RchiOBHm_Chr3g0481941

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0009688
Physical Location & Seq
Forward (+)
28048194 .. 28049862
1669 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ44685

Sequence Viewer

Length: 981 bp
ATGGTAGTCCTTTTATATGTGGATGATATGATAGTAACCGGAAGTGATGAAGGTGAGATTGCAAAGCTAAGGGCAGAATTATCTACTCGGTTCGATATGAAGATTTTGGGTGAGCTAAGCCATTTTCTTGGTTTAGAAGTGAAAAATATGAAGGATGGTGTTCTGTTATCACAAGAAGGTTATGCTAAGAAGTTGGTTGAGAAATATGGCCTGAAACTTAGCAAGAGACGATCTACTCCACTTGACATAAGTGAGAAATTAAGGCGAGATGTAGGATCTCTCTTGCCAGATCCTAAGTCTTATCGTTCTCTTGTTGGTGGTCTTCTTTATTTGACAATCACAAGGCCAGACATTGCCTTTTCAGTTGGGCTCATAAGCCGATACTTGCAAGAGCCTCGGAAGCCACATCTAGAAGCAGCAAAGAAGATTCTCAAGTATGTTAATTGTACTCTTGATCTGGGTCTCTTTTACAAAAGAGGTGGTGGTTTCTTGTTAAATGGCTATACAGATGCTGATTTTGGTGGAGATTTAGACAAAAGAAGATCCACTTCTGGTTATGTCTTTCTGTGCAACAATACAAGTGTTTCTTGGTGCAGCAAGAAACAAGATGCAGTGGTTTTATCTACAACTGAAGCAGAGTACAAGGCTGCTACACTTGCTGCACAGGAGTGTGTTTGGCTTCGAAGACTTATTACGGATGTTTATCATCAAATTCATAAGGCTACTGATCTGTTTGGTGATAATCAGAGTGCCATCAAGCTTGCTTATAATCCAGTGTGCCATGCTAGAACTAAACACATTGAGATTGAGCATCATTTTATTCGAGAGAAGGTTCTTGATGGAACAATTGACAACAAGGAGGTGAGAAGTGATCTTAATGTTGCAGATATCTTTACAAAGACTCTCTCCAAAGGTCCATTCGAGTTTCTTCGTGCAAGGCTGGGGCTGATCTCCAAAAACAACTTTAAGGGGGAGTGTTGA
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
DUF4219 RVT_2 Retrotran_gag_2 Retrotran_gag_3 gag_pre-integrs rve zf-CCHC

Protein Analysis

326

Amino Acids

36.73

Weight (kDa)

9.02

Isoelectric Point (pI)

41.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 1 - 81 4.9e-16 Reverse transcriptase (RNA-dependent DNA polymerase)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 768
AclWI GGATC 3 cut(s) 283, 284, 537
AcsI RAATTY 1 cut(s) 711
AcuI CTGAAG 1 cut(s) 651
AfaI GTAC 2 cut(s) 448, 641
AjuI GAANNNNNNNTTGG 2 cut(s) 902, 934
AleI CACNNNNGTG 1 cut(s) 667
AluBI AGCT 3 cut(s) 67, 115, 760
AluI AGCT 3 cut(s) 67, 115, 760
Alw26I GTCTC 2 cut(s) 220, 467
AlwI GGATC 3 cut(s) 283, 284, 537
AlwNI CAGNNNCTG 1 cut(s) 512
AoxI GGCC 2 cut(s) 208, 344
ApeKI GCWGC 4 cut(s) 416, 594, 647, 659
ApoI RAATTY 1 cut(s) 711
AspS9I GGNCC 1 cut(s) 914
AsuHPI GGTGA 4 cut(s) 65, 122, 749, 874
AsuII TTCGAA 1 cut(s) 682
AvaII GGWCC 1 cut(s) 914
BanII GRGCYC 1 cut(s) 372
BarI GAAGNNNNNNTAC 2 cut(s) 676, 708
BbsI GAAGAC 2 cut(s) 314, 691
BbvI GCAGC 4 cut(s) 428, 606, 634, 646
BccI CCATC 3 cut(s) 149, 761, 833
BcgI CGANNNNNNTGC 2 cut(s) 377, 411
BcoDI GTCTC 2 cut(s) 220, 467
BfaI CTAG 2 cut(s) 410, 786
BisI GCNGC 4 cut(s) 417, 595, 648, 660
BlpI GCTNAGC 1 cut(s) 116
BlsI GCNGC 4 cut(s) 418, 596, 649, 661
Bme18I GGWCC 1 cut(s) 914
BmgT120I GGNCC 1 cut(s) 914
BmsI GCATC 3 cut(s) 499, 598, 820
BpiI GAAGAC 2 cut(s) 314, 691
Bpu10I CCTNAGC 1 cut(s) 68
Bpu1102I GCTNAGC 1 cut(s) 116
Bpu14I TTCGAA 1 cut(s) 682
BpuEI CTTGAG 1 cut(s) 416
BsaBI GATNNNNATC 1 cut(s) 702
BsaI GGTCTC 1 cut(s) 467
BsaJI CCNNGG 1 cut(s) 395
BsaWI WCCGGW 1 cut(s) 38
Bse1I ACTGG 1 cut(s) 773
Bse3DI GCAATG 1 cut(s) 351
Bse8I GATNNNNATC 1 cut(s) 702
BseDI CCNNGG 1 cut(s) 395
BseGI GGATG 3 cut(s) 28, 160, 703
BseJI GATNNNNATC 1 cut(s) 702
BseMI GCAATG 1 cut(s) 351
BseNI ACTGG 1 cut(s) 773
BseXI GCAGC 4 cut(s) 428, 606, 634, 646
BseYI CCCAGC 1 cut(s) 940
BsgI GTGCAG 2 cut(s) 613, 645
BshFI GGCC 2 cut(s) 210, 346
BsiSI CCGG 1 cut(s) 39
BsmAI GTCTC 2 cut(s) 220, 467
BsmBI CGTCTC 1 cut(s) 220
BsnI GGCC 2 cut(s) 210, 346
Bso31I GGTCTC 1 cut(s) 467
Bsp119I TTCGAA 1 cut(s) 682
Bsp1286I GDGCHC 1 cut(s) 372
Bsp143I GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
Bsp1720I GCTNAGC 1 cut(s) 116
BspANI GGCC 2 cut(s) 210, 346
BspPI GGATC 3 cut(s) 283, 284, 537
BspT104I TTCGAA 1 cut(s) 682
BspTNI GGTCTC 1 cut(s) 467
BsrDI GCAATG 1 cut(s) 351
BsrI ACTGG 1 cut(s) 773
BssECI CCNNGG 1 cut(s) 395
BssMI GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
BstBI TTCGAA 1 cut(s) 682
BstC8I GCNNGC 1 cut(s) 762
BstDEI CTNAG 5 cut(s) 68, 116, 186, 218, 294
BstF5I GGATG 3 cut(s) 28, 160, 703
BstKTI GATC 8 cut(s) 233, 278, 292, 457, 545, 730, 874, 951
BstMAI GTCTC 2 cut(s) 220, 467
BstMBI GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
BstMWI GCNNNNNNNGC 2 cut(s) 400, 656
BstV1I GCAGC 4 cut(s) 428, 606, 634, 646
BstV2I GAAGAC 2 cut(s) 314, 691
BstX2I RGATCY 3 cut(s) 275, 289, 542
BstXI CCANNNNNNTGG 1 cut(s) 128
BstYI RGATCY 3 cut(s) 275, 289, 542
BsuRI GGCC 2 cut(s) 210, 346
BtsCI GGATG 3 cut(s) 28, 160, 703
BtsI GCAGTG 1 cut(s) 618
BtsIMutI CAGTG 2 cut(s) 618, 780
Cac8I GCNNGC 1 cut(s) 762
CaiI CAGNNNCTG 1 cut(s) 512
Cfr13I GGNCC 1 cut(s) 914
Csp6I GTAC 2 cut(s) 447, 640
CspCI CAANNNNNGTGG 2 cut(s) 460, 495
CviAII CATG 1 cut(s) 782
CviQI GTAC 2 cut(s) 447, 640
DdeI CTNAG 5 cut(s) 68, 116, 186, 218, 294
DpnI GATC 8 cut(s) 232, 277, 291, 456, 544, 729, 873, 950
DpnII GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
Eco24I GRGCYC 1 cut(s) 372
Eco31I GGTCTC 1 cut(s) 467
Eco32I GATATC 1 cut(s) 889
Eco47I GGWCC 1 cut(s) 914
Eco57I CTGAAG 1 cut(s) 651
EcoRV GATATC 1 cut(s) 889
EcoT38I GRGCYC 1 cut(s) 372
Esp3I CGTCTC 1 cut(s) 220
FaeI CATG 1 cut(s) 785
FalI AAGNNNNNCTT 4 cut(s) 532, 564, 571, 603
FatI CATG 1 cut(s) 781
Fnu4HI GCNGC 4 cut(s) 417, 595, 648, 660
FokI GGATG 3 cut(s) 35, 167, 710
FriOI GRGCYC 1 cut(s) 372
Fsp4HI GCNGC 4 cut(s) 417, 595, 648, 660
FspBI CTAG 2 cut(s) 410, 786
GluI GCNGC 4 cut(s) 417, 595, 648, 660
GsaI CCCAGC 1 cut(s) 944
HaeIII GGCC 2 cut(s) 210, 346
HapII CCGG 1 cut(s) 39
Hin1II CATG 1 cut(s) 785
HindIII AAGCTT 1 cut(s) 758
HinfI GANTC 2 cut(s) 427, 901
HpaII CCGG 1 cut(s) 39
HphI GGTGA 4 cut(s) 65, 122, 749, 874
Hpy188I TCNGA 2 cut(s) 399, 747
Hpy188III TCNNGA 4 cut(s) 410, 452, 824, 836
HpyAV CCTTC 4 cut(s) 44, 145, 170, 823
HpyCH4V TGCA 8 cut(s) 62, 388, 570, 594, 611, 662, 884, 935
HpyF10VI GCNNNNNNNGC 2 cut(s) 400, 656
HpyF3I CTNAG 5 cut(s) 68, 116, 186, 218, 294
Hsp92II CATG 1 cut(s) 785
Kzo9I GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
LpnPI CCDG 9 cut(s) 52, 224, 300, 360, 443, 537, 650, 786, 926
Lsp1109I GCAGC 4 cut(s) 428, 606, 634, 646
LweI GCATC 3 cut(s) 499, 598, 820
MaeI CTAG 2 cut(s) 410, 786
MaeIII GTNAC 1 cut(s) 34
MalI GATC 8 cut(s) 232, 277, 291, 456, 544, 729, 873, 950
MboI GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
MboII GAAGA 6 cut(s) 112, 314, 436, 552, 696, 920
MfeI CAATTG 1 cut(s) 846
MflI RGATCY 3 cut(s) 275, 289, 542
MhlI GDGCHC 1 cut(s) 372
MluCI AATT 5 cut(s) 77, 257, 442, 711, 846
MlyI GAGTC 1 cut(s) 895
MnlI CCTC 3 cut(s) 405, 470, 853
MseI TTAA 5 cut(s) 260, 441, 494, 876, 966
MslI CAYNNNNRTG 1 cut(s) 667
MspI CCGG 1 cut(s) 39
MunI CAATTG 1 cut(s) 846
MwoI GCNNNNNNNGC 2 cut(s) 400, 656
NdeII GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
NlaIII CATG 1 cut(s) 785
NspV TTCGAA 1 cut(s) 682
OliI CACNNNNGTG 1 cut(s) 667
PfeI GAWTC 1 cut(s) 427
PkrI GCNGC 4 cut(s) 418, 596, 649, 661
PleI GAGTC 1 cut(s) 895
PpsI GAGTC 1 cut(s) 895
PsiI TTATAA 1 cut(s) 768
PspFI CCCAGC 1 cut(s) 940
PspPI GGNCC 1 cut(s) 914
PstNI CAGNNNCTG 1 cut(s) 512
PsuI RGATCY 3 cut(s) 275, 289, 542
RsaI GTAC 2 cut(s) 448, 641
RsaNI GTAC 2 cut(s) 447, 640
RseI CAYNNNNRTG 1 cut(s) 667
SaqAI TTAA 5 cut(s) 260, 441, 494, 876, 966
SatI GCNGC 4 cut(s) 417, 595, 648, 660
Sau3AI GATC 8 cut(s) 230, 275, 289, 454, 542, 727, 871, 948
Sau96I GGNCC 1 cut(s) 914
SchI GAGTC 1 cut(s) 895
SduI GDGCHC 1 cut(s) 372
SetI ASST 9 cut(s) 55, 69, 117, 181, 481, 762, 834, 864, 916
SfaNI GCATC 3 cut(s) 499, 598, 820
SfuI TTCGAA 1 cut(s) 682
SinI GGWCC 1 cut(s) 914
SmiMI CAYNNNNRTG 1 cut(s) 667
SmlI CTYRAG 1 cut(s) 431
SmoI CTYRAG 1 cut(s) 431
Sse9I AATT 5 cut(s) 77, 257, 442, 711, 846
SspMI CTAG 2 cut(s) 410, 786
TaqI TCGA 4 cut(s) 93, 682, 823, 921
TasI AATT 5 cut(s) 77, 257, 442, 711, 846
TatI WGTACW 2 cut(s) 446, 639
TfiI GAWTC 1 cut(s) 427
Tru1I TTAA 5 cut(s) 260, 441, 494, 876, 966
Tru9I TTAA 5 cut(s) 260, 441, 494, 876, 966
TscAI CASTG 2 cut(s) 618, 780
TseI GCWGC 4 cut(s) 416, 594, 647, 659
TspDTI ATGAA 4 cut(s) 63, 113, 164, 704
TspGWI ACGGA 1 cut(s) 710
TspRI CASTG 2 cut(s) 618, 780
VpaK11BI GGWCC 1 cut(s) 914
XapI RAATTY 1 cut(s) 711
XbaI TCTAGA 1 cut(s) 409
XspI CTAG 2 cut(s) 410, 786
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.