RchiOBHm_Chr4g0388371

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000562
Physical Location & Seq
Forward (+)
3576152 .. 3578007
1856 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ36160

Sequence Viewer

Length: 1119 bp
ATGTCCAGAGGAGATAGCTCCATTTCTTCTTCCTCTACACCAAAAAGTTATGAGAGTGATTCAAACCCAAATCAACGTTTGTGTTCAGTTTTACTCAATGAGTTCAACTATATATCTTGGTCAAGAGCGATCACTCTTGCTCTTGGTGGAAGATCCAAGCTTGGCTACATCAATGGTGACATTCAAATCCCACCACCTCTATCCGCTGATTATGAAGCATGGCTCAGCAAAGATCAGCTAGTCATGTCATGGCTCCTAAATTCTATGGAGCCATCTGTTGCTGTGATCTTTAACTATTCTGAGTCTTCTCAGCATATATGGAAATCTGTGAAAGAAATGTATGGCAACCAAAATAATTGTGCCAGAGTTTTTCAACTTCAAAGAGACATCACCAATCTCAAGCAAGGAGCAACCTCTTTTGTTCATCATCTTGGAAGCATGAAAAACATGTGGAATGAGGTAAATATCTATAGGCCTCACACCACAGATGCAGCTATTCTACAAAAAAGGGCCGAAGAAGATAAAGTGTTCCAGCTCCTAGCCAGTTTAGGACCTGAGTATGAAGATCTTCGCAGCCACATACTCATGACTCCTGAACTACCAACTTTGACCAGCATCTGCTCTACCATTCAACGTGAAGAGACTCGGAGAAAAGTCATGAATGAAGACTTAAAGACATCTGTTTCTGAAGCTAGAGCTTTTGCAAGTGATCATAAGCCAGCTGAGAAGAAACCTTACAGAGGTAAACGCCCTGATCTTCACTGTACTTACTGTGATCATCCTGGACATCTCAGAGACAGGTGCTGGATACTACATCCAGAACTCAAACCCAAGTTTGATAAGCAAGCCAGAGATACCAGGTTCTTTCCAAAAAATCATGGTCACAAGGCAAATCATGTGGCTTCTGCTACTGAGGGATTACTAAACTTCACTGCAAATCCAGCTGCACTGATAAATGAATTTGCAGCCTACATCAAATTGAAGCAAGGAAATGAAAAAGAGGCTGTTACTGAAGACTCAACAGCTTTACTTGGAAAATTCGCTGGTTTTCTAGCAGAGGCAGATGGAATAACTCAACATGATGTGTCAGGATCTAGCCACCAAGGAGCAGATTGGTGA
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

372

Amino Acids

41.9

Weight (kDa)

6.95

Isoelectric Point (pI)

41.31

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 22 - 65 1.3e-14 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 51 - 220 5.1e-15 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)
AciI CCGC 1 cut(s) 204
AclI AACGTT 1 cut(s) 76
AclWI GGATC 2 cut(s) 147, 1099
AcsI RAATTY 3 cut(s) 259, 959, 1037
AcuI CTGAAG 2 cut(s) 708, 1032
AfaI GTAC 1 cut(s) 766
AfiI CCNNNNNNNGG 1 cut(s) 740
AflIII ACRYGT 1 cut(s) 447
AgsI TTSAA 7 cut(s) 63, 106, 185, 374, 380, 632, 982
AjnI CCWGG 2 cut(s) 781, 857
Alw26I GTCTC 3 cut(s) 378, 635, 789
AlwI GGATC 2 cut(s) 147, 1099
AlwNI CAGNNNCTG 2 cut(s) 618, 804
AoxI GGCC 2 cut(s) 473, 510
ApeKI GCWGC 4 cut(s) 491, 573, 944, 965
ApoI RAATTY 3 cut(s) 259, 959, 1037
Asp700I GAANNNNTTC 1 cut(s) 567
AspS9I GGNCC 2 cut(s) 510, 551
AsuHPI GGTGA 2 cut(s) 188, 382
AvaII GGWCC 1 cut(s) 551
BarI GAAGNNNNNNTAC 2 cut(s) 719, 751
BbsI GAAGAC 3 cut(s) 297, 672, 1020
BbvI GCAGC 4 cut(s) 503, 585, 931, 977
BccI CCATC 2 cut(s) 280, 1058
BciT130I CCWGG 2 cut(s) 783, 859
BciVI GTATCC 1 cut(s) 801
BclI TGATCA 2 cut(s) 709, 775
BcoDI GTCTC 3 cut(s) 378, 635, 789
BfaI CTAG 5 cut(s) 239, 539, 693, 1052, 1095
BfmI CTRYAG 1 cut(s) 469
BfuI GTATCC 1 cut(s) 801
BglII AGATCT 1 cut(s) 565
BisI GCNGC 4 cut(s) 492, 574, 945, 966
BlpI GCTNAGC 1 cut(s) 224
BlsI GCNGC 4 cut(s) 493, 575, 946, 967
Bme1390I CCNGG 2 cut(s) 783, 859
Bme18I GGWCC 1 cut(s) 551
BmgT120I GGNCC 2 cut(s) 510, 551
BmiI GGNNCC 2 cut(s) 254, 270
BmrFI CCNGG 2 cut(s) 783, 859
BmsI GCATC 2 cut(s) 478, 624
BpiI GAAGAC 3 cut(s) 297, 672, 1020
Bpu1102I GCTNAGC 1 cut(s) 224
BpuEI CTTGAG 1 cut(s) 383
BsaJI CCNNGG 1 cut(s) 1102
Bsc4I CCNNNNNNNGG 1 cut(s) 740
Bse1I ACTGG 1 cut(s) 543
BseBI CCWGG 2 cut(s) 783, 859
BseDI CCNNGG 1 cut(s) 1102
BseGI GGATG 2 cut(s) 778, 814
BseLI CCNNNNNNNGG 1 cut(s) 740
BseMII CTCAG 7 cut(s) 238, 291, 323, 546, 714, 805, 903
BseNI ACTGG 1 cut(s) 543
BseRI GAGGAG 1 cut(s) 24
BseXI GCAGC 4 cut(s) 503, 585, 931, 977
BsgI GTGCAG 1 cut(s) 930
BshFI GGCC 2 cut(s) 475, 512
BslI CCNNNNNNNGG 1 cut(s) 740
BsmAI GTCTC 3 cut(s) 378, 635, 789
BsnI GGCC 2 cut(s) 475, 512
Bsp143I GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
Bsp1720I GCTNAGC 1 cut(s) 224
BspACI CCGC 1 cut(s) 204
BspANI GGCC 2 cut(s) 475, 512
BspCNI CTCAG 7 cut(s) 237, 292, 322, 547, 715, 804, 904
BspHI TCATGA 2 cut(s) 585, 657
BspLI GGNNCC 2 cut(s) 254, 270
BspPI GGATC 2 cut(s) 147, 1099
BsrI ACTGG 1 cut(s) 543
BssECI CCNNGG 1 cut(s) 1102
BssMI GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
BssT1I CCWWGG 1 cut(s) 1102
Bst2UI CCWGG 2 cut(s) 783, 859
Bst4CI ACNGT 2 cut(s) 764, 773
Bst6I CTCTTC 1 cut(s) 633
BstC8I GCNNGC 2 cut(s) 720, 846
BstDEI CTNAG 7 cut(s) 224, 300, 309, 555, 723, 791, 912
BstENI CCTNNNNNAGG 1 cut(s) 738
BstF5I GGATG 2 cut(s) 778, 814
BstKTI GATC 9 cut(s) 132, 155, 235, 288, 568, 712, 757, 778, 1094
BstMAI GTCTC 3 cut(s) 378, 635, 789
BstMBI GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
BstMWI GCNNNNNNNGC 1 cut(s) 941
BstNI CCWGG 2 cut(s) 783, 859
BstNSI RCATGY 1 cut(s) 451
BstSCI CCNGG 2 cut(s) 781, 857
BstSFI CTRYAG 1 cut(s) 469
BstV1I GCAGC 4 cut(s) 503, 585, 931, 977
BstV2I GAAGAC 3 cut(s) 297, 672, 1020
BstX2I RGATCY 3 cut(s) 152, 565, 1091
BstYI RGATCY 3 cut(s) 152, 565, 1091
BsuI GTATCC 1 cut(s) 801
BsuRI GGCC 2 cut(s) 475, 512
BtsCI GGATG 2 cut(s) 778, 814
BtsI GCAGTG 1 cut(s) 930
BtsIMutI CAGTG 3 cut(s) 760, 930, 947
Cac8I GCNNGC 2 cut(s) 720, 846
CaiI CAGNNNCTG 2 cut(s) 618, 804
CciI TCATGA 2 cut(s) 585, 657
Cfr13I GGNCC 2 cut(s) 510, 551
CsiI ACCWGGT 1 cut(s) 857
Csp6I GTAC 1 cut(s) 765
CspCI CAANNNNNGTGG 2 cut(s) 879, 914
CviQI GTAC 1 cut(s) 765
DdeI CTNAG 7 cut(s) 224, 300, 309, 555, 723, 791, 912
DpnI GATC 9 cut(s) 131, 154, 234, 287, 567, 711, 756, 777, 1093
DpnII GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
Eam1104I CTCTTC 1 cut(s) 633
EarI CTCTTC 1 cut(s) 633
Eco130I CCWWGG 1 cut(s) 1102
Eco147I AGGCCT 1 cut(s) 475
Eco47I GGWCC 1 cut(s) 551
Eco57I CTGAAG 2 cut(s) 708, 1032
EcoNI CCTNNNNNAGG 1 cut(s) 738
EcoO109I RGGNCCY 1 cut(s) 551
EcoRII CCWGG 2 cut(s) 781, 857
EcoT14I CCWWGG 1 cut(s) 1102
ErhI CCWWGG 1 cut(s) 1102
FbaI TGATCA 2 cut(s) 709, 775
Fnu4HI GCNGC 4 cut(s) 492, 574, 945, 966
FokI GGATG 2 cut(s) 765, 801
Fsp4HI GCNGC 4 cut(s) 492, 574, 945, 966
FspBI CTAG 5 cut(s) 239, 539, 693, 1052, 1095
GluI GCNGC 4 cut(s) 492, 574, 945, 966
HaeIII GGCC 2 cut(s) 475, 512
HindIII AAGCTT 1 cut(s) 158
HinfI GANTC 5 cut(s) 59, 302, 589, 643, 1016
HphI GGTGA 2 cut(s) 188, 382
Hpy166II GTNNAC 1 cut(s) 746
Hpy188I TCNGA 4 cut(s) 301, 648, 688, 794
Hpy188III TCNNGA 7 cut(s) 6, 123, 586, 593, 658, 818, 1089
Hpy8I GTNNAC 1 cut(s) 746
HpyCH4III ACNGT 2 cut(s) 764, 773
HpyCH4IV ACGT 2 cut(s) 76, 634
HpyCH4V TGCA 5 cut(s) 491, 704, 935, 947, 965
HpyF10VI GCNNNNNNNGC 1 cut(s) 941
HpyF3I CTNAG 7 cut(s) 224, 300, 309, 555, 723, 791, 912
HpySE526I ACGT 2 cut(s) 76, 634
Ksp22I TGATCA 2 cut(s) 709, 775
Kzo9I GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
LmnI GCTCC 6 cut(s) 23, 258, 268, 407, 540, 1106
Lsp1109I GCAGC 4 cut(s) 503, 585, 931, 977
LweI GCATC 2 cut(s) 478, 624
MabI ACCWGGT 1 cut(s) 857
MaeI CTAG 5 cut(s) 239, 539, 693, 1052, 1095
MaeII ACGT 2 cut(s) 76, 634
MaeIII GTNAC 3 cut(s) 176, 881, 1006
MalI GATC 9 cut(s) 131, 154, 234, 287, 567, 711, 756, 777, 1093
MboI GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
MflI RGATCY 3 cut(s) 152, 565, 1091
MluCI AATT 5 cut(s) 259, 355, 959, 977, 1037
MlyI GAGTC 4 cut(s) 311, 583, 637, 1010
MnlI CCTC 9 cut(s) 43, 207, 424, 451, 486, 734, 907, 994, 1051
MroXI GAANNNNTTC 1 cut(s) 567
MseI TTAA 2 cut(s) 291, 671
MslI CAYNNNNRTG 1 cut(s) 584
MspA1I CMGCKG 3 cut(s) 206, 722, 944
MspR9I CCNGG 2 cut(s) 783, 859
MvaI CCWGG 2 cut(s) 783, 859
MwoI GCNNNNNNNGC 1 cut(s) 941
NdeII GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
NlaIV GGNNCC 2 cut(s) 254, 270
NmuCI GTSAC 2 cut(s) 176, 881
NspI RCATGY 1 cut(s) 451
PagI TCATGA 2 cut(s) 585, 657
PceI AGGCCT 1 cut(s) 475
PciI ACATGT 1 cut(s) 447
PdmI GAANNNNTTC 1 cut(s) 567
PfeI GAWTC 1 cut(s) 59
PfoI TCCNGGA 1 cut(s) 781
PkrI GCNGC 4 cut(s) 493, 575, 946, 967
PleI GAGTC 4 cut(s) 310, 583, 637, 1010
PpsI GAGTC 4 cut(s) 310, 583, 637, 1010
PpuMI RGGWCCY 1 cut(s) 551
PscI ACATGT 1 cut(s) 447
Psp1406I AACGTT 1 cut(s) 76
Psp5II RGGWCCY 1 cut(s) 551
Psp6I CCWGG 2 cut(s) 781, 857
PspGI CCWGG 2 cut(s) 781, 857
PspN4I GGNNCC 2 cut(s) 254, 270
PspPI GGNCC 2 cut(s) 510, 551
PspPPI RGGWCCY 1 cut(s) 551
PstNI CAGNNNCTG 2 cut(s) 618, 804
PsuI RGATCY 3 cut(s) 152, 565, 1091
PvuII CAGCTG 2 cut(s) 722, 944
RsaI GTAC 1 cut(s) 766
RsaNI GTAC 1 cut(s) 765
RseI CAYNNNNRTG 1 cut(s) 584
SaqAI TTAA 2 cut(s) 291, 671
SatI GCNGC 4 cut(s) 492, 574, 945, 966
Sau3AI GATC 9 cut(s) 129, 152, 232, 285, 565, 709, 754, 775, 1091
Sau96I GGNCC 2 cut(s) 510, 551
SchI GAGTC 4 cut(s) 311, 583, 637, 1010
ScrFI CCNGG 2 cut(s) 783, 859
SexAI ACCWGGT 1 cut(s) 857
SfaNI GCATC 2 cut(s) 478, 624
SfcI CTRYAG 1 cut(s) 469
SinI GGWCC 1 cut(s) 551
SmiMI CAYNNNNRTG 1 cut(s) 584
SmlI CTYRAG 1 cut(s) 398
SmoI CTYRAG 1 cut(s) 398
Sse9I AATT 5 cut(s) 259, 355, 959, 977, 1037
SseBI AGGCCT 1 cut(s) 475
SsiI CCGC 1 cut(s) 204
SspMI CTAG 5 cut(s) 239, 539, 693, 1052, 1095
StuI AGGCCT 1 cut(s) 475
StyD4I CCNGG 2 cut(s) 781, 857
StyI CCWWGG 1 cut(s) 1102
TaaI ACNGT 2 cut(s) 764, 773
TaiI ACGT 2 cut(s) 79, 637
TasI AATT 5 cut(s) 259, 355, 959, 977, 1037
TatI WGTACW 1 cut(s) 764
TfiI GAWTC 1 cut(s) 59
Tru1I TTAA 2 cut(s) 291, 671
Tru9I TTAA 2 cut(s) 291, 671
TscAI CASTG 3 cut(s) 767, 937, 954
TseFI GTSAC 2 cut(s) 176, 881
TseI GCWGC 4 cut(s) 491, 573, 944, 965
Tsp45I GTSAC 2 cut(s) 176, 881
TspDTI ATGAA 8 cut(s) 228, 413, 455, 576, 674, 678, 972, 1008
TspRI CASTG 3 cut(s) 767, 937, 954
VpaK11BI GGWCC 1 cut(s) 551
XagI CCTNNNNNAGG 1 cut(s) 738
XapI RAATTY 3 cut(s) 259, 959, 1037
XceI RCATGY 1 cut(s) 451
XmnI GAANNNNTTC 1 cut(s) 567
XspI CTAG 5 cut(s) 239, 539, 693, 1052, 1095
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.