Rroxscaffold_6G00388250

Zinc knuckle

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0004851
Physical Location & Seq
Forward (+)
1102766 .. 1108053
5288 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00388250.1

Sequence Viewer

Length: 696 bp
ATGGAGCAAGTCAAACAACCCAGAGCTAAGACCTATGCCATCGATCCGGCTATGGCTGAAAGTTTGATCACCCGACTTGAGACTGAGTTATTGCATTTGAGGCAAGGTGACATGACGGTGTTGGAATATGGGCGACGTTTCAATAGCTTGTATCGTTTTGCGCCTGCCTTGGTGGCTAATGAGAGGGATAAAATCCACAAATTTCTACAAGGACTACGCGATCAACTCCGTGTTATGTTAGCGGCTACCTTATTTACCGAGTTCAGTCAAGTATTTTTGGCCGCCATGAAGTGCGAGGACAGACTTTTGAAATGTGTACAACCATTAGAGGCGGGTTCCCCTAGCCCAAGTCCATCCGAGAGGGCTACCGCTATTTCGAGGTCCGAGGCTTTGACCGGTAGTAGACCTGACAGTTTTGGGTCCGACTCTCGACAGAATTACAGAAGACGTGAACGGAGGTGGGGCAAGCACAAGCGACGAACCAAACAGTCCAGGAGTAGTGTTAGCGGTTATAGTAGAGGTTCTAGAAGACTTCCCATTAAGAGAGACCGTCCACAATGTCAGACATGTGGCAGACACCATGATGGACAGTGCCAAGTAGGACTATACACGATAGGGAGTGTGGTATGTTATCATTGTGGCCAACATGGTCACTACTTGAGGAAGTGCCCTCAACTGACTCAGGGAGCTACTTAA
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 zf-CCHC

Protein Analysis

231

Amino Acids

26.37

Weight (kDa)

10.07

Isoelectric Point (pI)

72.01

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 24 - 74 2e-09 Retrotransposon gag protein
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 403
AccII CGCG 1 cut(s) 219
AciI CCGC 5 cut(s) 242, 282, 332, 369, 507
AclWI GGATC 1 cut(s) 38
AcoI YGGCCR 2 cut(s) 279, 640
AcsI RAATTY 1 cut(s) 200
AfaI GTAC 1 cut(s) 318
AflIII ACRYGT 1 cut(s) 566
AgeI ACCGGT 1 cut(s) 395
AgsI TTSAA 2 cut(s) 142, 310
AjiI CACGTC 1 cut(s) 449
AjnI CCWGG 1 cut(s) 491
AluBI AGCT 3 cut(s) 26, 147, 689
AluI AGCT 3 cut(s) 26, 147, 689
Alw26I GTCTC 2 cut(s) 74, 540
AlwI GGATC 1 cut(s) 38
AoxI GGCC 2 cut(s) 279, 640
ApoI RAATTY 1 cut(s) 200
AsiGI ACCGGT 1 cut(s) 395
AspLEI GCGC 1 cut(s) 163
AspS9I GGNCC 2 cut(s) 381, 420
AsuHPI GGTGA 2 cut(s) 61, 119
AvaII GGWCC 2 cut(s) 381, 420
BaeGI GKGCMC 1 cut(s) 671
BalI TGGCCA 1 cut(s) 642
BbsI GAAGAC 2 cut(s) 451, 535
BccI CCATC 3 cut(s) 47, 361, 578
BciT130I CCWGG 1 cut(s) 493
BclI TGATCA 1 cut(s) 66
BcoDI GTCTC 2 cut(s) 74, 540
BfaI CTAG 2 cut(s) 342, 525
BglI GCCNNNNNGGC 1 cut(s) 173
BisI GCNGC 2 cut(s) 243, 282
BlsI GCNGC 2 cut(s) 244, 283
Bme1390I CCNGG 1 cut(s) 493
Bme18I GGWCC 2 cut(s) 381, 420
BmgBI CACGTC 1 cut(s) 449
BmgT120I GGNCC 2 cut(s) 381, 420
BmiI GGNNCC 2 cut(s) 337, 421
BmrFI CCNGG 1 cut(s) 493
BpiI GAAGAC 2 cut(s) 451, 535
BpuEI CTTGAG 2 cut(s) 98, 679
Bsa29I ATCGAT 1 cut(s) 42
BsaI GGTCTC 1 cut(s) 540
BsaJI CCNNGG 2 cut(s) 168, 384
BsaWI WCCGGW 1 cut(s) 395
Bse118I RCCGGY 1 cut(s) 395
BseBI CCWGG 1 cut(s) 493
BseCI ATCGAT 1 cut(s) 42
BseDI CCNNGG 2 cut(s) 168, 384
BseGI GGATG 1 cut(s) 353
BseMII CTCAG 2 cut(s) 75, 695
BseSI GKGCMC 1 cut(s) 671
Bsh1236I CGCG 1 cut(s) 219
BshFI GGCC 2 cut(s) 281, 642
BshTI ACCGGT 1 cut(s) 395
BshVI ATCGAT 1 cut(s) 42
BsiSI CCGG 2 cut(s) 47, 396
BsmAI GTCTC 2 cut(s) 74, 540
BsnI GGCC 2 cut(s) 281, 642
Bso31I GGTCTC 1 cut(s) 540
Bsp1286I GDGCHC 1 cut(s) 671
Bsp1407I TGTACA 1 cut(s) 316
Bsp143I GATC 3 cut(s) 43, 66, 220
BspACI CCGC 5 cut(s) 242, 282, 332, 369, 507
BspANI GGCC 2 cut(s) 281, 642
BspCNI CTCAG 2 cut(s) 76, 694
BspDI ATCGAT 1 cut(s) 42
BspFNI CGCG 1 cut(s) 219
BspLI GGNNCC 2 cut(s) 337, 421
BspPI GGATC 1 cut(s) 38
BspTNI GGTCTC 1 cut(s) 540
BsrFI RCCGGY 1 cut(s) 395
BsrGI TGTACA 1 cut(s) 316
BssAI RCCGGY 1 cut(s) 395
BssECI CCNNGG 2 cut(s) 168, 384
BssMI GATC 3 cut(s) 43, 66, 220
BssT1I CCWWGG 1 cut(s) 168
Bst2UI CCWGG 1 cut(s) 493
Bst4CI ACNGT 5 cut(s) 118, 413, 489, 551, 591
BstAUI TGTACA 1 cut(s) 316
BstC8I GCNNGC 2 cut(s) 165, 467
BstDEI CTNAG 3 cut(s) 27, 84, 681
BstF5I GGATG 1 cut(s) 353
BstFNI CGCG 1 cut(s) 219
BstHHI GCGC 1 cut(s) 163
BstKTI GATC 3 cut(s) 46, 69, 223
BstMAI GTCTC 2 cut(s) 74, 540
BstMBI GATC 3 cut(s) 43, 66, 220
BstMWI GCNNNNNNNGC 2 cut(s) 100, 173
BstNI CCWGG 1 cut(s) 493
BstNSI RCATGY 1 cut(s) 570
BstSCI CCNGG 1 cut(s) 491
BstSLI GKGCMC 1 cut(s) 671
BstUI CGCG 1 cut(s) 219
BstV2I GAAGAC 2 cut(s) 451, 535
Bsu15I ATCGAT 1 cut(s) 42
BsuRI GGCC 2 cut(s) 281, 642
BsuTUI ATCGAT 1 cut(s) 42
BtrI CACGTC 1 cut(s) 449
BtsCI GGATG 1 cut(s) 353
BtsIMutI CAGTG 1 cut(s) 596
Cac8I GCNNGC 2 cut(s) 165, 467
CfoI GCGC 1 cut(s) 163
Cfr10I RCCGGY 1 cut(s) 395
Cfr13I GGNCC 2 cut(s) 381, 420
ClaI ATCGAT 1 cut(s) 42
Csp6I GTAC 1 cut(s) 317
CspAI ACCGGT 1 cut(s) 395
CviAII CATG 5 cut(s) 112, 286, 567, 581, 647
CviQI GTAC 1 cut(s) 317
DdeI CTNAG 3 cut(s) 27, 84, 681
DpnI GATC 3 cut(s) 45, 68, 222
DpnII GATC 3 cut(s) 43, 66, 220
EaeI YGGCCR 2 cut(s) 279, 640
Eco130I CCWWGG 1 cut(s) 168
Eco31I GGTCTC 1 cut(s) 540
Eco47I GGWCC 2 cut(s) 381, 420
EcoRII CCWGG 1 cut(s) 491
EcoT14I CCWWGG 1 cut(s) 168
ErhI CCWWGG 1 cut(s) 168
FaeI CATG 5 cut(s) 115, 289, 570, 584, 650
FatI CATG 5 cut(s) 111, 285, 566, 580, 646
FauI CCCGC 1 cut(s) 325
FbaI TGATCA 1 cut(s) 66
FblI GTMKAC 1 cut(s) 403
Fnu4HI GCNGC 2 cut(s) 243, 282
FokI GGATG 1 cut(s) 340
Fsp4HI GCNGC 2 cut(s) 243, 282
FspBI CTAG 2 cut(s) 342, 525
GlaI GCGC 1 cut(s) 162
GluI GCNGC 2 cut(s) 243, 282
HaeIII GGCC 2 cut(s) 281, 642
HapII CCGG 2 cut(s) 47, 396
HhaI GCGC 1 cut(s) 163
Hin1II CATG 5 cut(s) 115, 289, 570, 584, 650
Hin6I GCGC 1 cut(s) 161
HinP1I GCGC 1 cut(s) 161
HinfI GANTC 2 cut(s) 425, 679
HpaII CCGG 2 cut(s) 47, 396
HphI GGTGA 2 cut(s) 61, 119
Hpy166II GTNNAC 4 cut(s) 317, 404, 452, 554
Hpy188I TCNGA 4 cut(s) 358, 385, 424, 564
Hpy188III TCNNGA 2 cut(s) 429, 525
Hpy8I GTNNAC 4 cut(s) 317, 404, 452, 554
Hpy99I CGWCG 2 cut(s) 138, 480
HpyCH4III ACNGT 5 cut(s) 118, 413, 489, 551, 591
HpyCH4IV ACGT 2 cut(s) 136, 448
HpyCH4V TGCA 1 cut(s) 94
HpyF10VI GCNNNNNNNGC 2 cut(s) 100, 173
HpyF3I CTNAG 3 cut(s) 27, 84, 681
HpySE526I ACGT 2 cut(s) 136, 448
Hsp92II CATG 5 cut(s) 115, 289, 570, 584, 650
HspAI GCGC 1 cut(s) 161
Ksp22I TGATCA 1 cut(s) 66
Kzo9I GATC 3 cut(s) 43, 66, 220
LmnI GCTCC 2 cut(s) 4, 686
LpnPI CCDG 8 cut(s) 34, 60, 177, 409, 420, 478, 505, 668
MaeI CTAG 2 cut(s) 342, 525
MaeII ACGT 2 cut(s) 136, 448
MaeIII GTNAC 2 cut(s) 107, 650
MalI GATC 3 cut(s) 45, 68, 222
MboI GATC 3 cut(s) 43, 66, 220
MboII GAAGA 2 cut(s) 456, 540
MhlI GDGCHC 1 cut(s) 671
MlsI TGGCCA 1 cut(s) 642
MluCI AATT 2 cut(s) 200, 436
MluNI TGGCCA 1 cut(s) 642
MlyI GAGTC 2 cut(s) 419, 673
MmeI TCCRAC 2 cut(s) 102, 447
Mox20I TGGCCA 1 cut(s) 642
MscI TGGCCA 1 cut(s) 642
MseI TTAA 2 cut(s) 540, 694
MslI CAYNNNNRTG 2 cut(s) 116, 582
Msp20I TGGCCA 1 cut(s) 642
MspI CCGG 2 cut(s) 47, 396
MspR9I CCNGG 1 cut(s) 493
MvaI CCWGG 1 cut(s) 493
MvnI CGCG 1 cut(s) 219
MwoI GCNNNNNNNGC 2 cut(s) 100, 173
NdeII GATC 3 cut(s) 43, 66, 220
NlaIII CATG 5 cut(s) 115, 289, 570, 584, 650
NlaIV GGNNCC 2 cut(s) 337, 421
NmuCI GTSAC 2 cut(s) 107, 650
NspI RCATGY 1 cut(s) 570
PciI ACATGT 1 cut(s) 566
PfoI TCCNGGA 1 cut(s) 491
PinAI ACCGGT 1 cut(s) 395
PkrI GCNGC 2 cut(s) 244, 283
PleI GAGTC 2 cut(s) 419, 673
PpsI GAGTC 2 cut(s) 419, 673
PscI ACATGT 1 cut(s) 566
Psp6I CCWGG 1 cut(s) 491
PspGI CCWGG 1 cut(s) 491
PspN4I GGNNCC 2 cut(s) 337, 421
PspPI GGNCC 2 cut(s) 381, 420
RsaI GTAC 1 cut(s) 318
RsaNI GTAC 1 cut(s) 317
RseI CAYNNNNRTG 2 cut(s) 116, 582
SaqAI TTAA 2 cut(s) 540, 694
SatI GCNGC 2 cut(s) 243, 282
Sau3AI GATC 3 cut(s) 43, 66, 220
Sau96I GGNCC 2 cut(s) 381, 420
SchI GAGTC 2 cut(s) 419, 673
ScrFI CCNGG 1 cut(s) 493
SduI GDGCHC 1 cut(s) 671
SinI GGWCC 2 cut(s) 381, 420
SmiMI CAYNNNNRTG 2 cut(s) 116, 582
SmlI CTYRAG 2 cut(s) 77, 658
SmoI CTYRAG 2 cut(s) 77, 658
Sse9I AATT 2 cut(s) 200, 436
SsiI CCGC 5 cut(s) 242, 282, 332, 369, 507
SspMI CTAG 2 cut(s) 342, 525
StyD4I CCNGG 1 cut(s) 491
StyI CCWWGG 1 cut(s) 168
TaaI ACNGT 5 cut(s) 118, 413, 489, 551, 591
TaiI ACGT 2 cut(s) 139, 451
TaqI TCGA 3 cut(s) 42, 377, 430
TasI AATT 2 cut(s) 200, 436
TatI WGTACW 1 cut(s) 316
TauI GCSGC 2 cut(s) 245, 284
Tru1I TTAA 2 cut(s) 540, 694
Tru9I TTAA 2 cut(s) 540, 694
TscAI CASTG 1 cut(s) 596
TseFI GTSAC 2 cut(s) 107, 650
Tsp45I GTSAC 2 cut(s) 107, 650
TspDTI ATGAA 1 cut(s) 302
TspGWI ACGGA 2 cut(s) 218, 469
TspRI CASTG 1 cut(s) 596
VpaK11BI GGWCC 2 cut(s) 381, 420
XapI RAATTY 1 cut(s) 200
XbaI TCTAGA 1 cut(s) 524
XceI RCATGY 1 cut(s) 570
XmiI GTMKAC 1 cut(s) 403
XspI CTAG 2 cut(s) 342, 525
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.