Rh5AG504400

Cleavage site for pathogenic type III effector avirulence factor Avr

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0008210
Physical Location & Seq
Reverse (-)
85407027 .. 85410203
3177 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG504400.1

Sequence Viewer

Length: 258 bp
ATGGGAAATTTTACTGATATCCAACAGGAAAAGGGTAGACCTCTCCCAAAATTTGGTGAATGGGATGTCAATGATCCTGCTTCAGCAGAAGGGTTTACTGTGATTTTTAACAAGGCTAGGGATGAAAAAAAGACAGGTGGCAAACCTGAGTCACCAACCAAGGCTGCTCAGAATAATGTCAGGCCTGGAGTGGATCCTAACAGGCCACCATCTAAAAAATGGTTTTGCTGCATGGCCCAACCACCTACACAATCTTGA
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

85

Amino Acids

9.4

Weight (kDa)

9.06

Isoelectric Point (pI)

47.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AvrRpt-cleavage PF05627 10 - 44 3.1e-20 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)
AccB7I CCANNNNNTGG 1 cut(s) 53
AccI GTMKAC 1 cut(s) 37
AclWI GGATC 3 cut(s) 68, 188, 201
AcsI RAATTY 2 cut(s) 7, 50
AcuI CTGAAG 1 cut(s) 66
AfiI CCNNNNNNNGG 1 cut(s) 53
AjnI CCWGG 1 cut(s) 184
AlwI GGATC 3 cut(s) 68, 188, 201
AoxI GGCC 3 cut(s) 182, 203, 234
ApeKI GCWGC 2 cut(s) 164, 228
ApoI RAATTY 2 cut(s) 7, 50
AspS9I GGNCC 1 cut(s) 235
AsuHPI GGTGA 2 cut(s) 68, 144
BamHI GGATCC 1 cut(s) 193
BbvI GCAGC 2 cut(s) 151, 215
BccI CCATC 1 cut(s) 217
BciT130I CCWGG 1 cut(s) 186
BfaI CTAG 1 cut(s) 117
BisI GCNGC 2 cut(s) 165, 229
BlsI GCNGC 2 cut(s) 166, 230
Bme1390I CCNGG 1 cut(s) 186
BmgT120I GGNCC 1 cut(s) 235
BmiI GGNNCC 1 cut(s) 195
BmrFI CCNGG 1 cut(s) 186
BpmI CTGGAG 1 cut(s) 207
BsaJI CCNNGG 1 cut(s) 159
Bsc4I CCNNNNNNNGG 1 cut(s) 53
BseBI CCWGG 1 cut(s) 186
BseDI CCNNGG 1 cut(s) 159
BseGI GGATG 2 cut(s) 70, 127
BseLI CCNNNNNNNGG 1 cut(s) 53
BseMII CTCAG 2 cut(s) 138, 182
BseXI GCAGC 2 cut(s) 151, 215
BshFI GGCC 3 cut(s) 184, 205, 236
BslI CCNNNNNNNGG 1 cut(s) 53
BsnI GGCC 3 cut(s) 184, 205, 236
Bsp143I GATC 2 cut(s) 73, 193
BspANI GGCC 3 cut(s) 184, 205, 236
BspCNI CTCAG 2 cut(s) 139, 181
BspLI GGNNCC 1 cut(s) 195
BspPI GGATC 3 cut(s) 68, 188, 201
BssECI CCNNGG 1 cut(s) 159
BssMI GATC 2 cut(s) 73, 193
BssT1I CCWWGG 1 cut(s) 159
Bst2UI CCWGG 1 cut(s) 186
Bst4CI ACNGT 1 cut(s) 100
BstDEI CTNAG 2 cut(s) 147, 168
BstF5I GGATG 2 cut(s) 70, 127
BstKTI GATC 2 cut(s) 76, 196
BstMBI GATC 2 cut(s) 73, 193
BstNI CCWGG 1 cut(s) 186
BstSCI CCNGG 1 cut(s) 184
BstV1I GCAGC 2 cut(s) 151, 215
BstX2I RGATCY 1 cut(s) 193
BstYI RGATCY 1 cut(s) 193
BsuRI GGCC 3 cut(s) 184, 205, 236
BtsCI GGATG 2 cut(s) 70, 127
Cfr13I GGNCC 1 cut(s) 235
CviAII CATG 1 cut(s) 232
CviJI RGCY 5 cut(s) 116, 164, 184, 205, 236
CviKI_1 RGCY 5 cut(s) 116, 164, 184, 205, 236
DdeI CTNAG 2 cut(s) 147, 168
DpnI GATC 2 cut(s) 75, 195
DpnII GATC 2 cut(s) 73, 193
Eco130I CCWWGG 1 cut(s) 159
Eco147I AGGCCT 1 cut(s) 184
Eco32I GATATC 1 cut(s) 19
Eco57I CTGAAG 1 cut(s) 66
EcoRII CCWGG 1 cut(s) 184
EcoRV GATATC 1 cut(s) 19
EcoT14I CCWWGG 1 cut(s) 159
ErhI CCWWGG 1 cut(s) 159
FaeI CATG 1 cut(s) 235
FaiI YATR 1 cut(s) 233
FatI CATG 1 cut(s) 231
FblI GTMKAC 1 cut(s) 37
Fnu4HI GCNGC 2 cut(s) 165, 229
FokI GGATG 2 cut(s) 77, 134
Fsp4HI GCNGC 2 cut(s) 165, 229
FspBI CTAG 1 cut(s) 117
GluI GCNGC 2 cut(s) 165, 229
GsuI CTGGAG 1 cut(s) 207
HaeIII GGCC 3 cut(s) 184, 205, 236
Hin1II CATG 1 cut(s) 235
HinfI GANTC 1 cut(s) 149
HphI GGTGA 2 cut(s) 68, 144
Hpy166II GTNNAC 2 cut(s) 38, 96
Hpy188I TCNGA 1 cut(s) 171
Hpy188III TCNNGA 1 cut(s) 255
Hpy8I GTNNAC 2 cut(s) 38, 96
HpyAV CCTTC 1 cut(s) 83
HpyCH4III ACNGT 1 cut(s) 100
HpyCH4V TGCA 1 cut(s) 231
HpyF3I CTNAG 2 cut(s) 147, 168
Hsp92II CATG 1 cut(s) 235
Kzo9I GATC 2 cut(s) 73, 193
LpnPI CCDG 8 cut(s) 11, 90, 120, 159, 166, 171, 187, 198
Lsp1109I GCAGC 2 cut(s) 151, 215
MaeI CTAG 1 cut(s) 117
MaeIII GTNAC 1 cut(s) 150
MalI GATC 2 cut(s) 75, 195
MboI GATC 2 cut(s) 73, 193
MflI RGATCY 1 cut(s) 193
MluCI AATT 2 cut(s) 7, 50
MlyI GAGTC 1 cut(s) 158
MmeI TCCRAC 1 cut(s) 46
MnlI CCTC 1 cut(s) 51
MseI TTAA 1 cut(s) 108
MspR9I CCNGG 1 cut(s) 186
MvaI CCWGG 1 cut(s) 186
NdeII GATC 2 cut(s) 73, 193
NlaIII CATG 1 cut(s) 235
NlaIV GGNNCC 1 cut(s) 195
NmuCI GTSAC 1 cut(s) 150
PceI AGGCCT 1 cut(s) 184
PflMI CCANNNNNTGG 1 cut(s) 53
PkrI GCNGC 2 cut(s) 166, 230
PleI GAGTC 1 cut(s) 157
PpsI GAGTC 1 cut(s) 157
Psp6I CCWGG 1 cut(s) 184
PspGI CCWGG 1 cut(s) 184
PspN4I GGNNCC 1 cut(s) 195
PspPI GGNCC 1 cut(s) 235
PsuI RGATCY 1 cut(s) 193
SaqAI TTAA 1 cut(s) 108
SatI GCNGC 2 cut(s) 165, 229
Sau3AI GATC 2 cut(s) 73, 193
Sau96I GGNCC 1 cut(s) 235
SchI GAGTC 1 cut(s) 158
ScrFI CCNGG 1 cut(s) 186
SetI ASST 4 cut(s) 43, 139, 148, 247
Sse9I AATT 2 cut(s) 7, 50
SseBI AGGCCT 1 cut(s) 184
SspMI CTAG 1 cut(s) 117
StuI AGGCCT 1 cut(s) 184
StyD4I CCNGG 1 cut(s) 184
StyI CCWWGG 1 cut(s) 159
TaaI ACNGT 1 cut(s) 100
TasI AATT 2 cut(s) 7, 50
Tru1I TTAA 1 cut(s) 108
Tru9I TTAA 1 cut(s) 108
TseFI GTSAC 1 cut(s) 150
TseI GCWGC 2 cut(s) 164, 228
Tsp45I GTSAC 1 cut(s) 150
TspDTI ATGAA 1 cut(s) 138
Van91I CCANNNNNTGG 1 cut(s) 53
XapI RAATTY 2 cut(s) 7, 50
XcmI CCANNNNNNNNNTGG 1 cut(s) 216
XmiI GTMKAC 1 cut(s) 37
XspI CTAG 1 cut(s) 117
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.