Rmu_sc0002646.1_g000018

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0002646.1
OG0006436
Physical Location & Seq
Forward (+)
77484 .. 79336
1853 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 576 bp
atgtgtagttttctcaaaggaagcaagctatggcgttatgctactagagatattactcaaccaaccaagctcaataacgaaactgatgacaagtttgctgaacgacttgaagattgggacaataagaaccaccaggtcatcacttggtttcgcaacaccttatcttcctcaatcaaccatcaatttggcctgttcaacacagccaaggacatttggaattttttaaagaagcgctatacaaccacagatcttgctcacagatatcaacttttgagcacccttcatcgtatgcgccaagaacctgaggatggtcgtacgtccttcagcccgtccggcgctgctgcggtgtcctcccatcattttgcaatgggaagattgaccggtcaaggattgtcgacggtggtccatggtgacgcatatgatgacgaaacccgcagacattgccggattcaatctccggtgagagaagaaatcagtgaggggggaggagagagagaagagattgaagaggggggggaagagagagtcggagaggagtcaaagggcgacggcattgctggattcagtctccggtga
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 Retrotran_gag_2 gag_pre-integrs rve

Protein Analysis

191

Amino Acids

21.82

Weight (kDa)

6.07

Isoelectric Point (pI)

45.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 4 - 100 1.1e-08 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 395
AciI CCGC 2 cut(s) 344, 433
AcsI RAATTY 1 cut(s) 217
AcuI CTGAAG 1 cut(s) 307
AfaI GTAC 1 cut(s) 316
AfeI AGCGCT 1 cut(s) 233
AfiI CCNNNNNNNGG 1 cut(s) 308
AgeI ACCGGT 1 cut(s) 380
AgsI TTSAA 4 cut(s) 110, 196, 452, 506
AjnI CCWGG 1 cut(s) 132
AluBI AGCT 2 cut(s) 28, 70
AluI AGCT 2 cut(s) 28, 70
Alw21I GWGCWC 1 cut(s) 278
Alw26I GTCTC 1 cut(s) 572
Aor51HI AGCGCT 1 cut(s) 233
AoxI GGCC 1 cut(s) 187
ApeKI GCWGC 2 cut(s) 338, 341
ApoI RAATTY 1 cut(s) 217
AsiGI ACCGGT 1 cut(s) 380
AspLEI GCGC 3 cut(s) 234, 294, 338
AspS9I GGNCC 1 cut(s) 403
AsuHPI GGTGA 2 cut(s) 422, 472
AvaII GGWCC 1 cut(s) 403
AxyI CCTNAGG 1 cut(s) 303
Bbv12I GWGCWC 1 cut(s) 278
BbvI GCAGC 2 cut(s) 325, 328
BccI CCATC 3 cut(s) 186, 302, 363
BceAI ACGGC 1 cut(s) 565
BcgI CGANNNNNNTGC 2 cut(s) 536, 570
BciT130I CCWGG 1 cut(s) 134
BcoDI GTCTC 1 cut(s) 572
BfaI CTAG 1 cut(s) 45
BfoI RGCGCY 2 cut(s) 235, 339
BglI GCCNNNNNGGC 1 cut(s) 333
BglII AGATCT 1 cut(s) 247
BisI GCNGC 2 cut(s) 339, 342
BlsI GCNGC 2 cut(s) 340, 343
Bme1390I CCNGG 1 cut(s) 134
Bme18I GGWCC 1 cut(s) 403
BmgT120I GGNCC 1 cut(s) 403
BmrFI CCNGG 1 cut(s) 134
BoxI GACNNNNGTC 1 cut(s) 401
BsaJI CCNNGG 2 cut(s) 204, 406
BsaWI WCCGGW 3 cut(s) 380, 457, 570
Bsc4I CCNNNNNNNGG 1 cut(s) 308
Bse118I RCCGGY 1 cut(s) 380
Bse21I CCTNAGG 1 cut(s) 303
Bse3DI GCAATG 3 cut(s) 372, 439, 552
BseBI CCWGG 1 cut(s) 134
BseDI CCNNGG 2 cut(s) 204, 406
BseGI GGATG 1 cut(s) 313
BseLI CCNNNNNNNGG 1 cut(s) 308
BseMI GCAATG 3 cut(s) 372, 439, 552
BseMII CTCAG 1 cut(s) 294
BseRI GAGGAG 2 cut(s) 501, 548
BseXI GCAGC 2 cut(s) 325, 328
BshFI GGCC 1 cut(s) 189
BshTI ACCGGT 1 cut(s) 380
BsiHKAI GWGCWC 1 cut(s) 278
BsiSI CCGG 5 cut(s) 333, 381, 445, 458, 571
BsiWI CGTACG 1 cut(s) 314
BslFI GGGAC 1 cut(s) 131
BslI CCNNNNNNNGG 1 cut(s) 308
BsmAI GTCTC 1 cut(s) 572
BsmFI GGGAC 1 cut(s) 131
BsnI GGCC 1 cut(s) 189
Bsp1286I GDGCHC 1 cut(s) 278
Bsp143I GATC 1 cut(s) 247
Bsp19I CCATGG 1 cut(s) 406
BspACI CCGC 2 cut(s) 344, 433
BspANI GGCC 1 cut(s) 189
BspCNI CTCAG 1 cut(s) 295
BsrDI GCAATG 3 cut(s) 372, 439, 552
BsrFI RCCGGY 1 cut(s) 380
BssAI RCCGGY 1 cut(s) 380
BssECI CCNNGG 2 cut(s) 204, 406
BssMI GATC 1 cut(s) 247
BssT1I CCWWGG 2 cut(s) 204, 406
Bst2UI CCWGG 1 cut(s) 134
Bst4CI ACNGT 1 cut(s) 400
Bst6I CTCTTC 3 cut(s) 492, 501, 513
BstAPI GCANNNNNTGC 1 cut(s) 441
BstC8I GCNNGC 1 cut(s) 26
BstDEI CTNAG 1 cut(s) 303
BstDSI CCRYGG 1 cut(s) 406
BstF5I GGATG 1 cut(s) 313
BstH2I RGCGCY 2 cut(s) 235, 339
BstHHI GCGC 3 cut(s) 234, 294, 338
BstKTI GATC 1 cut(s) 250
BstMAI GTCTC 1 cut(s) 572
BstMBI GATC 1 cut(s) 247
BstMWI GCNNNNNNNGC 2 cut(s) 333, 441
BstNI CCWGG 1 cut(s) 134
BstPAI GACNNNNGTC 1 cut(s) 401
BstSCI CCNGG 1 cut(s) 132
BstV1I GCAGC 2 cut(s) 325, 328
BstX2I RGATCY 1 cut(s) 247
BstXI CCANNNNNNTGG 1 cut(s) 185
BstYI RGATCY 1 cut(s) 247
Bsu36I CCTNAGG 1 cut(s) 303
BsuRI GGCC 1 cut(s) 189
BtgI CCRYGG 1 cut(s) 406
BtsCI GGATG 1 cut(s) 313
BtsIMutI CAGTG 1 cut(s) 481
Cac8I GCNNGC 1 cut(s) 26
CfoI GCGC 3 cut(s) 234, 294, 338
Cfr10I RCCGGY 1 cut(s) 380
Cfr13I GGNCC 1 cut(s) 403
CseI GACGC 1 cut(s) 422
CsiI ACCWGGT 1 cut(s) 132
Csp6I GTAC 1 cut(s) 315
CspAI ACCGGT 1 cut(s) 380
CspCI CAANNNNNGTGG 2 cut(s) 232, 267
CviAII CATG 1 cut(s) 407
CviJI RGCY 5 cut(s) 28, 70, 189, 203, 327
CviKI_1 RGCY 5 cut(s) 28, 70, 189, 203, 327
CviQI GTAC 1 cut(s) 315
DdeI CTNAG 1 cut(s) 303
DpnI GATC 1 cut(s) 249
DpnII GATC 1 cut(s) 247
DraI TTTAAA 1 cut(s) 225
Eam1104I CTCTTC 3 cut(s) 492, 501, 513
EarI CTCTTC 3 cut(s) 492, 501, 513
Eco130I CCWWGG 2 cut(s) 204, 406
Eco32I GATATC 1 cut(s) 263
Eco47I GGWCC 1 cut(s) 403
Eco47III AGCGCT 1 cut(s) 233
Eco57I CTGAAG 1 cut(s) 307
Eco81I CCTNAGG 1 cut(s) 303
EcoRII CCWGG 1 cut(s) 132
EcoRV GATATC 1 cut(s) 263
EcoT14I CCWWGG 2 cut(s) 204, 406
ErhI CCWWGG 2 cut(s) 204, 406
FaeI CATG 1 cut(s) 410
FaiI YATR 7 cut(s) 31, 39, 237, 290, 408, 418, 420
FaqI GGGAC 1 cut(s) 131
FatI CATG 1 cut(s) 406
FauI CCCGC 1 cut(s) 440
FauNDI CATATG 1 cut(s) 418
FblI GTMKAC 1 cut(s) 395
Fnu4HI GCNGC 2 cut(s) 339, 342
FokI GGATG 1 cut(s) 320
Fsp4HI GCNGC 2 cut(s) 339, 342
FspBI CTAG 1 cut(s) 45
GlaI GCGC 3 cut(s) 233, 293, 337
GluI GCNGC 2 cut(s) 339, 342
HaeII RGCGCY 2 cut(s) 235, 339
HaeIII GGCC 1 cut(s) 189
HapII CCGG 5 cut(s) 333, 381, 445, 458, 571
HgaI GACGC 1 cut(s) 422
HhaI GCGC 3 cut(s) 234, 294, 338
Hin1II CATG 1 cut(s) 410
Hin6I GCGC 3 cut(s) 232, 292, 336
HinP1I GCGC 3 cut(s) 232, 292, 336
HincII GTYRAC 1 cut(s) 396
HindII GTYRAC 1 cut(s) 396
HinfI GANTC 4 cut(s) 448, 525, 536, 561
HpaII CCGG 5 cut(s) 333, 381, 445, 458, 571
HphI GGTGA 2 cut(s) 422, 472
Hpy166II GTNNAC 1 cut(s) 396
Hpy188I TCNGA 1 cut(s) 530
Hpy8I GTNNAC 1 cut(s) 396
Hpy99I CGWCG 2 cut(s) 400, 551
HpyAV CCTTC 2 cut(s) 290, 331
HpyCH4III ACNGT 1 cut(s) 400
HpyCH4IV ACGT 1 cut(s) 317
HpyCH4V TGCA 1 cut(s) 365
HpyF10VI GCNNNNNNNGC 2 cut(s) 333, 441
HpyF3I CTNAG 1 cut(s) 303
HpySE526I ACGT 1 cut(s) 317
Hsp92II CATG 1 cut(s) 410
HspAI GCGC 3 cut(s) 232, 292, 336
Kzo9I GATC 1 cut(s) 247
LpnPI CCDG 9 cut(s) 119, 146, 203, 315, 346, 394, 458, 471, 543
Lsp1109I GCAGC 2 cut(s) 325, 328
MabI ACCWGGT 1 cut(s) 132
MaeI CTAG 1 cut(s) 45
MaeII ACGT 1 cut(s) 317
MaeIII GTNAC 1 cut(s) 410
MalI GATC 1 cut(s) 249
MboI GATC 1 cut(s) 247
MboII GAAGA 7 cut(s) 122, 156, 384, 479, 509, 518, 530
MflI RGATCY 1 cut(s) 247
MhlI GDGCHC 1 cut(s) 278
MluCI AATT 2 cut(s) 182, 217
MlyI GAGTC 2 cut(s) 534, 545
MmeI TCCRAC 1 cut(s) 508
MnlI CCTC 7 cut(s) 178, 298, 361, 472, 479, 502, 526
MseI TTAA 1 cut(s) 224
MspI CCGG 5 cut(s) 333, 381, 445, 458, 571
MspR9I CCNGG 1 cut(s) 134
MvaI CCWGG 1 cut(s) 134
MwoI GCNNNNNNNGC 2 cut(s) 333, 441
NcoI CCATGG 1 cut(s) 406
NdeI CATATG 1 cut(s) 418
NdeII GATC 1 cut(s) 247
NlaIII CATG 1 cut(s) 410
NmuCI GTSAC 1 cut(s) 410
PfeI GAWTC 2 cut(s) 448, 561
Pfl23II CGTACG 1 cut(s) 314
PinAI ACCGGT 1 cut(s) 380
PkrI GCNGC 2 cut(s) 340, 343
PleI GAGTC 2 cut(s) 533, 544
PpsI GAGTC 2 cut(s) 533, 544
PshAI GACNNNNGTC 1 cut(s) 401
Psp6I CCWGG 1 cut(s) 132
PspGI CCWGG 1 cut(s) 132
PspLI CGTACG 1 cut(s) 314
PspPI GGNCC 1 cut(s) 403
PsuI RGATCY 1 cut(s) 247
RsaI GTAC 1 cut(s) 316
RsaNI GTAC 1 cut(s) 315
SalI GTCGAC 1 cut(s) 394
SaqAI TTAA 1 cut(s) 224
SatI GCNGC 2 cut(s) 339, 342
Sau3AI GATC 1 cut(s) 247
Sau96I GGNCC 1 cut(s) 403
SchI GAGTC 2 cut(s) 534, 545
ScrFI CCNGG 1 cut(s) 134
SduI GDGCHC 1 cut(s) 278
SetI ASST 6 cut(s) 30, 72, 138, 161, 304, 320
SexAI ACCWGGT 1 cut(s) 132
SinI GGWCC 1 cut(s) 403
Sse9I AATT 2 cut(s) 182, 217
SsiI CCGC 2 cut(s) 344, 433
SspMI CTAG 1 cut(s) 45
StyD4I CCNGG 1 cut(s) 132
StyI CCWWGG 2 cut(s) 204, 406
TaaI ACNGT 1 cut(s) 400
TaiI ACGT 1 cut(s) 320
TaqI TCGA 1 cut(s) 395
TasI AATT 2 cut(s) 182, 217
TfiI GAWTC 2 cut(s) 448, 561
Tru1I TTAA 1 cut(s) 224
Tru9I TTAA 1 cut(s) 224
TscAI CASTG 1 cut(s) 481
TseFI GTSAC 1 cut(s) 410
TseI GCWGC 2 cut(s) 338, 341
Tsp45I GTSAC 1 cut(s) 410
TspDTI ATGAA 1 cut(s) 272
TspRI CASTG 1 cut(s) 481
VpaK11BI GGWCC 1 cut(s) 403
XapI RAATTY 1 cut(s) 217
XmiI GTMKAC 1 cut(s) 395
XspI CTAG 1 cut(s) 45
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.