Rw1G012660

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0006436
Physical Location & Seq
Forward (+)
28093690 .. 28094391
702 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G012660.1

Sequence Viewer

Length: 702 bp
ATGGCTTCAGATGATAAGGTCCAATCGATAAGTACTAGGTTAAATAAAGATAATTATTCATACTGGGCAAGTGTGATGAAAAATTTTCTTGTTGGTCGAGGTAGATGGGGTTATGTTACTGGCATAACAGTCAAACCTTCAGATTCCAAAGTTGCAGACTTTGAAAAATCCATTGCCACATGGGAAATGGAGAATGCTCAGGTGCTTACTTGGTTCCATAACTCTGTTGAATCAAGCATTGGTCAGAACTTTTCAAAGTTCGAAACTGCAAAGAGAGTATGGGAGTATTTGCAACTGTTATATCAAGAGTCTAACTTTGCTAAGCAATATCAGCTGGAAATGGAAATTCGAGGTGCCCAGCAAGGTGATAAGACCATTCAAGACTTCTACAATCAGATGACTTGTTTCTGGGATCAATTAGCACTTATGGAACCAGCTGACCTCTTGGCATTAGATAGTTATGTTAACTATAGAGAGCGTCAGAGACTTGTCCAATTTCTTATGGCACTTAAGGAACAGTTTGAAACTTTGCGTGGTGCTATGCTGCATCGTATTCCTTTACCCACTGTTGATGGAGCGGTTAAAGAACTTCTAGCTGAGGAGACTCGATTTAAGGTTGCTCATAATGTTTCTCCCCCCCATCAGTGTTTGCAACCTCTATGTTGCAACCTCCTTTACTGCCTACCCCACCTCAAAGTTTGA
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 Retrotran_gag_3

Protein Analysis

233

Amino Acids

27.08

Weight (kDa)

6.22

Isoelectric Point (pI)

27.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 8 - 47 1.8e-10 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 26 - 204 4.7e-10 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)
AccB1I GGYRCC 1 cut(s) 353
AccBSI CCGCTC 1 cut(s) 578
AciI CCGC 1 cut(s) 578
AclWI GGATC 1 cut(s) 420
AcsI RAATTY 2 cut(s) 82, 345
AcuI CTGAAG 1 cut(s) 123
AfaI GTAC 1 cut(s) 34
AflII CTTAAG 1 cut(s) 509
AgsI TTSAA 5 cut(s) 164, 230, 255, 380, 524
AjuI GAANNNNNNNTTGG 2 cut(s) 222, 254
AluBI AGCT 3 cut(s) 334, 437, 596
AluI AGCT 3 cut(s) 334, 437, 596
Alw26I GTCTC 2 cut(s) 478, 596
AlwI GGATC 1 cut(s) 420
ApeKI GCWGC 1 cut(s) 544
ApoI RAATTY 2 cut(s) 82, 345
AspS9I GGNCC 1 cut(s) 19
AsuHPI GGTGA 1 cut(s) 377
AsuII TTCGAA 1 cut(s) 261
AvaII GGWCC 1 cut(s) 19
BaeGI GKGCMC 1 cut(s) 358
BanI GGYRCC 1 cut(s) 353
BbvCI CCTCAGC 1 cut(s) 597
BbvI GCAGC 1 cut(s) 531
BccI CCATC 3 cut(s) 99, 566, 648
BcoDI GTCTC 2 cut(s) 478, 596
BfaI CTAG 2 cut(s) 36, 593
BfmI CTRYAG 1 cut(s) 469
BfrI CTTAAG 1 cut(s) 509
BisI GCNGC 1 cut(s) 545
BlpI GCTNAGC 1 cut(s) 321
BlsI GCNGC 1 cut(s) 546
BmcAI AGTACT 1 cut(s) 34
Bme18I GGWCC 1 cut(s) 19
BmgT120I GGNCC 1 cut(s) 19
BmiI GGNNCC 3 cut(s) 215, 355, 432
BmrI ACTGGG 1 cut(s) 73
BmsI GCATC 1 cut(s) 556
BmuI ACTGGG 1 cut(s) 73
Bpu10I CCTNAGC 2 cut(s) 198, 597
Bpu1102I GCTNAGC 1 cut(s) 321
Bpu14I TTCGAA 1 cut(s) 261
Bsa29I ATCGAT 1 cut(s) 26
Bse1I ACTGG 2 cut(s) 68, 124
Bse3DI GCAATG 1 cut(s) 171
BseCI ATCGAT 1 cut(s) 26
BseMI GCAATG 1 cut(s) 171
BseMII CTCAG 2 cut(s) 212, 588
BseNI ACTGG 2 cut(s) 68, 124
BseRI GAGGAG 1 cut(s) 614
BseSI GKGCMC 1 cut(s) 358
BseXI GCAGC 1 cut(s) 531
BseYI CCCAGC 1 cut(s) 357
BshNI GGYRCC 1 cut(s) 353
BshVI ATCGAT 1 cut(s) 26
BsmAI GTCTC 2 cut(s) 478, 596
BsmI GAATGC 1 cut(s) 199
Bsp119I TTCGAA 1 cut(s) 261
Bsp1286I GDGCHC 1 cut(s) 358
Bsp143I GATC 1 cut(s) 412
Bsp1720I GCTNAGC 1 cut(s) 321
BspACI CCGC 1 cut(s) 578
BspCNI CTCAG 2 cut(s) 211, 589
BspDI ATCGAT 1 cut(s) 26
BspLI GGNNCC 3 cut(s) 215, 355, 432
BspPI GGATC 1 cut(s) 420
BspT104I TTCGAA 1 cut(s) 261
BspT107I GGYRCC 1 cut(s) 353
BspTI CTTAAG 1 cut(s) 509
BsrBI CCGCTC 1 cut(s) 578
BsrDI GCAATG 1 cut(s) 171
BsrI ACTGG 2 cut(s) 68, 124
BssMI GATC 1 cut(s) 412
Bst4CI ACNGT 4 cut(s) 130, 297, 519, 568
BstAFI CTTAAG 1 cut(s) 509
BstBI TTCGAA 1 cut(s) 261
BstDEI CTNAG 3 cut(s) 198, 321, 597
BstKTI GATC 1 cut(s) 415
BstMAI GTCTC 2 cut(s) 478, 596
BstMBI GATC 1 cut(s) 412
BstMWI GCNNNNNNNGC 1 cut(s) 331
BstSFI CTRYAG 1 cut(s) 469
BstSLI GKGCMC 1 cut(s) 358
BstV1I GCAGC 1 cut(s) 531
Bsu15I ATCGAT 1 cut(s) 26
BsuTUI ATCGAT 1 cut(s) 26
BtsIMutI CAGTG 2 cut(s) 564, 650
Cfr13I GGNCC 1 cut(s) 19
ClaI ATCGAT 1 cut(s) 26
CseI GACGC 1 cut(s) 467
Csp6I GTAC 1 cut(s) 33
CviAII CATG 1 cut(s) 180
CviJI RGCY 4 cut(s) 5, 334, 437, 596
CviKI_1 RGCY 4 cut(s) 5, 334, 437, 596
CviQI GTAC 1 cut(s) 33
DdeI CTNAG 3 cut(s) 198, 321, 597
DpnI GATC 1 cut(s) 414
DpnII GATC 1 cut(s) 412
Eco47I GGWCC 1 cut(s) 19
Eco57I CTGAAG 1 cut(s) 123
FaeI CATG 1 cut(s) 183
FatI CATG 1 cut(s) 179
Fnu4HI GCNGC 1 cut(s) 545
Fsp4HI GCNGC 1 cut(s) 545
FspBI CTAG 2 cut(s) 36, 593
GluI GCNGC 1 cut(s) 545
GsaI CCCAGC 1 cut(s) 361
HgaI GACGC 1 cut(s) 467
Hin1II CATG 1 cut(s) 183
HincII GTYRAC 1 cut(s) 466
HindII GTYRAC 1 cut(s) 466
HinfI GANTC 4 cut(s) 143, 230, 308, 604
HpaI GTTAAC 1 cut(s) 466
HphI GGTGA 1 cut(s) 377
Hpy166II GTNNAC 1 cut(s) 466
Hpy188I TCNGA 5 cut(s) 10, 142, 246, 396, 483
Hpy188III TCNNGA 2 cut(s) 305, 380
Hpy8I GTNNAC 1 cut(s) 466
HpyAV CCTTC 1 cut(s) 147
HpyCH4III ACNGT 4 cut(s) 130, 297, 519, 568
HpyCH4V TGCA 6 cut(s) 155, 269, 292, 547, 652, 666
HpyF10VI GCNNNNNNNGC 1 cut(s) 331
HpyF3I CTNAG 3 cut(s) 198, 321, 597
Hsp92II CATG 1 cut(s) 183
KspAI GTTAAC 1 cut(s) 466
Kzo9I GATC 1 cut(s) 412
LmnI GCTCC 1 cut(s) 575
LpnPI CCDG 7 cut(s) 49, 105, 185, 320, 371, 394, 447
Lsp1109I GCAGC 1 cut(s) 531
LweI GCATC 1 cut(s) 556
MaeI CTAG 2 cut(s) 36, 593
MaeIII GTNAC 1 cut(s) 115
MalI GATC 1 cut(s) 414
MbiI CCGCTC 1 cut(s) 578
MboI GATC 1 cut(s) 412
MhlI GDGCHC 1 cut(s) 358
MluCI AATT 5 cut(s) 52, 82, 345, 416, 494
MlyI GAGTC 2 cut(s) 317, 598
MnlI CCTC 7 cut(s) 92, 344, 452, 592, 666, 680, 701
MseI TTAA 5 cut(s) 41, 465, 510, 582, 612
MspA1I CMGCKG 2 cut(s) 334, 437
MspCI CTTAAG 1 cut(s) 509
Mva1269I GAATGC 1 cut(s) 199
MwoI GCNNNNNNNGC 1 cut(s) 331
NdeII GATC 1 cut(s) 412
NlaIII CATG 1 cut(s) 183
NlaIV GGNNCC 3 cut(s) 215, 355, 432
NspV TTCGAA 1 cut(s) 261
PctI GAATGC 1 cut(s) 199
PfeI GAWTC 2 cut(s) 143, 230
PkrI GCNGC 1 cut(s) 546
PleI GAGTC 2 cut(s) 316, 598
PpsI GAGTC 2 cut(s) 316, 598
PspFI CCCAGC 1 cut(s) 357
PspN4I GGNNCC 3 cut(s) 215, 355, 432
PspPI GGNCC 1 cut(s) 19
PvuII CAGCTG 2 cut(s) 334, 437
RsaI GTAC 1 cut(s) 34
RsaNI GTAC 1 cut(s) 33
SaqAI TTAA 5 cut(s) 41, 465, 510, 582, 612
SatI GCNGC 1 cut(s) 545
Sau3AI GATC 1 cut(s) 412
Sau96I GGNCC 1 cut(s) 19
ScaI AGTACT 1 cut(s) 34
SchI GAGTC 2 cut(s) 317, 598
SduI GDGCHC 1 cut(s) 358
SfaNI GCATC 1 cut(s) 556
SfcI CTRYAG 1 cut(s) 469
SfuI TTCGAA 1 cut(s) 261
SinI GGWCC 1 cut(s) 19
SmlI CTYRAG 1 cut(s) 509
SmoI CTYRAG 1 cut(s) 509
Sse9I AATT 5 cut(s) 52, 82, 345, 416, 494
SsiI CCGC 1 cut(s) 578
SspMI CTAG 2 cut(s) 36, 593
TaaI ACNGT 4 cut(s) 130, 297, 519, 568
TaqI TCGA 5 cut(s) 26, 97, 261, 349, 607
TasI AATT 5 cut(s) 52, 82, 345, 416, 494
TatI WGTACW 1 cut(s) 32
TfiI GAWTC 2 cut(s) 143, 230
Tru1I TTAA 5 cut(s) 41, 465, 510, 582, 612
Tru9I TTAA 5 cut(s) 41, 465, 510, 582, 612
TscAI CASTG 2 cut(s) 571, 650
TseI GCWGC 1 cut(s) 544
TspDTI ATGAA 2 cut(s) 48, 92
TspRI CASTG 2 cut(s) 571, 650
Vha464I CTTAAG 1 cut(s) 509
VpaK11BI GGWCC 1 cut(s) 19
XapI RAATTY 2 cut(s) 82, 345
XcmI CCANNNNNNNNNTGG 1 cut(s) 184
XspI CTAG 2 cut(s) 36, 593
ZrmI AGTACT 1 cut(s) 34
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.