Rroxscaffold_3G00224890

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000562
Physical Location & Seq
Reverse (-)
8141451 .. 8143462
2012 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00224890.1

Sequence Viewer

Length: 1152 bp
ATGACTGAGGCTTTATCTACTCTTGATACTGAGACTGTCTCCGTGGTTGAGGGGAATCCTAACCAAAGATTGTGTTTAGTTGTGCTAAATGAATTTAACTATTTGCCATGGTCTCGTGCTGTTACCTTGGCTCTAGGAGGAAGATCAAAGCTGAGCTTCATAAATGGAAGCTTGGAAGCTCCTGATATCACCTCACCTACTTATGAAGCTTGGTTGTGTAAAGACCAGCTTGTAATGTCTTGGTTGCTCAATTCAATGGAACCTAAACTCTCTGAGTTGTTCAGTTACTCGGAGTCATCCTATCATCTCTGGAGGTCAGTGTATGACATGTATGGCAACCAGAATAATGCGGCTCGTGTGTTTCAGTTGAAGAAAGAAATTGCAGGTCTGCAACAAGGGGACAAAACATTTGTCCAGCATCTGGGAAGCCTGAAGTCCATGTGGAATGAACTCAACCTGTACAAGCCACACACTACAGATGCTACAACTCTTCTGAAGAGGGCTTACGAAGATAAGGTATTTCAGCTACTTGCAAGCCTTGGGTCTAAGTATGAACACTTGAGGAGTCATCTCTTAATGAACTCTGAACTTCCTTCATTCTCAAGTGTGTGCAATACTATCCAGTGTGAAGAGATACGCAGGAAAGTGATGCAGGTGGAGACCAAACCCAGCAGCTCTGAAGCTAGAGCTTTTGCAGTGAATCAAAGGTACTCTGGAGATAAGGGTTACAAAGGAAAACGACCTGACTGGAAGTGTTCTTACTGCCAAGGTCTAGGCCATTTAAGAGAAAAGTGTTGGATTTTGCATCCAGAGCTAAAACCCAAGTTTGATAAGGATTACAAGGCCTCTTCTAGAGACAACAAGGGTTCACAGAGAGTTGCTATTATTTCTGATCACAAGCACAAGGCCAATCTAGCAAAATCTTCCTCAGCAGAAACAAGCAGATCTATTGATTTCTCGTCTAATCCTATTGCCTTACTTAATGAGTTTGCAGTATATTTGCAAAAAAGGAAGGGTAACTCTGAGAGTGAGATGCTCACTGATGGAAACTCTACTGCTTTGCTTGGTAAATTTGCAGGCTTTTTAGCCGATTCAGATTGTGTCAAGAGTGAAGACATACCAGGACCGAACTACCAAGAAGATGATTGGTGA
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
RVT_2 Retrotran_gag_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve

Protein Analysis

383

Amino Acids

43.31

Weight (kDa)

7.57

Isoelectric Point (pI)

39.99

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 24 - 62 2.1e-12 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 53 - 216 9.6e-13 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)
AarI CACCTGC 1 cut(s) 643
Acc36I ACCTGC 2 cut(s) 374, 643
AccB7I CCANNNNNTGG 1 cut(s) 421
AciI CCGC 1 cut(s) 350
AcsI RAATTY 2 cut(s) 92, 1070
AcuI CTGAAG 3 cut(s) 452, 515, 699
AfaI GTAC 2 cut(s) 461, 710
AfiI CCNNNNNNNGG 1 cut(s) 421
AflIII ACRYGT 1 cut(s) 327
AgsI TTSAA 2 cut(s) 255, 370
AjnI CCWGG 1 cut(s) 1120
Alw26I GTCTC 5 cut(s) 26, 43, 117, 653, 849
AlwNI CAGNNNCTG 1 cut(s) 421
AoxI GGCC 3 cut(s) 775, 843, 906
ApeKI GCWGC 1 cut(s) 672
ApoI RAATTY 2 cut(s) 92, 1070
ArsI GACNNNNNNTTYG 4 cut(s) 392, 396, 424, 428
AspS9I GGNCC 1 cut(s) 1124
AsuHPI GGTGA 2 cut(s) 181, 186
AvaII GGWCC 1 cut(s) 1124
BarI GAAGNNNNNNTAC 4 cut(s) 488, 520, 743, 775
BauI CACGAG 2 cut(s) 114, 354
BbsI GAAGAC 1 cut(s) 1119
BbvCI CCTCAGC 1 cut(s) 928
BbvI GCAGC 1 cut(s) 684
BccI CCATC 1 cut(s) 1037
BciT130I CCWGG 1 cut(s) 1122
BclI TGATCA 1 cut(s) 892
BcoDI GTCTC 5 cut(s) 26, 43, 117, 653, 849
BfaI CTAG 5 cut(s) 134, 684, 773, 852, 914
BfmI CTRYAG 1 cut(s) 474
BfuAI ACCTGC 2 cut(s) 374, 643
BglII AGATCT 1 cut(s) 944
BisI GCNGC 2 cut(s) 351, 673
BlpI GCTNAGC 1 cut(s) 152
BlsI GCNGC 2 cut(s) 352, 674
Bme1390I CCNGG 1 cut(s) 1122
Bme18I GGWCC 1 cut(s) 1124
BmgT120I GGNCC 1 cut(s) 1124
BmiI GGNNCC 1 cut(s) 261
BmrFI CCNGG 1 cut(s) 1122
BmsI GCATC 5 cut(s) 427, 469, 639, 814, 1023
BpiI GAAGAC 1 cut(s) 1119
BplI GAGNNNNNCTC 2 cut(s) 23, 55
BpmI CTGGAG 2 cut(s) 331, 735
Bpu10I CCTNAGC 1 cut(s) 928
Bpu1102I GCTNAGC 1 cut(s) 152
BpuEI CTTGAG 2 cut(s) 580, 586
BsaI GGTCTC 2 cut(s) 117, 653
BsaJI CCNNGG 5 cut(s) 42, 107, 126, 538, 766
Bsc4I CCNNNNNNNGG 1 cut(s) 421
Bse1I ACTGG 2 cut(s) 622, 752
BseBI CCWGG 1 cut(s) 1122
BseDI CCNNGG 5 cut(s) 42, 107, 126, 538, 766
BseGI GGATG 2 cut(s) 296, 805
BseLI CCNNNNNNNGG 1 cut(s) 421
BseMII CTCAG 5 cut(s) 21, 143, 264, 942, 1014
BseNI ACTGG 2 cut(s) 622, 752
BseRI GAGGAG 1 cut(s) 577
BseXI GCAGC 1 cut(s) 684
BseYI CCCAGC 1 cut(s) 668
BshFI GGCC 3 cut(s) 777, 845, 908
BslFI GGGAC 1 cut(s) 413
BslI CCNNNNNNNGG 1 cut(s) 421
BsmAI GTCTC 5 cut(s) 26, 43, 117, 653, 849
BsmFI GGGAC 1 cut(s) 413
BsnI GGCC 3 cut(s) 777, 845, 908
Bso31I GGTCTC 2 cut(s) 117, 653
Bsp1407I TGTACA 1 cut(s) 459
Bsp143I GATC 3 cut(s) 143, 892, 944
Bsp1720I GCTNAGC 1 cut(s) 152
Bsp19I CCATGG 1 cut(s) 107
BspACI CCGC 1 cut(s) 350
BspANI GGCC 3 cut(s) 777, 845, 908
BspCNI CTCAG 5 cut(s) 22, 144, 265, 941, 1015
BspLI GGNNCC 1 cut(s) 261
BspMI ACCTGC 2 cut(s) 374, 643
BspTNI GGTCTC 2 cut(s) 117, 653
BsrGI TGTACA 1 cut(s) 459
BsrI ACTGG 2 cut(s) 622, 752
BssECI CCNNGG 5 cut(s) 42, 107, 126, 538, 766
BssMI GATC 3 cut(s) 143, 892, 944
BssSI CACGAG 2 cut(s) 114, 354
BssT1I CCWWGG 4 cut(s) 107, 126, 538, 766
Bst2BI CACGAG 2 cut(s) 114, 354
Bst2UI CCWGG 1 cut(s) 1122
Bst4CI ACNGT 1 cut(s) 37
Bst6I CTCTTC 4 cut(s) 491, 495, 624, 853
BstAUI TGTACA 1 cut(s) 459
BstC8I GCNNGC 2 cut(s) 535, 1078
BstDEI CTNAG 7 cut(s) 6, 30, 152, 273, 546, 928, 1023
BstDSI CCRYGG 2 cut(s) 42, 107
BstF5I GGATG 2 cut(s) 296, 805
BstKTI GATC 3 cut(s) 146, 895, 947
BstMAI GTCTC 5 cut(s) 26, 43, 117, 653, 849
BstMBI GATC 3 cut(s) 143, 892, 944
BstMWI GCNNNNNNNGC 2 cut(s) 811, 914
BstNI CCWGG 1 cut(s) 1122
BstNSI RCATGY 1 cut(s) 331
BstSCI CCNGG 1 cut(s) 1120
BstSFI CTRYAG 1 cut(s) 474
BstV1I GCAGC 1 cut(s) 684
BstV2I GAAGAC 1 cut(s) 1119
BstX2I RGATCY 1 cut(s) 944
BstYI RGATCY 1 cut(s) 944
BsuRI GGCC 3 cut(s) 777, 845, 908
BtgI CCRYGG 2 cut(s) 42, 107
BtsCI GGATG 2 cut(s) 296, 805
BtsI GCAGTG 1 cut(s) 702
BtsIMutI CAGTG 4 cut(s) 324, 629, 702, 1038
BveI ACCTGC 2 cut(s) 374, 643
Cac8I GCNNGC 2 cut(s) 535, 1078
CaiI CAGNNNCTG 1 cut(s) 421
Cfr13I GGNCC 1 cut(s) 1124
Csp6I GTAC 2 cut(s) 460, 709
CviAII CATG 3 cut(s) 108, 328, 439
CviQI GTAC 2 cut(s) 460, 709
DdeI CTNAG 7 cut(s) 6, 30, 152, 273, 546, 928, 1023
DpnI GATC 3 cut(s) 145, 894, 946
DpnII GATC 3 cut(s) 143, 892, 944
Eam1104I CTCTTC 4 cut(s) 491, 495, 624, 853
EarI CTCTTC 4 cut(s) 491, 495, 624, 853
Eco130I CCWWGG 4 cut(s) 107, 126, 538, 766
Eco147I AGGCCT 1 cut(s) 845
Eco31I GGTCTC 2 cut(s) 117, 653
Eco32I GATATC 1 cut(s) 187
Eco47I GGWCC 1 cut(s) 1124
Eco57I CTGAAG 3 cut(s) 452, 515, 699
EcoRII CCWGG 1 cut(s) 1120
EcoRV GATATC 1 cut(s) 187
EcoT14I CCWWGG 4 cut(s) 107, 126, 538, 766
ErhI CCWWGG 4 cut(s) 107, 126, 538, 766
FaeI CATG 3 cut(s) 111, 331, 442
FalI AAGNNNNNCTT 4 cut(s) 140, 172, 213, 245
FaqI GGGAC 1 cut(s) 413
FatI CATG 3 cut(s) 107, 327, 438
FbaI TGATCA 1 cut(s) 892
Fnu4HI GCNGC 2 cut(s) 351, 673
FokI GGATG 2 cut(s) 283, 792
Fsp4HI GCNGC 2 cut(s) 351, 673
FspBI CTAG 5 cut(s) 134, 684, 773, 852, 914
GluI GCNGC 2 cut(s) 351, 673
GsaI CCCAGC 1 cut(s) 672
GsuI CTGGAG 2 cut(s) 331, 735
HaeIII GGCC 3 cut(s) 777, 845, 908
Hin1II CATG 3 cut(s) 111, 331, 442
HindIII AAGCTT 2 cut(s) 169, 207
HinfI GANTC 5 cut(s) 55, 293, 565, 700, 1091
HphI GGTGA 2 cut(s) 181, 186
Hpy166II GTNNAC 1 cut(s) 869
Hpy188I TCNGA 8 cut(s) 274, 292, 495, 586, 679, 892, 1024, 1096
Hpy188III TCNNGA 7 cut(s) 23, 182, 310, 714, 809, 852, 1105
Hpy8I GTNNAC 1 cut(s) 869
HpyAV CCTTC 2 cut(s) 603, 1006
HpyCH4III ACNGT 1 cut(s) 37
HpyF10VI GCNNNNNNNGC 2 cut(s) 811, 914
HpyF3I CTNAG 7 cut(s) 6, 30, 152, 273, 546, 928, 1023
Hsp92II CATG 3 cut(s) 111, 331, 442
Ksp22I TGATCA 1 cut(s) 892
Kzo9I GATC 3 cut(s) 143, 892, 944
LmnI GCTCC 1 cut(s) 184
Lsp1109I GCAGC 1 cut(s) 684
LweI GCATC 5 cut(s) 427, 469, 639, 814, 1023
MaeI CTAG 5 cut(s) 134, 684, 773, 852, 914
MaeIII GTNAC 4 cut(s) 121, 284, 725, 1016
MalI GATC 3 cut(s) 145, 894, 946
MboI GATC 3 cut(s) 143, 892, 944
MflI RGATCY 1 cut(s) 944
MluCI AATT 4 cut(s) 92, 250, 378, 1070
MlyI GAGTC 2 cut(s) 302, 574
MmeI TCCRAC 1 cut(s) 776
MnlI CCTC 8 cut(s) 43, 131, 202, 306, 492, 555, 856, 937
MseI TTAA 4 cut(s) 96, 575, 782, 981
MspR9I CCNGG 1 cut(s) 1122
MvaI CCWGG 1 cut(s) 1122
MwoI GCNNNNNNNGC 2 cut(s) 811, 914
NcoI CCATGG 1 cut(s) 107
NdeII GATC 3 cut(s) 143, 892, 944
NlaIII CATG 3 cut(s) 111, 331, 442
NlaIV GGNNCC 1 cut(s) 261
NspI RCATGY 1 cut(s) 331
PaqCI CACCTGC 1 cut(s) 643
PceI AGGCCT 1 cut(s) 845
PciI ACATGT 1 cut(s) 327
PfeI GAWTC 3 cut(s) 55, 700, 1091
PflMI CCANNNNNTGG 1 cut(s) 421
PkrI GCNGC 2 cut(s) 352, 674
PleI GAGTC 2 cut(s) 301, 573
PpsI GAGTC 2 cut(s) 301, 573
PscI ACATGT 1 cut(s) 327
Psp6I CCWGG 1 cut(s) 1120
PspFI CCCAGC 1 cut(s) 668
PspGI CCWGG 1 cut(s) 1120
PspN4I GGNNCC 1 cut(s) 261
PspPI GGNCC 1 cut(s) 1124
PstNI CAGNNNCTG 1 cut(s) 421
PsuI RGATCY 1 cut(s) 944
RsaI GTAC 2 cut(s) 461, 710
RsaNI GTAC 2 cut(s) 460, 709
SaqAI TTAA 4 cut(s) 96, 575, 782, 981
SatI GCNGC 2 cut(s) 351, 673
Sau3AI GATC 3 cut(s) 143, 892, 944
Sau96I GGNCC 1 cut(s) 1124
SchI GAGTC 2 cut(s) 302, 574
ScrFI CCNGG 1 cut(s) 1122
SfaNI GCATC 5 cut(s) 427, 469, 639, 814, 1023
SfcI CTRYAG 1 cut(s) 474
SinI GGWCC 1 cut(s) 1124
SmlI CTYRAG 2 cut(s) 559, 601
SmoI CTYRAG 2 cut(s) 559, 601
Sse9I AATT 4 cut(s) 92, 250, 378, 1070
SseBI AGGCCT 1 cut(s) 845
SsiI CCGC 1 cut(s) 350
SspMI CTAG 5 cut(s) 134, 684, 773, 852, 914
StuI AGGCCT 1 cut(s) 845
StyD4I CCNGG 1 cut(s) 1120
StyI CCWWGG 4 cut(s) 107, 126, 538, 766
TaaI ACNGT 1 cut(s) 37
TaqII GACCGA 1 cut(s) 1141
TasI AATT 4 cut(s) 92, 250, 378, 1070
TatI WGTACW 1 cut(s) 459
TauI GCSGC 1 cut(s) 353
TfiI GAWTC 3 cut(s) 55, 700, 1091
Tru1I TTAA 4 cut(s) 96, 575, 782, 981
Tru9I TTAA 4 cut(s) 96, 575, 782, 981
TscAI CASTG 4 cut(s) 324, 629, 702, 1045
TseI GCWGC 1 cut(s) 672
TspDTI ATGAA 7 cut(s) 105, 148, 219, 462, 567, 585, 593
TspGWI ACGGA 1 cut(s) 31
TspRI CASTG 4 cut(s) 324, 629, 702, 1045
Van91I CCANNNNNTGG 1 cut(s) 421
VpaK11BI GGWCC 1 cut(s) 1124
XapI RAATTY 2 cut(s) 92, 1070
XbaI TCTAGA 1 cut(s) 851
XceI RCATGY 1 cut(s) 331
XspI CTAG 5 cut(s) 134, 684, 773, 852, 914
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.