Rroxscaffold_3G00254550

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0002557
Physical Location & Seq
Forward (+)
48790930 .. 48795609
4680 bp
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UTR
Exon/CDS
Intron
Rroxscaffold_3G00254550.1

Sequence Viewer

Length: 447 bp
ATGGAGAATTTGCTTAGGGCAAAGGGTCTTTGGAGCTTGGTGGAGAATGGCTTTGAAGAGCCAAGAGCGAGGACGATGCGGACCGAGGCGCGGCAAACACGGCTTGAAGATGCCGTAACCAAGGATCACCAAGTCAAGCATTATCTCTTCCGGGCACTTGATCGGACTATCTTCGAACAAATCTTGGACCGTCACACGCCCAAGATTGTTTGGGACTCGATGAAGCGGAAGTTTGGAGGAAATATCGGGGTGAAGAGATCTCTTCTTAACTCACTAAGAAGAGAGTTTGAGGTTCTAGCGATGAAGAAGGATGAAACCATCACCGAGTATTTTGCAAGAGTGATGACGGTCTCCAACAAGATGAGGAGCAATGGAGAAGATATGCCTAACTCAAAGATTGTTGAGAAGATCCTACGAACCCTAGCGAGAGGTTCACATATGTTGTAA
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

Protein Analysis

148

Amino Acids

17.41

Weight (kDa)

10.1

Isoelectric Point (pI)

47.86

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 1 - 142 5.6e-19 gag-polypeptide of LTR copia-type
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)
AccII CGCG 1 cut(s) 91
AciI CCGC 3 cut(s) 79, 91, 226
AclWI GGATC 2 cut(s) 132, 403
AcsI RAATTY 1 cut(s) 7
AfiI CCNNNNNNNGG 1 cut(s) 90
AgsI TTSAA 2 cut(s) 56, 107
AluBI AGCT 1 cut(s) 36
AluI AGCT 1 cut(s) 36
Alw26I GTCTC 1 cut(s) 355
AlwI GGATC 2 cut(s) 132, 403
ApoI RAATTY 1 cut(s) 7
AspLEI GCGC 1 cut(s) 91
AspS9I GGNCC 2 cut(s) 81, 187
AsuC2I CCSGG 1 cut(s) 152
AsuHPI GGTGA 3 cut(s) 119, 262, 313
AsuII TTCGAA 1 cut(s) 174
AvaII GGWCC 2 cut(s) 81, 187
BaeGI GKGCMC 1 cut(s) 157
BccI CCATC 1 cut(s) 326
BceAI ACGGC 2 cut(s) 98, 116
BcgI CGANNNNNNTGC 4 cut(s) 58, 92, 314, 348
BcnI CCSGG 1 cut(s) 152
BcoDI GTCTC 1 cut(s) 355
BfaI CTAG 2 cut(s) 296, 422
BglII AGATCT 1 cut(s) 257
BisI GCNGC 1 cut(s) 92
BlsI GCNGC 1 cut(s) 93
Bme1390I CCNGG 1 cut(s) 152
Bme18I GGWCC 2 cut(s) 81, 187
BmgT120I GGNCC 2 cut(s) 81, 187
BmrFI CCNGG 1 cut(s) 152
BmsI GCATC 2 cut(s) 66, 100
Bpu10I CCTNAGC 1 cut(s) 14
Bpu14I TTCGAA 1 cut(s) 174
BpuMI CCSGG 1 cut(s) 152
BsaI GGTCTC 1 cut(s) 355
BsaJI CCNNGG 2 cut(s) 84, 120
Bsc4I CCNNNNNNNGG 1 cut(s) 90
Bse3DI GCAATG 1 cut(s) 376
BseDI CCNNGG 2 cut(s) 84, 120
BseGI GGATG 1 cut(s) 316
BseLI CCNNNNNNNGG 1 cut(s) 90
BseMI GCAATG 1 cut(s) 376
BseRI GAGGAG 1 cut(s) 379
BseSI GKGCMC 1 cut(s) 157
Bsh1236I CGCG 1 cut(s) 91
BsiSI CCGG 1 cut(s) 151
BslFI GGGAC 1 cut(s) 227
BslI CCNNNNNNNGG 1 cut(s) 90
BsmAI GTCTC 1 cut(s) 355
BsmFI GGGAC 1 cut(s) 227
Bso31I GGTCTC 1 cut(s) 355
Bsp119I TTCGAA 1 cut(s) 174
Bsp1286I GDGCHC 1 cut(s) 157
Bsp143I GATC 4 cut(s) 124, 160, 257, 408
BspACI CCGC 3 cut(s) 79, 91, 226
BspFNI CGCG 1 cut(s) 91
BspPI GGATC 2 cut(s) 132, 403
BspQI GCTCTTC 1 cut(s) 51
BspT104I TTCGAA 1 cut(s) 174
BspTNI GGTCTC 1 cut(s) 355
BsrDI GCAATG 1 cut(s) 376
BssECI CCNNGG 2 cut(s) 84, 120
BssMI GATC 4 cut(s) 124, 160, 257, 408
BssT1I CCWWGG 1 cut(s) 120
Bst4CI ACNGT 2 cut(s) 191, 349
Bst6I CTCTTC 5 cut(s) 51, 152, 248, 267, 274
BstBI TTCGAA 1 cut(s) 174
BstDEI CTNAG 2 cut(s) 14, 275
BstF5I GGATG 1 cut(s) 316
BstFNI CGCG 1 cut(s) 91
BstHHI GCGC 1 cut(s) 91
BstKTI GATC 4 cut(s) 127, 163, 260, 411
BstMAI GTCTC 1 cut(s) 355
BstMBI GATC 4 cut(s) 124, 160, 257, 408
BstMWI GCNNNNNNNGC 1 cut(s) 100
BstSCI CCNGG 1 cut(s) 150
BstSLI GKGCMC 1 cut(s) 157
BstUI CGCG 1 cut(s) 91
BstX2I RGATCY 2 cut(s) 257, 408
BstYI RGATCY 2 cut(s) 257, 408
BtgZI GCGATG 1 cut(s) 314
BtsCI GGATG 1 cut(s) 316
CfoI GCGC 1 cut(s) 91
Cfr13I GGNCC 2 cut(s) 81, 187
CpoI CGGWCCG 1 cut(s) 81
CspI CGGWCCG 1 cut(s) 81
CviJI RGCY 4 cut(s) 36, 51, 61, 103
CviKI_1 RGCY 4 cut(s) 36, 51, 61, 103
DdeI CTNAG 2 cut(s) 14, 275
DpnI GATC 4 cut(s) 126, 162, 259, 410
DpnII GATC 4 cut(s) 124, 160, 257, 408
Eam1104I CTCTTC 5 cut(s) 51, 152, 248, 267, 274
EarI CTCTTC 5 cut(s) 51, 152, 248, 267, 274
Eco130I CCWWGG 1 cut(s) 120
Eco31I GGTCTC 1 cut(s) 355
Eco47I GGWCC 2 cut(s) 81, 187
EcoT14I CCWWGG 1 cut(s) 120
ErhI CCWWGG 1 cut(s) 120
FaiI YATR 3 cut(s) 383, 438, 440
FaqI GGGAC 1 cut(s) 227
FauNDI CATATG 1 cut(s) 438
Fnu4HI GCNGC 1 cut(s) 92
FokI GGATG 1 cut(s) 323
Fsp4HI GCNGC 1 cut(s) 92
FspBI CTAG 2 cut(s) 296, 422
GlaI GCGC 1 cut(s) 90
GluI GCNGC 1 cut(s) 92
HapII CCGG 1 cut(s) 151
HhaI GCGC 1 cut(s) 91
Hin6I GCGC 1 cut(s) 89
HinP1I GCGC 1 cut(s) 89
HinfI GANTC 1 cut(s) 215
HpaII CCGG 1 cut(s) 151
HphI GGTGA 3 cut(s) 119, 262, 313
Hpy166II GTNNAC 1 cut(s) 434
Hpy188I TCNGA 1 cut(s) 165
Hpy8I GTNNAC 1 cut(s) 434
HpyAV CCTTC 1 cut(s) 301
HpyCH4III ACNGT 2 cut(s) 191, 349
HpyCH4V TGCA 1 cut(s) 335
HpyF10VI GCNNNNNNNGC 1 cut(s) 100
HpyF3I CTNAG 2 cut(s) 14, 275
HspAI GCGC 1 cut(s) 89
Kzo9I GATC 4 cut(s) 124, 160, 257, 408
LguI GCTCTTC 1 cut(s) 51
LmnI GCTCC 2 cut(s) 33, 366
LpnPI CCDG 1 cut(s) 164
LweI GCATC 2 cut(s) 66, 100
MaeI CTAG 2 cut(s) 296, 422
MaeIII GTNAC 2 cut(s) 115, 191
MalI GATC 4 cut(s) 126, 162, 259, 410
MboI GATC 4 cut(s) 124, 160, 257, 408
MflI RGATCY 2 cut(s) 257, 408
MhlI GDGCHC 1 cut(s) 157
MluCI AATT 1 cut(s) 7
MlyI GAGTC 1 cut(s) 209
MmeI TCCRAC 1 cut(s) 378
MnlI CCTC 6 cut(s) 63, 79, 230, 283, 357, 422
MseI TTAA 1 cut(s) 267
MspI CCGG 1 cut(s) 151
MspR9I CCNGG 1 cut(s) 152
MvnI CGCG 1 cut(s) 91
MwoI GCNNNNNNNGC 1 cut(s) 100
NciI CCSGG 1 cut(s) 152
NdeI CATATG 1 cut(s) 438
NdeII GATC 4 cut(s) 124, 160, 257, 408
NmuCI GTSAC 1 cut(s) 191
NspV TTCGAA 1 cut(s) 174
PciSI GCTCTTC 1 cut(s) 51
PkrI GCNGC 1 cut(s) 93
PleI GAGTC 1 cut(s) 209
PpsI GAGTC 1 cut(s) 209
PspPI GGNCC 2 cut(s) 81, 187
PsuI RGATCY 2 cut(s) 257, 408
Rsr2I CGGWCCG 1 cut(s) 81
RsrII CGGWCCG 1 cut(s) 81
SapI GCTCTTC 1 cut(s) 51
SaqAI TTAA 1 cut(s) 267
SatI GCNGC 1 cut(s) 92
Sau3AI GATC 4 cut(s) 124, 160, 257, 408
Sau96I GGNCC 2 cut(s) 81, 187
SchI GAGTC 1 cut(s) 209
ScrFI CCNGG 1 cut(s) 152
SduI GDGCHC 1 cut(s) 157
SetI ASST 3 cut(s) 38, 294, 433
SfaNI GCATC 2 cut(s) 66, 100
SfuI TTCGAA 1 cut(s) 174
SinI GGWCC 2 cut(s) 81, 187
Sse9I AATT 1 cut(s) 7
SsiI CCGC 3 cut(s) 79, 91, 226
SspMI CTAG 2 cut(s) 296, 422
StyD4I CCNGG 1 cut(s) 150
StyI CCWWGG 1 cut(s) 120
TaaI ACNGT 2 cut(s) 191, 349
TaqI TCGA 2 cut(s) 174, 218
TaqII GACCGA 1 cut(s) 98
TasI AATT 1 cut(s) 7
TauI GCSGC 1 cut(s) 94
Tru1I TTAA 1 cut(s) 267
Tru9I TTAA 1 cut(s) 267
TseFI GTSAC 1 cut(s) 191
Tsp45I GTSAC 1 cut(s) 191
TspDTI ATGAA 3 cut(s) 236, 317, 327
VpaK11BI GGWCC 2 cut(s) 81, 187
XapI RAATTY 1 cut(s) 7
XspI CTAG 2 cut(s) 296, 422
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.