RchiOBHm_Chr3g0453341

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000562
Physical Location & Seq
Forward (+)
3784415 .. 3786729
2315 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ42043

Sequence Viewer

Length: 1143 bp
ATGGCTGGGAAATCTGGTTCAAAAAATGAGGATTCTCTTCTAACCTCAATTTCTTCCGATGTTGAGTTTAATCCGAACCAACGTCTTAGCTCTGTTTTGTTGAATGAATTCAACTATCTTTCTTGGGCTAGAGCTGTTACACTTGCTCTTGGAGGAAGGTCCAAGCTTGGTTATATCAATGGAGTTATACAGATGCCAGAAGCTAAGTCCCCTACATATGATTCTTGGCTTTGCAATGATCAACTTGTTATGTCTTGGTTACTCAATTCCATGGAGAGCAGAATAAGGGAGATTTTTAGTTTTTCTGAGTCTTCTATGCATCTCTGGAAATATGTTAAAGAGATGTATGGAAATCAGAATAATGCTGCTCGAGTGTTTCAACTCAAGCGAGATATTGCTGATCTACAACAAGAGGGTAAATCCTTTGTTCAACACCTTGGTAGCCTTACAAGTATGTGGAATGAGCTAGATGTTTACAGACCTCATACCACAGAGGCGAGTGTTTTGTTAAAGAGAGCAGATGAGGACAAGATTTTTCAACTCCTTGCAAGTTTAAACTCAGATTATGAAGATTTGAGAAGCCACATTCTCATGAATTCTGAGCTTCCATCTTTCAACACCGTATGTGCTACGATTCAAAGGGAAGAAGTTCGAAAAAAGGTGATGAATATGGAGAACAAGTCTAGTCTGTCTGAAACTAGAGCCTATGTTTCAAATCATAGGCAAGTTGAAGAGAGAACATACAAAGGCAAGAGAACTGATTTGAAGTGCACTTACTGTGAAGGTGTTGGGCATGTCAAGGACAGATGTTGGATTCTCCATCCTGAGCAGAAGCCAAAGTTTTCAAAAGAAGGCAAAATTCTTCAAAAAGGCTGGAGTACTCCATCACACAGAGCAAAACTTGCTGATGCTTCTTATACTAGGAGTATGATGAATTTCACCTCCAATCCCACTGCGCTTATTAATGAATTTGCTACCTATCTCAACATGAGGCAGATGCATGGTGGAAAAGAAGAACCAGCTATAACTGGGAGTGAAAACCACACTGCACTCCTTGGAAAGTTTGCTGGCTTTCTTGCAGAAACTGATTGTGTCTCACATGAGGAAGCTTCAGGATCTCATCACCAAGGAGACGATTGGTGA
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 Retrotran_gag_3 rve

Protein Analysis

380

Amino Acids

43.25

Weight (kDa)

6.68

Isoelectric Point (pI)

41.89

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 27 - 67 1.5e-13 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 53 - 221 3.6e-14 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
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Orthologous Genes (Group: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclWI GGATC 1 cut(s) 1123
AcsI RAATTY 5 cut(s) 107, 595, 858, 934, 968
AcuI CTGAAG 1 cut(s) 1095
AfaI GTAC 1 cut(s) 880
AloI GAACNNNNNNTCC 1 cut(s) 33
AluBI AGCT 8 cut(s) 90, 134, 166, 203, 466, 604, 1022, 1109
AluI AGCT 8 cut(s) 90, 134, 166, 203, 466, 604, 1022, 1109
Alw21I GWGCWC 1 cut(s) 773
Alw26I GTCTC 2 cut(s) 1099, 1125
Alw44I GTGCAC 1 cut(s) 769
AlwI GGATC 1 cut(s) 1123
AlwNI CAGNNNCTG 1 cut(s) 1085
Ama87I CYCGRG 1 cut(s) 369
ApaLI GTGCAC 1 cut(s) 769
ApeKI GCWGC 1 cut(s) 365
ApoI RAATTY 5 cut(s) 107, 595, 858, 934, 968
AseI ATTAAT 1 cut(s) 963
Asp700I GAANNNNTTC 2 cut(s) 107, 648
AspLEI GCGC 1 cut(s) 958
AspS9I GGNCC 1 cut(s) 159
AsuHPI GGTGA 3 cut(s) 673, 931, 1115
AsuII TTCGAA 1 cut(s) 652
AvaI CYCGRG 1 cut(s) 369
AvaII GGWCC 1 cut(s) 159
BaeGI GKGCMC 1 cut(s) 773
BarI GAAGNNNNNNTAC 2 cut(s) 758, 790
BbsI GAAGAC 1 cut(s) 303
Bbv12I GWGCWC 1 cut(s) 773
BbvI GCAGC 1 cut(s) 352
BccI CCATC 3 cut(s) 616, 828, 892
BclI TGATCA 1 cut(s) 238
BcoDI GTCTC 2 cut(s) 1099, 1125
BfaI CTAG 5 cut(s) 129, 467, 684, 699, 921
BisI GCNGC 1 cut(s) 366
BlsI GCNGC 1 cut(s) 367
BmcAI AGTACT 1 cut(s) 880
Bme18I GGWCC 1 cut(s) 159
BmeT110I CYCGRG 1 cut(s) 369
BmgT120I GGNCC 1 cut(s) 159
BmrI ACTGGG 1 cut(s) 1038
BmsI GCATC 4 cut(s) 183, 328, 898, 987
BmuI ACTGGG 1 cut(s) 1038
BpiI GAAGAC 1 cut(s) 303
BpmI CTGGAG 1 cut(s) 895
Bpu10I CCTNAGC 1 cut(s) 825
Bpu14I TTCGAA 1 cut(s) 652
BpuEI CTTGAG 1 cut(s) 368
BsaJI CCNNGG 4 cut(s) 270, 436, 1054, 1126
BsaXI ACNNNNNCTCC 2 cut(s) 665, 695
Bse1I ACTGG 1 cut(s) 1033
Bse3DI GCAATG 1 cut(s) 241
BseDI CCNNGG 4 cut(s) 270, 436, 1054, 1126
BseGI GGATG 1 cut(s) 820
BseMI GCAATG 1 cut(s) 241
BseMII CTCAG 4 cut(s) 297, 573, 591, 816
BseNI ACTGG 1 cut(s) 1033
BseSI GKGCMC 1 cut(s) 773
BseXI GCAGC 1 cut(s) 352
BseYI CCCAGC 1 cut(s) 5
BsgI GTGCAG 1 cut(s) 1032
BsiHKAI GWGCWC 1 cut(s) 773
BsiHKCI CYCGRG 1 cut(s) 369
BslFI GGGAC 1 cut(s) 193
BsmAI GTCTC 2 cut(s) 1099, 1125
BsmBI CGTCTC 1 cut(s) 1125
BsmFI GGGAC 1 cut(s) 193
BsoBI CYCGRG 1 cut(s) 369
Bsp119I TTCGAA 1 cut(s) 652
Bsp1286I GDGCHC 1 cut(s) 773
Bsp143I GATC 3 cut(s) 238, 400, 1115
Bsp19I CCATGG 1 cut(s) 270
BspCNI CTCAG 4 cut(s) 298, 572, 592, 817
BspHI TCATGA 1 cut(s) 591
BspPI GGATC 1 cut(s) 1123
BspT104I TTCGAA 1 cut(s) 652
BsrDI GCAATG 1 cut(s) 241
BsrI ACTGG 1 cut(s) 1033
BssECI CCNNGG 4 cut(s) 270, 436, 1054, 1126
BssMI GATC 3 cut(s) 238, 400, 1115
BssT1I CCWWGG 4 cut(s) 270, 436, 1054, 1126
Bst4CI ACNGT 2 cut(s) 622, 779
Bst6I CTCTTC 2 cut(s) 42, 726
BstAPI GCANNNNNTGC 1 cut(s) 902
BstBI TTCGAA 1 cut(s) 652
BstC8I GCNNGC 1 cut(s) 1069
BstDEI CTNAG 6 cut(s) 86, 204, 306, 559, 600, 825
BstDSI CCRYGG 1 cut(s) 270
BstF5I GGATG 1 cut(s) 820
BstHHI GCGC 1 cut(s) 958
BstKTI GATC 3 cut(s) 241, 403, 1118
BstMAI GTCTC 2 cut(s) 1099, 1125
BstMBI GATC 3 cut(s) 238, 400, 1115
BstMWI GCNNNNNNNGC 1 cut(s) 902
BstNSI RCATGY 1 cut(s) 797
BstSLI GKGCMC 1 cut(s) 773
BstV1I GCAGC 1 cut(s) 352
BstV2I GAAGAC 1 cut(s) 303
BstX2I RGATCY 1 cut(s) 1115
BstYI RGATCY 1 cut(s) 1115
BtgI CCRYGG 1 cut(s) 270
BtsCI GGATG 1 cut(s) 820
BtsI GCAGTG 2 cut(s) 951, 1044
BtsIMutI CAGTG 2 cut(s) 951, 1044
Cac8I GCNNGC 1 cut(s) 1069
CaiI CAGNNNCTG 1 cut(s) 1085
CciI TCATGA 1 cut(s) 591
CfoI GCGC 1 cut(s) 958
Cfr13I GGNCC 1 cut(s) 159
Csp6I GTAC 1 cut(s) 879
CviAII CATG 6 cut(s) 271, 592, 794, 988, 1001, 1100
CviQI GTAC 1 cut(s) 879
DdeI CTNAG 6 cut(s) 86, 204, 306, 559, 600, 825
DpnI GATC 3 cut(s) 240, 402, 1117
DpnII GATC 3 cut(s) 238, 400, 1115
DraI TTTAAA 1 cut(s) 555
Eam1104I CTCTTC 2 cut(s) 42, 726
EarI CTCTTC 2 cut(s) 42, 726
Eco130I CCWWGG 4 cut(s) 270, 436, 1054, 1126
Eco47I GGWCC 1 cut(s) 159
Eco57I CTGAAG 1 cut(s) 1095
Eco88I CYCGRG 1 cut(s) 369
EcoRI GAATTC 2 cut(s) 107, 595
EcoT14I CCWWGG 4 cut(s) 270, 436, 1054, 1126
EcoT22I ATGCAT 2 cut(s) 321, 1002
ErhI CCWWGG 4 cut(s) 270, 436, 1054, 1126
Esp3I CGTCTC 1 cut(s) 1125
FaeI CATG 6 cut(s) 274, 595, 797, 991, 1004, 1103
FaqI GGGAC 1 cut(s) 193
FatI CATG 6 cut(s) 270, 591, 793, 987, 1000, 1099
FauNDI CATATG 1 cut(s) 217
FbaI TGATCA 1 cut(s) 238
Fnu4HI GCNGC 1 cut(s) 366
FokI GGATG 1 cut(s) 807
Fsp4HI GCNGC 1 cut(s) 366
FspBI CTAG 5 cut(s) 129, 467, 684, 699, 921
GlaI GCGC 1 cut(s) 957
GluI GCNGC 1 cut(s) 366
GsaI CCCAGC 1 cut(s) 9
GsuI CTGGAG 1 cut(s) 895
HhaI GCGC 1 cut(s) 958
Hin1II CATG 6 cut(s) 274, 595, 797, 991, 1004, 1103
Hin6I GCGC 1 cut(s) 956
HinP1I GCGC 1 cut(s) 956
HindIII AAGCTT 2 cut(s) 164, 1107
HinfI GANTC 5 cut(s) 32, 221, 308, 634, 814
HphI GGTGA 3 cut(s) 673, 931, 1115
Hpy166II GTNNAC 2 cut(s) 475, 771
Hpy188I TCNGA 7 cut(s) 58, 75, 307, 357, 562, 601, 694
Hpy188III TCNNGA 4 cut(s) 325, 592, 824, 1113
Hpy8I GTNNAC 2 cut(s) 475, 771
HpyAV CCTTC 3 cut(s) 150, 776, 845
HpyCH4III ACNGT 2 cut(s) 622, 779
HpyCH4IV ACGT 1 cut(s) 82
HpyCH4V TGCA 7 cut(s) 234, 319, 548, 771, 1000, 1049, 1079
HpyF10VI GCNNNNNNNGC 1 cut(s) 902
HpyF3I CTNAG 6 cut(s) 86, 204, 306, 559, 600, 825
HpySE526I ACGT 1 cut(s) 82
Hsp92II CATG 6 cut(s) 274, 595, 797, 991, 1004, 1103
HspAI GCGC 1 cut(s) 956
Ksp22I TGATCA 1 cut(s) 238
Kzo9I GATC 3 cut(s) 238, 400, 1115
LpnPI CCDG 8 cut(s) 210, 310, 837, 859, 1014, 1032, 1053, 1098
Lsp1109I GCAGC 1 cut(s) 352
LweI GCATC 4 cut(s) 183, 328, 898, 987
MaeI CTAG 5 cut(s) 129, 467, 684, 699, 921
MaeII ACGT 1 cut(s) 82
MaeIII GTNAC 2 cut(s) 136, 258
MalI GATC 3 cut(s) 240, 402, 1117
MboI GATC 3 cut(s) 238, 400, 1115
MboII GAAGA 8 cut(s) 29, 45, 303, 581, 656, 743, 854, 1025
MflI RGATCY 1 cut(s) 1115
MhlI GDGCHC 1 cut(s) 773
MluCI AATT 7 cut(s) 48, 107, 265, 595, 858, 934, 968
MlyI GAGTC 1 cut(s) 317
MmeI TCCRAC 1 cut(s) 791
Mph1103I ATGCAT 2 cut(s) 321, 1002
MroXI GAANNNNTTC 2 cut(s) 107, 648
MseI TTAA 5 cut(s) 69, 336, 509, 554, 963
MslI CAYNNNNRTG 1 cut(s) 590
MssI GTTTAAAC 1 cut(s) 555
MwoI GCNNNNNNNGC 1 cut(s) 902
NcoI CCATGG 1 cut(s) 270
NdeI CATATG 1 cut(s) 217
NdeII GATC 3 cut(s) 238, 400, 1115
NlaIII CATG 6 cut(s) 274, 595, 797, 991, 1004, 1103
NsiI ATGCAT 2 cut(s) 321, 1002
NspI RCATGY 1 cut(s) 797
NspV TTCGAA 1 cut(s) 652
PaeR7I CTCGAG 1 cut(s) 369
PagI TCATGA 1 cut(s) 591
PdmI GAANNNNTTC 2 cut(s) 107, 648
PfeI GAWTC 4 cut(s) 32, 221, 634, 814
PkrI GCNGC 1 cut(s) 367
PleI GAGTC 1 cut(s) 316
PmeI GTTTAAAC 1 cut(s) 555
PpsI GAGTC 1 cut(s) 316
PshBI ATTAAT 1 cut(s) 963
PspFI CCCAGC 1 cut(s) 5
PspPI GGNCC 1 cut(s) 159
PspXI VCTCGAGB 1 cut(s) 369
PstNI CAGNNNCTG 1 cut(s) 1085
PsuI RGATCY 1 cut(s) 1115
RsaI GTAC 1 cut(s) 880
RsaNI GTAC 1 cut(s) 879
RseI CAYNNNNRTG 1 cut(s) 590
SaqAI TTAA 5 cut(s) 69, 336, 509, 554, 963
SatI GCNGC 1 cut(s) 366
Sau3AI GATC 3 cut(s) 238, 400, 1115
Sau96I GGNCC 1 cut(s) 159
ScaI AGTACT 1 cut(s) 880
SchI GAGTC 1 cut(s) 317
SduI GDGCHC 1 cut(s) 773
SfaNI GCATC 4 cut(s) 183, 328, 898, 987
Sfr274I CTCGAG 1 cut(s) 369
SfuI TTCGAA 1 cut(s) 652
SinI GGWCC 1 cut(s) 159
SlaI CTCGAG 1 cut(s) 369
SmiMI CAYNNNNRTG 1 cut(s) 590
SmlI CTYRAG 2 cut(s) 369, 383
SmoI CTYRAG 2 cut(s) 369, 383
Sse9I AATT 7 cut(s) 48, 107, 265, 595, 858, 934, 968
SspMI CTAG 5 cut(s) 129, 467, 684, 699, 921
StyI CCWWGG 4 cut(s) 270, 436, 1054, 1126
TaaI ACNGT 2 cut(s) 622, 779
TaiI ACGT 1 cut(s) 85
TaqI TCGA 2 cut(s) 370, 652
TasI AATT 7 cut(s) 48, 107, 265, 595, 858, 934, 968
TatI WGTACW 1 cut(s) 878
TfiI GAWTC 4 cut(s) 32, 221, 634, 814
Tru1I TTAA 5 cut(s) 69, 336, 509, 554, 963
Tru9I TTAA 5 cut(s) 69, 336, 509, 554, 963
TscAI CASTG 2 cut(s) 958, 1051
TseI GCWGC 1 cut(s) 365
TspDTI ATGAA 6 cut(s) 120, 582, 608, 680, 947, 981
TspRI CASTG 2 cut(s) 958, 1051
VneI GTGCAC 1 cut(s) 769
VpaK11BI GGWCC 1 cut(s) 159
VspI ATTAAT 1 cut(s) 963
XapI RAATTY 5 cut(s) 107, 595, 858, 934, 968
XceI RCATGY 1 cut(s) 797
XhoI CTCGAG 1 cut(s) 369
XmnI GAANNNNTTC 2 cut(s) 107, 648
XspI CTAG 5 cut(s) 129, 467, 684, 699, 921
ZrmI AGTACT 1 cut(s) 880
Zsp2I ATGCAT 2 cut(s) 321, 1002
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.