_5g37451 FvH4_5g39631 FvH4_6g04721 FvH4_6g11661 FvH4_6g20571 FvH4_6g32791 FvH4_7g23184
prunus_persica Prupe.1G090900_v2.0.a1 Prupe.1G241200_v2.0.a1 Prupe.1G534100_v2.0.a1 Prupe.3G076700_v2.0.a1 Prupe.4G150800_v2.0.a1 Prupe.4G181800_v2.0.a1 Prupe.4G240900_v2.0.a1 Prupe.4G247600_v2.0.a1 Prupe.6G115900_v2.0.a1 Prupe.6G327500_v2.0.a1 Prupe.8G071700_v2.0.a1
pyrus_communis pycom06g11480 pycom10g08330 pycom15g04320 pycom15g04350 pycom15g12620 pycom2874g00060
rosa_chinensis RchiOBHm_Chr1g0317241 RchiOBHm_Chr1g0341801 RchiOBHm_Chr1g0341931 RchiOBHm_Chr1g0359621 RchiOBHm_Chr2g0113741 RchiOBHm_Chr2g0117261 RchiOBHm_Chr2g0138831 RchiOBHm_Chr2g0141421 RchiOBHm_Chr2g0145281 RchiOBHm_Chr2g0152991 RchiOBHm_Chr3g0448001 RchiOBHm_Chr3g0450981 RchiOBHm_Chr3g0455161 RchiOBHm_Chr3g0457401 RchiOBHm_Chr3g0460001 RchiOBHm_Chr4g0387431 RchiOBHm_Chr4g0388741 RchiOBHm_Chr4g0444201 RchiOBHm_Chr4g0444261 RchiOBHm_Chr5g0010221 RchiOBHm_Chr6g0271721 RchiOBHm_Chr6g0274641 RchiOBHm_Chr6g0294691 RchiOBHm_Chr7g0237031 RchiOBHm_Chr7g0238461 RchiOBHm_Chr7g0239981
rosa_laevigata RLG00000009017
rosa_multiflora Rmu_co7986768.1_g000001 Rmu_co8302239.1_g000001 Rmu_co8485799.1_g000001 Rmu_sc0000061.1_g000013 Rmu_sc0000303.1_g000034 Rmu_sc0000303.1_g000035 Rmu_sc0000315.1_g000017 Rmu_sc0000349.1_g000003 Rmu_sc0000498.1_g000068 Rmu_sc0000508.1_g000014 Rmu_sc0000602.1_g000001 Rmu_sc0000633.1_g000002 Rmu_sc0000638.1_g000030 Rmu_sc0000756.1_g000016 Rmu_sc0000756.1_g000017 Rmu_sc0000785.1_g000037 Rmu_sc0000795.1_g000017 Rmu_sc0000796.1_g000030 Rmu_sc0000863.1_g000023 Rmu_sc0000920.1_g000021 Rmu_sc0000960.1_g000015 Rmu_sc0000982.1_g000102 Rmu_sc0001036.1_g000008 Rmu_sc0001036.1_g000009 Rmu_sc0001643.1_g000029 Rmu_sc0001687.1_g000026 Rmu_sc0001708.1_g000037 Rmu_sc0001768.1_g000015 Rmu_sc0001790.1_g000022 Rmu_sc0002180.1_g000007 Rmu_sc0002211.1_g000006 Rmu_sc0002270.1_g000010 Rmu_sc0002404.1_g000031 Rmu_sc0002858.1_g000016 Rmu_sc0003063.1_g000028 Rmu_sc0003730.1_g000017 Rmu_sc0004087.1_g000020 Rmu_sc0004618.1_g000048 Rmu_sc0004724.1_g000005 Rmu_sc0005167.1_g000036 Rmu_sc0005781.1_g000003 Rmu_sc0005878.1_g000012 Rmu_sc0006011.1_g000003 Rmu_sc0006343.1_g000011 Rmu_sc0006573.1_g000007 Rmu_sc0006599.1_g000007 Rmu_sc0006803.1_g000014 Rmu_sc0006836.1_g000002 Rmu_sc0006849.1_g000002 Rmu_sc0007109.1_g000009 Rmu_sc0009268.1_g000016 Rmu_sc0009618.1_g000017 Rmu_sc0009674.1_g000009 Rmu_sc0010244.1_g000009 Rmu_sc0011151.1_g000004 Rmu_sc0011356.1_g000001 Rmu_sc0011674.1_g000002 Rmu_sc0011778.1_g000016 Rmu_sc0012342.1_g000001 Rmu_sc0012467.1_g000002 Rmu_sc0012574.1_g000003 Rmu_sc0012913.1_g000005 Rmu_sc0013612.1_g000020 Rmu_sc0014824.1_g000001 Rmu_sc0017869.1_g000002 Rmu_sc0018085.1_g000003 Rmu_sc0024789.1_g000001 Rmu_sc0025106.1_g000013 Rmu_sc0034502.1_g000001 Rmu_sc0034547.1_g000001 Rmu_sc0035094.1_g000001 Rmu_sc0035095.1_g000001 Rmu_ssc0000100.1_g000027 Rmu_ssc0000244.1_g000005 Rmu_ssc0000371.1_g000029 Rmu_ssc0000381.1_g000004
rosa_roxburghii Rroxscaffold_1G00015480 Rroxscaffold_1G00023580 Rroxscaffold_1G00039340 Rroxscaffold_1G00047080 Rroxscaffold_2G00095820 Rroxscaffold_2G00125200 Rroxscaffold_2G00128330 Rroxscaffold_3G00270860
rosa_rugosa Rorug06G0120700
rosa_samantha Rh3BG173100 Rh6AG089600 Rh7AG488100 Rh7DG389600
rosa_wichuraiana Rw0G001150 Rw0G001990 Rw0G002010 Rw0G019540 Rw1G013730 Rw1G024110 Rw1G029190 Rw2G018850 Rw2G021090 Rw2G022260 Rw2G023180 Rw2G027280 Rw3G010190 Rw3G020660 Rw3G029380 Rw4G002390 Rw4G002690 Rw4G033260 Rw5G011960 Rw5G023110 Rw5G025250 Rw5G028950 Rw5G033740 Rw5G033950 Rw5G037900 Rw6G009640 Rw6G011620 Rw6G027720 Rw7G010680 Rw7G042070

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 133
AccBSI CCGCTC 1 cut(s) 71
AciI CCGC 3 cut(s) 69, 307, 338
AclI AACGTT 1 cut(s) 86
AcsI RAATTY 1 cut(s) 221
AgsI TTSAA 2 cut(s) 84, 227
AluBI AGCT 1 cut(s) 197
AluI AGCT 1 cut(s) 197
Alw21I GWGCWC 1 cut(s) 163
AoxI GGCC 1 cut(s) 234
ApeKI GCWGC 2 cut(s) 14, 197
ApoI RAATTY 1 cut(s) 221
AspS9I GGNCC 1 cut(s) 234
BaeGI GKGCMC 1 cut(s) 136
BanI GGYRCC 1 cut(s) 133
BauI CACGAG 1 cut(s) 162
BbsI GAAGAC 2 cut(s) 12, 353
Bbv12I GWGCWC 1 cut(s) 163
BbvI GCAGC 1 cut(s) 184
BccI CCATC 1 cut(s) 292
BisI GCNGC 2 cut(s) 15, 198
BlsI GCNGC 2 cut(s) 16, 199
BmgT120I GGNCC 1 cut(s) 234
BmiI GGNNCC 3 cut(s) 135, 190, 282
BpiI GAAGAC 2 cut(s) 12, 353
BpmI CTGGAG 1 cut(s) 207
BpuEI CTTGAG 1 cut(s) 127
Bse1I ACTGG 1 cut(s) 190
BseNI ACTGG 1 cut(s) 190
BseSI GKGCMC 1 cut(s) 136
BseXI GCAGC 1 cut(s) 184
BsgI GTGCAG 1 cut(s) 183
BshFI GGCC 1 cut(s) 236
BshNI GGYRCC 1 cut(s) 133
BsiHKAI GWGCWC 1 cut(s) 163
BsnI GGCC 1 cut(s) 236
Bsp1286I GDGCHC 2 cut(s) 136, 163
BspACI CCGC 3 cut(s) 69, 307, 338
BspANI GGCC 1 cut(s) 236
BspHI TCATGA 1 cut(s) 291
BspLI GGNNCC 3 cut(s) 135, 190, 282
BspT107I GGYRCC 1 cut(s) 133
BsrBI CCGCTC 1 cut(s) 71
BsrI ACTGG 1 cut(s) 190
BssSI CACGAG 1 cut(s) 162
Bst2BI CACGAG 1 cut(s) 162
Bst6I CTCTTC 1 cut(s) 251
BstMWI GCNNNNNNNGC 2 cut(s) 23, 197
BstNSI RCATGY 1 cut(s) 40
BstSLI GKGCMC 1 cut(s) 136
BstV1I GCAGC 1 cut(s) 184
BstV2I GAAGAC 2 cut(s) 12, 353
BsuRI GGCC 1 cut(s) 236
BtsIMutI CAGTG 1 cut(s) 267
CciI TCATGA 1 cut(s) 291
Cfr13I GGNCC 1 cut(s) 234
CseI GACGC 1 cut(s) 20
CviAII CATG 2 cut(s) 37, 292
CviJI RGCY 6 cut(s) 177, 191, 197, 236, 283, 320
CviKI_1 RGCY 6 cut(s) 177, 191, 197, 236, 283, 320
Eam1104I CTCTTC 1 cut(s) 251
EarI CTCTTC 1 cut(s) 251
EciI GGCGGA 1 cut(s) 296
FaeI CATG 2 cut(s) 40, 295
FatI CATG 2 cut(s) 36, 291
FauNDI CATATG 1 cut(s) 128
Fnu4HI GCNGC 2 cut(s) 15, 198
Fsp4HI GCNGC 2 cut(s) 15, 198
GluI GCNGC 2 cut(s) 15, 198
GsuI CTGGAG 1 cut(s) 207
HaeIII GGCC 1 cut(s) 236
HgaI GACGC 1 cut(s) 20
Hin1II CATG 2 cut(s) 40, 295
HinfI GANTC 4 cut(s) 113, 272, 295, 362
Hpy188III TCNNGA 2 cut(s) 218, 292
Hpy99I CGWCG 1 cut(s) 14
HpyCH4IV ACGT 1 cut(s) 86
HpyCH4V TGCA 2 cut(s) 26, 200
HpyF10VI GCNNNNNNNGC 2 cut(s) 23, 197
HpySE526I ACGT 1 cut(s) 86
Hsp92II CATG 2 cut(s) 40, 295
LmnI GCTCC 3 cut(s) 158, 188, 280
LpnPI CCDG 2 cut(s) 171, 231
Lsp1109I GCAGC 1 cut(s) 184
MaeII ACGT 1 cut(s) 86
MaeIII GTNAC 1 cut(s) 265
MbiI CCGCTC 1 cut(s) 71
MboII GAAGA 4 cut(s) 17, 157, 268, 358
MhlI GDGCHC 2 cut(s) 136, 163
MluCI AATT 2 cut(s) 79, 221
MmeI TCCRAC 1 cut(s) 141
MnlI CCTC 4 cut(s) 51, 144, 147, 320
MwoI GCNNNNNNNGC 2 cut(s) 23, 197
NdeI CATATG 1 cut(s) 128
NlaIII CATG 2 cut(s) 40, 295
NlaIV GGNNCC 3 cut(s) 135, 190, 282
NmuCI GTSAC 1 cut(s) 265
NspI RCATGY 1 cut(s) 40
PagI TCATGA 1 cut(s) 291
PfeI GAWTC 4 cut(s) 113, 272, 295, 362
PkrI GCNGC 2 cut(s) 16, 199
Psp1406I AACGTT 1 cut(s) 86
PspN4I GGNNCC 3 cut(s) 135, 190, 282
PspPI GGNCC 1 cut(s) 234
SatI GCNGC 2 cut(s) 15, 198
Sau96I GGNCC 1 cut(s) 234
SduI GDGCHC 2 cut(s) 136, 163
SetI ASST 5 cut(s) 89, 139, 174, 183, 199
SgeI CNNG 9 cut(s) 35, 49, 118, 174, 176, 198, 230, 304, 388
SmlI CTYRAG 1 cut(s) 106
SmoI CTYRAG 1 cut(s) 106
Sse9I AATT 2 cut(s) 79, 221
SsiI CCGC 3 cut(s) 69, 307, 338
TaiI ACGT 1 cut(s) 89
TasI AATT 2 cut(s) 79, 221
TfiI GAWTC 4 cut(s) 113, 272, 295, 362
TscAI CASTG 1 cut(s) 274
TseFI GTSAC 1 cut(s) 265
TseI GCWGC 2 cut(s) 14, 197
Tsp45I GTSAC 1 cut(s) 265
TspDTI ATGAA 4 cut(s) 158, 261, 308, 384
TspRI CASTG 1 cut(s) 274
XapI RAATTY 1 cut(s) 221
XceI RCATGY 1 cut(s) 40
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.