Rroxscaffold_3G00238340

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000756
Physical Location & Seq
Reverse (-)
26487198 .. 26491048
3851 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00238340.1

Sequence Viewer

Length: 501 bp
ATGAGCAAGACAGCTTTTAGAACTCATAATGGTCACTATGAGTTTCTAGTCATGCCATTTGGACTAACAAATGCACCATCTACTTTTCAGTCCGTAATGAATGATGTGTTGCGAGATTATTTGAGGAAGTTTGCCCTAGTATTATTTGATGACATCTTAATTTACAGCTCTTCTTTACAAGCTCACTTGGAACATTTGGAGAAGATCTTCAAGAGATTACACGCTAATGCTTTGAAGATTAAAGAGAGTAAATGCAGTTTTGGAGTGTCACAAGTCGAATATTTAGGTCACATAATCAGCAAGGAGGGCGTGGCGATTGATCCAACAAAAATCGAGTGCATAAAAAGCGGAACAAACCTCAAACTCTCAAAGGGCTCGGGGGCCGGCTATTATAGAAAGTTTGTGAGGAATTTTGGCCTCATTGCCAAGCCACTCACTAATATGTTGAAGGTTGGTGAGTTTCAATGGACACAAGAATCGAAGTTGCTTTTGAAGCCTTGA
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
RVP_2 RVT_1 Retrotrans_gag rve

Protein Analysis

166

Amino Acids

18.83

Weight (kDa)

9.59

Isoelectric Point (pI)

30.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_1 PF00078 7 - 99 9.3e-24 Reverse transcriptase (RNA-dependent DNA polymerase)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 348
AclWI GGATC 1 cut(s) 314
AcsI RAATTY 1 cut(s) 409
AgsI TTSAA 5 cut(s) 211, 235, 448, 464, 493
AluBI AGCT 3 cut(s) 14, 168, 182
AluI AGCT 3 cut(s) 14, 168, 182
AlwI GGATC 1 cut(s) 314
Ama87I CYCGRG 1 cut(s) 376
AoxI GGCC 2 cut(s) 381, 415
ApoI RAATTY 1 cut(s) 409
Asp700I GAANNNNTTC 1 cut(s) 206
AspS9I GGNCC 1 cut(s) 381
AsuHPI GGTGA 1 cut(s) 467
AvaI CYCGRG 1 cut(s) 376
BanII GRGCYC 1 cut(s) 377
BccI CCATC 1 cut(s) 85
BfaI CTAG 2 cut(s) 47, 137
BglII AGATCT 1 cut(s) 204
BmeT110I CYCGRG 1 cut(s) 376
BmgT120I GGNCC 1 cut(s) 381
BmiI GGNNCC 1 cut(s) 382
Bse118I RCCGGY 1 cut(s) 383
Bse3DI GCAATG 1 cut(s) 420
BseMI GCAATG 1 cut(s) 420
BshFI GGCC 2 cut(s) 383, 417
BsiHKCI CYCGRG 1 cut(s) 376
BsiSI CCGG 1 cut(s) 384
BsnI GGCC 2 cut(s) 383, 417
BsoBI CYCGRG 1 cut(s) 376
Bsp1286I GDGCHC 1 cut(s) 377
Bsp143I GATC 2 cut(s) 204, 319
BspACI CCGC 1 cut(s) 348
BspANI GGCC 2 cut(s) 383, 417
BspLI GGNNCC 1 cut(s) 382
BspPI GGATC 1 cut(s) 314
BspQI GCTCTTC 1 cut(s) 175
BsrDI GCAATG 1 cut(s) 420
BsrFI RCCGGY 1 cut(s) 383
BssAI RCCGGY 1 cut(s) 383
BssMI GATC 2 cut(s) 204, 319
Bst6I CTCTTC 1 cut(s) 175
BstC8I GCNNGC 1 cut(s) 385
BstKTI GATC 2 cut(s) 207, 322
BstMBI GATC 2 cut(s) 204, 319
BstMWI GCNNNNNNNGC 3 cut(s) 306, 345, 493
BstX2I RGATCY 1 cut(s) 204
BstYI RGATCY 1 cut(s) 204
BsuRI GGCC 2 cut(s) 383, 417
Cac8I GCNNGC 1 cut(s) 385
Cfr10I RCCGGY 1 cut(s) 383
Cfr13I GGNCC 1 cut(s) 381
CviAII CATG 1 cut(s) 52
CviJI RGCY 9 cut(s) 14, 168, 182, 375, 383, 387, 417, 430, 496
CviKI_1 RGCY 9 cut(s) 14, 168, 182, 375, 383, 387, 417, 430, 496
DpnI GATC 2 cut(s) 206, 321
DpnII GATC 2 cut(s) 204, 319
Eam1104I CTCTTC 1 cut(s) 175
EarI CTCTTC 1 cut(s) 175
Eco24I GRGCYC 1 cut(s) 377
Eco88I CYCGRG 1 cut(s) 376
EcoT38I GRGCYC 1 cut(s) 377
FaeI CATG 1 cut(s) 55
FaiI YATR 7 cut(s) 27, 39, 53, 293, 341, 393, 443
FatI CATG 1 cut(s) 51
FriOI GRGCYC 1 cut(s) 377
FspBI CTAG 2 cut(s) 47, 137
HaeIII GGCC 2 cut(s) 383, 417
HapII CCGG 1 cut(s) 384
Hin1II CATG 1 cut(s) 55
HinfI GANTC 1 cut(s) 476
HpaII CCGG 1 cut(s) 384
HphI GGTGA 1 cut(s) 467
Hpy188III TCNNGA 1 cut(s) 211
HpyAV CCTTC 1 cut(s) 442
HpyCH4V TGCA 3 cut(s) 74, 255, 339
HpyF10VI GCNNNNNNNGC 3 cut(s) 306, 345, 493
Hsp92II CATG 1 cut(s) 55
KroI GCCGGC 1 cut(s) 383
KroNI GCCGGC 1 cut(s) 385
Kzo9I GATC 2 cut(s) 204, 319
LguI GCTCTTC 1 cut(s) 175
LpnPI CCDG 1 cut(s) 397
MaeI CTAG 2 cut(s) 47, 137
MaeIII GTNAC 3 cut(s) 32, 267, 287
MalI GATC 2 cut(s) 206, 321
MboI GATC 2 cut(s) 204, 319
MboII GAAGA 4 cut(s) 162, 199, 214, 247
MflI RGATCY 1 cut(s) 204
MhlI GDGCHC 1 cut(s) 377
MluCI AATT 2 cut(s) 159, 409
MmeI TCCRAC 1 cut(s) 347
MnlI CCTC 5 cut(s) 117, 298, 368, 399, 428
MroNI GCCGGC 1 cut(s) 383
MroXI GAANNNNTTC 1 cut(s) 206
MseI TTAA 2 cut(s) 158, 240
MslI CAYNNNNRTG 2 cut(s) 225, 440
MspI CCGG 1 cut(s) 384
MwoI GCNNNNNNNGC 3 cut(s) 306, 345, 493
NaeI GCCGGC 1 cut(s) 385
NdeII GATC 2 cut(s) 204, 319
NgoMIV GCCGGC 1 cut(s) 383
NlaIII CATG 1 cut(s) 55
NlaIV GGNNCC 1 cut(s) 382
NmuCI GTSAC 3 cut(s) 32, 267, 287
PciSI GCTCTTC 1 cut(s) 175
PdiI GCCGGC 1 cut(s) 385
PdmI GAANNNNTTC 1 cut(s) 206
PfeI GAWTC 1 cut(s) 476
PspN4I GGNNCC 1 cut(s) 382
PspPI GGNCC 1 cut(s) 381
PsuI RGATCY 1 cut(s) 204
RseI CAYNNNNRTG 2 cut(s) 225, 440
SapI GCTCTTC 1 cut(s) 175
SaqAI TTAA 2 cut(s) 158, 240
Sau3AI GATC 2 cut(s) 204, 319
Sau96I GGNCC 1 cut(s) 381
SduI GDGCHC 1 cut(s) 377
SetI ASST 6 cut(s) 16, 170, 184, 289, 360, 453
SmiMI CAYNNNNRTG 2 cut(s) 225, 440
Sse9I AATT 2 cut(s) 159, 409
SsiI CCGC 1 cut(s) 348
SspI AATATT 1 cut(s) 281
SspMI CTAG 2 cut(s) 47, 137
TaqI TCGA 3 cut(s) 276, 333, 479
TasI AATT 2 cut(s) 159, 409
TfiI GAWTC 1 cut(s) 476
Tru1I TTAA 2 cut(s) 158, 240
Tru9I TTAA 2 cut(s) 158, 240
TseFI GTSAC 3 cut(s) 32, 267, 287
Tsp45I GTSAC 3 cut(s) 32, 267, 287
TspDTI ATGAA 1 cut(s) 113
TspGWI ACGGA 1 cut(s) 82
XapI RAATTY 1 cut(s) 409
XmnI GAANNNNTTC 1 cut(s) 206
XspI CTAG 2 cut(s) 47, 137
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.