Rmu_sc0002680.1_g000014

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0002680.1
N/A
Physical Location & Seq
Reverse (-)
54459 .. 55407
949 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 456 bp
ctgaaccggccgactgaaagtccggcagaaaaaccggcagaaggaaaagaagaaaaaaaaaggaaggagaagctgcagcccagaggcccaagtcgtgccccagcagtagcccaggtgcccaagcccaagcctagaagcccaagctgcagcccaggagtccaagccgcagccccagccgctgatgtcaactcagccacgtcagctacgccgcgtcatcagacagtcagcagccaggtcagcggatctgccacgtcagcaactcgtaacctgaacaaattagactttgctccattgggaacaactggctctgaatatcacaggtgggttcgtgatatccgccagcatctcaaggctgatggaatcttggatacgattctcgagcctagccaatacgtgctaactgttgagcaagctcaaactttggaagccaatatagcagccttagaggcaaaataa
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

151

Amino Acids

16.15

Weight (kDa)

9.52

Isoelectric Point (pI)

61.1

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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

Orthologous Genes

No orthologs found for this gene in the current database.

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 115
AccII CGCG 1 cut(s) 211
AciI CCGC 5 cut(s) 165, 177, 209, 240, 337
AclWI GGATC 1 cut(s) 250
AcoI YGGCCR 1 cut(s) 8
AfiI CCNNNNNNNGG 1 cut(s) 41
AhdI GACNNNNNGTC 1 cut(s) 18
AjiI CACGTC 2 cut(s) 198, 252
AjnI CCWGG 3 cut(s) 111, 151, 231
AluBI AGCT 4 cut(s) 73, 144, 203, 413
AluI AGCT 4 cut(s) 73, 144, 203, 413
AlwI GGATC 1 cut(s) 250
AlwNI CAGNNNCTG 1 cut(s) 179
Ama87I CYCGRG 1 cut(s) 377
AoxI GGCC 2 cut(s) 8, 85
ApeKI GCWGC 7 cut(s) 73, 76, 144, 147, 167, 228, 437
AspS9I GGNCC 1 cut(s) 86
AvaI CYCGRG 1 cut(s) 377
BaeGI GKGCMC 2 cut(s) 100, 120
BanI GGYRCC 1 cut(s) 115
BbvI GCAGC 7 cut(s) 60, 88, 131, 159, 179, 240, 449
BccI CCATC 1 cut(s) 350
BciT130I CCWGG 3 cut(s) 113, 153, 233
BciVI GTATCC 1 cut(s) 361
BfaI CTAG 2 cut(s) 132, 384
BfmI CTRYAG 2 cut(s) 74, 145
BfuI GTATCC 1 cut(s) 361
BglI GCCNNNNNGGC 1 cut(s) 446
Bme1390I CCNGG 3 cut(s) 113, 153, 233
BmeRI GACNNNNNGTC 1 cut(s) 18
BmeT110I CYCGRG 1 cut(s) 377
BmgBI CACGTC 2 cut(s) 198, 252
BmgT120I GGNCC 1 cut(s) 86
BmiI GGNNCC 1 cut(s) 117
BmrFI CCNGG 3 cut(s) 113, 153, 233
BmsI GCATC 1 cut(s) 352
BpuEI CTTGAG 1 cut(s) 332
BsaAI YACGTR 1 cut(s) 394
BsaJI CCNNGG 2 cut(s) 111, 151
Bsc4I CCNNNNNNNGG 1 cut(s) 41
Bse118I RCCGGY 2 cut(s) 6, 34
Bse1I ACTGG 1 cut(s) 307
BseBI CCWGG 3 cut(s) 113, 153, 233
BseDI CCNNGG 2 cut(s) 111, 151
BseLI CCNNNNNNNGG 1 cut(s) 41
BseMII CTCAG 1 cut(s) 204
BseNI ACTGG 1 cut(s) 307
BseSI GKGCMC 2 cut(s) 100, 120
BseX3I CGGCCG 1 cut(s) 8
BseXI GCAGC 7 cut(s) 60, 88, 131, 159, 179, 240, 449
BseYI CCCAGC 2 cut(s) 100, 172
Bsh1236I CGCG 1 cut(s) 211
Bsh1285I CGRYCG 1 cut(s) 11
BshFI GGCC 2 cut(s) 10, 87
BshNI GGYRCC 1 cut(s) 115
BsiEI CGRYCG 1 cut(s) 11
BsiHKCI CYCGRG 1 cut(s) 377
BsiSI CCGG 3 cut(s) 7, 23, 35
BslI CCNNNNNNNGG 1 cut(s) 41
BsnI GGCC 2 cut(s) 10, 87
BsoBI CYCGRG 1 cut(s) 377
Bsp1286I GDGCHC 2 cut(s) 100, 120
Bsp143I GATC 1 cut(s) 242
BspACI CCGC 5 cut(s) 165, 177, 209, 240, 337
BspANI GGCC 2 cut(s) 10, 87
BspCNI CTCAG 1 cut(s) 203
BspFNI CGCG 1 cut(s) 211
BspLI GGNNCC 1 cut(s) 117
BspMAI CTGCAG 2 cut(s) 78, 149
BspPI GGATC 1 cut(s) 250
BspT107I GGYRCC 1 cut(s) 115
BsrFI RCCGGY 2 cut(s) 6, 34
BsrI ACTGG 1 cut(s) 307
BssAI RCCGGY 2 cut(s) 6, 34
BssECI CCNNGG 2 cut(s) 111, 151
BssMI GATC 1 cut(s) 242
Bst2UI CCWGG 3 cut(s) 113, 153, 233
Bst4CI ACNGT 2 cut(s) 223, 403
BstBAI YACGTR 1 cut(s) 394
BstC8I GCNNGC 2 cut(s) 341, 411
BstDEI CTNAG 2 cut(s) 190, 442
BstFNI CGCG 1 cut(s) 211
BstKTI GATC 1 cut(s) 245
BstMBI GATC 1 cut(s) 242
BstMCI CGRYCG 1 cut(s) 11
BstMWI GCNNNNNNNGC 8 cut(s) 144, 173, 176, 200, 237, 254, 434, 446
BstNI CCWGG 3 cut(s) 113, 153, 233
BstSCI CCNGG 3 cut(s) 111, 151, 231
BstSFI CTRYAG 2 cut(s) 74, 145
BstSLI GKGCMC 2 cut(s) 100, 120
BstUI CGCG 1 cut(s) 211
BstV1I GCAGC 7 cut(s) 60, 88, 131, 159, 179, 240, 449
BstX2I RGATCY 1 cut(s) 242
BstYI RGATCY 1 cut(s) 242
BstZI CGGCCG 1 cut(s) 8
BsuI GTATCC 1 cut(s) 361
BsuRI GGCC 2 cut(s) 10, 87
BtrI CACGTC 2 cut(s) 198, 252
Cac8I GCNNGC 2 cut(s) 341, 411
CaiI CAGNNNCTG 1 cut(s) 179
Cfr10I RCCGGY 2 cut(s) 6, 34
Cfr13I GGNCC 1 cut(s) 86
CseI GACGC 1 cut(s) 200
DdeI CTNAG 2 cut(s) 190, 442
DpnI GATC 1 cut(s) 244
DpnII GATC 1 cut(s) 242
DriI GACNNNNNGTC 1 cut(s) 18
EaeI YGGCCR 1 cut(s) 8
EagI CGGCCG 1 cut(s) 8
Eam1105I GACNNNNNGTC 1 cut(s) 18
EciI GGCGGA 1 cut(s) 326
EclXI CGGCCG 1 cut(s) 8
Eco32I GATATC 1 cut(s) 334
Eco52I CGGCCG 1 cut(s) 8
Eco88I CYCGRG 1 cut(s) 377
EcoRII CCWGG 3 cut(s) 111, 151, 231
EcoRV GATATC 1 cut(s) 334
FaiI YATR 1 cut(s) 434
FspBI CTAG 2 cut(s) 132, 384
GsaI CCCAGC 2 cut(s) 104, 176
HaeIII GGCC 2 cut(s) 10, 87
HapII CCGG 3 cut(s) 7, 23, 35
HgaI GACGC 1 cut(s) 200
HincII GTYRAC 1 cut(s) 187
HindII GTYRAC 1 cut(s) 187
HinfI GANTC 3 cut(s) 156, 360, 373
HpaII CCGG 3 cut(s) 7, 23, 35
Hpy166II GTNNAC 1 cut(s) 187
Hpy188I TCNGA 2 cut(s) 219, 310
Hpy188III TCNNGA 2 cut(s) 329, 377
Hpy8I GTNNAC 1 cut(s) 187
HpyAV CCTTC 2 cut(s) 35, 58
HpyCH4III ACNGT 2 cut(s) 223, 403
HpyCH4IV ACGT 3 cut(s) 197, 251, 393
HpyCH4V TGCA 2 cut(s) 76, 147
HpyF10VI GCNNNNNNNGC 8 cut(s) 144, 173, 176, 200, 237, 254, 434, 446
HpyF3I CTNAG 2 cut(s) 190, 442
HpySE526I ACGT 3 cut(s) 197, 251, 393
Kzo9I GATC 1 cut(s) 242
LmnI GCTCC 1 cut(s) 292
Lsp1109I GCAGC 7 cut(s) 60, 88, 131, 159, 179, 240, 449
LweI GCATC 1 cut(s) 352
MaeI CTAG 2 cut(s) 132, 384
MaeII ACGT 3 cut(s) 197, 251, 393
MaeIII GTNAC 1 cut(s) 263
MalI GATC 1 cut(s) 244
MboI GATC 1 cut(s) 242
MboII GAAGA 1 cut(s) 62
MflI RGATCY 1 cut(s) 242
MhlI GDGCHC 2 cut(s) 100, 120
MluCI AATT 1 cut(s) 275
MlyI GAGTC 1 cut(s) 165
MnlI CCTC 2 cut(s) 77, 439
MspA1I CMGCKG 2 cut(s) 179, 240
MspI CCGG 3 cut(s) 7, 23, 35
MspR9I CCNGG 3 cut(s) 113, 153, 233
MvaI CCWGG 3 cut(s) 113, 153, 233
MvnI CGCG 1 cut(s) 211
MwoI GCNNNNNNNGC 8 cut(s) 144, 173, 176, 200, 237, 254, 434, 446
NdeII GATC 1 cut(s) 242
NlaIV GGNNCC 1 cut(s) 117
PaeR7I CTCGAG 1 cut(s) 377
PfeI GAWTC 2 cut(s) 360, 373
PleI GAGTC 1 cut(s) 164
PpsI GAGTC 1 cut(s) 164
Ppu21I YACGTR 1 cut(s) 394
Psp6I CCWGG 3 cut(s) 111, 151, 231
PspFI CCCAGC 2 cut(s) 100, 172
PspGI CCWGG 3 cut(s) 111, 151, 231
PspN4I GGNNCC 1 cut(s) 117
PspPI GGNCC 1 cut(s) 86
PstI CTGCAG 2 cut(s) 78, 149
PstNI CAGNNNCTG 1 cut(s) 179
PsuI RGATCY 1 cut(s) 242
Sau3AI GATC 1 cut(s) 242
Sau96I GGNCC 1 cut(s) 86
SchI GAGTC 1 cut(s) 165
ScrFI CCNGG 3 cut(s) 113, 153, 233
SduI GDGCHC 2 cut(s) 100, 120
SfaNI GCATC 1 cut(s) 352
SfcI CTRYAG 2 cut(s) 74, 145
Sfr274I CTCGAG 1 cut(s) 377
SlaI CTCGAG 1 cut(s) 377
SmlI CTYRAG 2 cut(s) 347, 377
SmoI CTYRAG 2 cut(s) 347, 377
Sse9I AATT 1 cut(s) 275
SsiI CCGC 5 cut(s) 165, 177, 209, 240, 337
SspMI CTAG 2 cut(s) 132, 384
StyD4I CCNGG 3 cut(s) 111, 151, 231
TaaI ACNGT 2 cut(s) 223, 403
TaiI ACGT 3 cut(s) 200, 254, 396
TaqI TCGA 1 cut(s) 378
TasI AATT 1 cut(s) 275
TauI GCSGC 3 cut(s) 167, 179, 211
TfiI GAWTC 2 cut(s) 360, 373
TseI GCWGC 7 cut(s) 73, 76, 144, 147, 167, 228, 437
XhoI CTCGAG 1 cut(s) 377
XspI CTAG 2 cut(s) 132, 384
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.