Rh6BG376700

Cleavage site for pathogenic type III effector avirulence factor Avr

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6B
OG0005965
Physical Location & Seq
Reverse (-)
60534366 .. 60541077
6712 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6BG376700.1

Sequence Viewer

Length: 477 bp
ATGCCAAAGTTCGGAGAATGGGACGTCAGTGATCCAGCATCAGCAGAGGGATTCACAGTAATCTTCAACAAGCTGGCAAGGACTGAGGAAAAGACTGGTGGCAGACCTGAGTCACCAGCAGAGGATGACTGCACATATAAGCATGGAGCAGTTCTCGGAAAGCCTACCATTGTAAACAATGCAGGAGTGGTTGGATGCATACTAAACCCTGAAACTTTTAGAGCAGTACTCAATAAGACATTCTGTGTATCTTCTACACAGGTAAGTCATGCCATTTCCAGGCATCTTATTGACCAGATGCATTATCTTCATCATGATCACCTCCGTGATTTTTTATCTACAACCGCAGAAACTGCAAGAACCATAAATACGAGGATGAAGATAATAAATACACCTACCCCTGTTAAGATTTCCATGAATGTAGCTGGTGTGGAGCTCATTTGGGGATCGAGTAATGCAGGAGGAAGAATTGCTTGA
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
AvrRpt-cleavage

Protein Analysis

158

Amino Acids

17.23

Weight (kDa)

7.05

Isoelectric Point (pI)

39.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AvrRpt-cleavage PF05627 2 - 26 6.8e-14 Cleavage site for pathogenic type III effector avirulence factor Avr
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)
AatII GACGTC 1 cut(s) 27
AciI CCGC 1 cut(s) 345
AclWI GGATC 2 cut(s) 26, 454
AcyI GRCGYC 1 cut(s) 24
AfaI GTAC 1 cut(s) 228
AfiI CCNNNNNNNGG 2 cut(s) 11, 279
AgsI TTSAA 1 cut(s) 67
AjnI CCWGG 1 cut(s) 278
AleI CACNNNNGTG 1 cut(s) 324
AluBI AGCT 3 cut(s) 73, 425, 436
AluI AGCT 3 cut(s) 73, 425, 436
Alw21I GWGCWC 1 cut(s) 438
AlwI GGATC 2 cut(s) 26, 454
AlwNI CAGNNNCTG 1 cut(s) 353
AsuHPI GGTGA 2 cut(s) 105, 311
BanII GRGCYC 1 cut(s) 438
Bbv12I GWGCWC 1 cut(s) 438
BciT130I CCWGG 1 cut(s) 280
BclI TGATCA 1 cut(s) 316
BmcAI AGTACT 1 cut(s) 228
Bme1390I CCNGG 1 cut(s) 280
BmrFI CCNGG 1 cut(s) 280
BmsI GCATC 4 cut(s) 47, 185, 288, 292
BoxI GACNNNNGTC 1 cut(s) 109
BplI GAGNNNNNCTC 4 cut(s) 138, 170, 213, 245
BsaHI GRCGYC 1 cut(s) 24
Bsc4I CCNNNNNNNGG 2 cut(s) 11, 279
Bse1I ACTGG 1 cut(s) 100
BseBI CCWGG 1 cut(s) 280
BseGI GGATG 3 cut(s) 130, 200, 381
BseLI CCNNNNNNNGG 2 cut(s) 11, 279
BseMII CTCAG 2 cut(s) 75, 99
BseNI ACTGG 1 cut(s) 100
BsgI GTGCAG 1 cut(s) 115
BsiHKAI GWGCWC 1 cut(s) 438
BslFI GGGAC 1 cut(s) 35
BslI CCNNNNNNNGG 2 cut(s) 11, 279
BsmFI GGGAC 1 cut(s) 35
Bsp1286I GDGCHC 1 cut(s) 438
Bsp143I GATC 3 cut(s) 31, 316, 446
BspACI CCGC 1 cut(s) 345
BspCNI CTCAG 2 cut(s) 76, 100
BspHI TCATGA 1 cut(s) 313
BspPI GGATC 2 cut(s) 26, 454
BsrI ACTGG 1 cut(s) 100
BssMI GATC 3 cut(s) 31, 316, 446
BssNI GRCGYC 1 cut(s) 24
Bst2UI CCWGG 1 cut(s) 280
Bst4CI ACNGT 1 cut(s) 58
BstACI GRCGYC 1 cut(s) 24
BstAPI GCANNNNNTGC 1 cut(s) 353
BstC8I GCNNGC 1 cut(s) 75
BstDEI CTNAG 2 cut(s) 84, 108
BstF5I GGATG 3 cut(s) 130, 200, 381
BstKTI GATC 3 cut(s) 34, 319, 449
BstMBI GATC 3 cut(s) 31, 316, 446
BstMWI GCNNNNNNNGC 1 cut(s) 353
BstNI CCWGG 1 cut(s) 280
BstPAI GACNNNNGTC 1 cut(s) 109
BstSCI CCNGG 1 cut(s) 278
BtsCI GGATG 3 cut(s) 130, 200, 381
BtsIMutI CAGTG 1 cut(s) 34
Cac8I GCNNGC 1 cut(s) 75
CaiI CAGNNNCTG 1 cut(s) 353
CciI TCATGA 1 cut(s) 313
Csp6I GTAC 1 cut(s) 227
CviAII CATG 4 cut(s) 143, 269, 314, 415
CviJI RGCY 4 cut(s) 73, 163, 425, 436
CviKI_1 RGCY 4 cut(s) 73, 163, 425, 436
CviQI GTAC 1 cut(s) 227
DdeI CTNAG 2 cut(s) 84, 108
DpnI GATC 3 cut(s) 33, 318, 448
DpnII GATC 3 cut(s) 31, 316, 446
Ecl136II GAGCTC 1 cut(s) 436
Eco24I GRGCYC 1 cut(s) 438
Eco53kI GAGCTC 1 cut(s) 436
EcoICRI GAGCTC 1 cut(s) 436
EcoRII CCWGG 1 cut(s) 278
EcoT22I ATGCAT 2 cut(s) 200, 303
EcoT38I GRGCYC 1 cut(s) 438
FaeI CATG 4 cut(s) 146, 272, 317, 418
FaiI YATR 8 cut(s) 136, 138, 144, 200, 270, 315, 365, 416
FalI AAGNNNNNCTT 1 cut(s) 457
FaqI GGGAC 1 cut(s) 35
FatI CATG 4 cut(s) 142, 268, 313, 414
FbaI TGATCA 1 cut(s) 316
FokI GGATG 3 cut(s) 137, 207, 388
FriOI GRGCYC 1 cut(s) 438
Hin1I GRCGYC 1 cut(s) 24
Hin1II CATG 4 cut(s) 146, 272, 317, 418
HinfI GANTC 2 cut(s) 51, 110
HphI GGTGA 2 cut(s) 105, 311
Hpy166II GTNNAC 1 cut(s) 175
Hpy188I TCNGA 2 cut(s) 14, 158
Hpy188III TCNNGA 1 cut(s) 314
Hpy8I GTNNAC 1 cut(s) 175
HpyCH4III ACNGT 1 cut(s) 58
HpyCH4IV ACGT 1 cut(s) 24
HpyCH4V TGCA 6 cut(s) 132, 182, 198, 301, 356, 458
HpyF10VI GCNNNNNNNGC 1 cut(s) 353
HpyF3I CTNAG 2 cut(s) 84, 108
HpySE526I ACGT 1 cut(s) 24
Hsp92I GRCGYC 1 cut(s) 24
Hsp92II CATG 4 cut(s) 146, 272, 317, 418
Ksp22I TGATCA 1 cut(s) 316
Kzo9I GATC 3 cut(s) 31, 316, 446
LmnI GCTCC 2 cut(s) 146, 433
LweI GCATC 4 cut(s) 47, 185, 288, 292
MaeII ACGT 1 cut(s) 24
MaeIII GTNAC 1 cut(s) 111
MalI GATC 3 cut(s) 33, 318, 448
MboI GATC 3 cut(s) 31, 316, 446
MboII GAAGA 5 cut(s) 55, 243, 299, 391, 477
MhlI GDGCHC 1 cut(s) 438
MluCI AATT 1 cut(s) 468
MlyI GAGTC 1 cut(s) 119
MmeI TCCRAC 1 cut(s) 172
MnlI CCTC 6 cut(s) 40, 79, 115, 332, 366, 455
Mph1103I ATGCAT 2 cut(s) 200, 303
MseI TTAA 1 cut(s) 405
MslI CAYNNNNRTG 1 cut(s) 324
MspR9I CCNGG 1 cut(s) 280
MvaI CCWGG 1 cut(s) 280
MwoI GCNNNNNNNGC 1 cut(s) 353
NdeII GATC 3 cut(s) 31, 316, 446
NlaIII CATG 4 cut(s) 146, 272, 317, 418
NmuCI GTSAC 1 cut(s) 111
NsiI ATGCAT 2 cut(s) 200, 303
OliI CACNNNNGTG 1 cut(s) 324
PagI TCATGA 1 cut(s) 313
PfeI GAWTC 1 cut(s) 51
PleI GAGTC 1 cut(s) 118
PpsI GAGTC 1 cut(s) 118
PshAI GACNNNNGTC 1 cut(s) 109
Psp124BI GAGCTC 1 cut(s) 438
Psp6I CCWGG 1 cut(s) 278
PspGI CCWGG 1 cut(s) 278
PsrI GAACNNNNNNTAC 2 cut(s) 352, 384
PstNI CAGNNNCTG 1 cut(s) 353
RsaI GTAC 1 cut(s) 228
RsaNI GTAC 1 cut(s) 227
RseI CAYNNNNRTG 1 cut(s) 324
SacI GAGCTC 1 cut(s) 438
SaqAI TTAA 1 cut(s) 405
Sau3AI GATC 3 cut(s) 31, 316, 446
ScaI AGTACT 1 cut(s) 228
SchI GAGTC 1 cut(s) 119
ScrFI CCNGG 1 cut(s) 280
SduI GDGCHC 1 cut(s) 438
SetI ASST 8 cut(s) 27, 75, 109, 264, 324, 397, 427, 438
SfaNI GCATC 4 cut(s) 47, 185, 288, 292
SmiMI CAYNNNNRTG 1 cut(s) 324
Sse9I AATT 1 cut(s) 468
SsiI CCGC 1 cut(s) 345
SstI GAGCTC 1 cut(s) 438
StyD4I CCNGG 1 cut(s) 278
TaaI ACNGT 1 cut(s) 58
TaiI ACGT 1 cut(s) 27
TaqI TCGA 1 cut(s) 449
TasI AATT 1 cut(s) 468
TatI WGTACW 1 cut(s) 226
TfiI GAWTC 1 cut(s) 51
Tru1I TTAA 1 cut(s) 405
Tru9I TTAA 1 cut(s) 405
TscAI CASTG 1 cut(s) 34
TseFI GTSAC 1 cut(s) 111
Tsp45I GTSAC 1 cut(s) 111
TspDTI ATGAA 3 cut(s) 299, 392, 431
TspGWI ACGGA 1 cut(s) 314
TspRI CASTG 1 cut(s) 34
ZraI GACGTC 1 cut(s) 25
ZrmI AGTACT 1 cut(s) 228
Zsp2I ATGCAT 2 cut(s) 200, 303
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.