Rh5DG538200

Cleavage site for pathogenic type III effector avirulence factor Avr

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0008210
Physical Location & Seq
Reverse (-)
83001561 .. 83004715
3155 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG538200.1

Sequence Viewer

Length: 237 bp
ATGTCGGAAAAGGGTAGACCTCTCCCAAAATTTGGTGAATGGGATGTCAATGATCCTGCTTCAGCAGAAGGGTTTACTGTGATTTTTAACAAGGCTAGGGATGAAAAAAAGACAGGTGGCAAACCTGAGTCACCAACCAAGGATGCTCAGAATAATGTCAGGCCTGGAGTGGATCCTGGCAGGCCACCATCTAAAAAATGGTTTTGCTGCATGGCCCAACCACCTACACAATCTTGA
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

78

Amino Acids

8.57

Weight (kDa)

9.06

Isoelectric Point (pI)

56.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AvrRpt-cleavage PF05627 3 - 37 2.6e-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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 32
AccI GTMKAC 1 cut(s) 16
AclWI GGATC 3 cut(s) 47, 167, 180
AcsI RAATTY 1 cut(s) 29
AcuI CTGAAG 1 cut(s) 45
AfiI CCNNNNNNNGG 1 cut(s) 32
AjnI CCWGG 2 cut(s) 163, 175
AlwI GGATC 3 cut(s) 47, 167, 180
AoxI GGCC 3 cut(s) 161, 182, 213
ApeKI GCWGC 1 cut(s) 207
ApoI RAATTY 1 cut(s) 29
AspS9I GGNCC 1 cut(s) 214
AsuHPI GGTGA 2 cut(s) 47, 123
BamHI GGATCC 1 cut(s) 172
BbvI GCAGC 1 cut(s) 194
BccI CCATC 1 cut(s) 196
BciT130I CCWGG 2 cut(s) 165, 177
BfaI CTAG 1 cut(s) 96
BisI GCNGC 1 cut(s) 208
BlsI GCNGC 1 cut(s) 209
Bme1390I CCNGG 2 cut(s) 165, 177
BmgT120I GGNCC 1 cut(s) 214
BmiI GGNNCC 1 cut(s) 174
BmrFI CCNGG 2 cut(s) 165, 177
BmsI GCATC 1 cut(s) 133
BpmI CTGGAG 1 cut(s) 186
BsaJI CCNNGG 1 cut(s) 138
Bsc4I CCNNNNNNNGG 1 cut(s) 32
BseBI CCWGG 2 cut(s) 165, 177
BseDI CCNNGG 1 cut(s) 138
BseGI GGATG 3 cut(s) 49, 106, 148
BseLI CCNNNNNNNGG 1 cut(s) 32
BseMII CTCAG 2 cut(s) 117, 161
BseXI GCAGC 1 cut(s) 194
BshFI GGCC 3 cut(s) 163, 184, 215
BslI CCNNNNNNNGG 1 cut(s) 32
BsnI GGCC 3 cut(s) 163, 184, 215
Bsp143I GATC 2 cut(s) 52, 172
BspANI GGCC 3 cut(s) 163, 184, 215
BspCNI CTCAG 2 cut(s) 118, 160
BspLI GGNNCC 1 cut(s) 174
BspPI GGATC 3 cut(s) 47, 167, 180
BssECI CCNNGG 1 cut(s) 138
BssMI GATC 2 cut(s) 52, 172
BssT1I CCWWGG 1 cut(s) 138
Bst2UI CCWGG 2 cut(s) 165, 177
Bst4CI ACNGT 1 cut(s) 79
BstC8I GCNNGC 1 cut(s) 182
BstDEI CTNAG 2 cut(s) 126, 147
BstF5I GGATG 3 cut(s) 49, 106, 148
BstKTI GATC 2 cut(s) 55, 175
BstMBI GATC 2 cut(s) 52, 172
BstNI CCWGG 2 cut(s) 165, 177
BstSCI CCNGG 2 cut(s) 163, 175
BstV1I GCAGC 1 cut(s) 194
BstX2I RGATCY 1 cut(s) 172
BstYI RGATCY 1 cut(s) 172
BsuRI GGCC 3 cut(s) 163, 184, 215
BtsCI GGATG 3 cut(s) 49, 106, 148
Cac8I GCNNGC 1 cut(s) 182
Cfr13I GGNCC 1 cut(s) 214
CviAII CATG 1 cut(s) 211
CviJI RGCY 4 cut(s) 95, 163, 184, 215
CviKI_1 RGCY 4 cut(s) 95, 163, 184, 215
DdeI CTNAG 2 cut(s) 126, 147
DpnI GATC 2 cut(s) 54, 174
DpnII GATC 2 cut(s) 52, 172
Eco130I CCWWGG 1 cut(s) 138
Eco147I AGGCCT 1 cut(s) 163
Eco57I CTGAAG 1 cut(s) 45
EcoRII CCWGG 2 cut(s) 163, 175
EcoT14I CCWWGG 1 cut(s) 138
ErhI CCWWGG 1 cut(s) 138
FaeI CATG 1 cut(s) 214
FaiI YATR 1 cut(s) 212
FatI CATG 1 cut(s) 210
FblI GTMKAC 1 cut(s) 16
Fnu4HI GCNGC 1 cut(s) 208
FokI GGATG 3 cut(s) 56, 113, 155
Fsp4HI GCNGC 1 cut(s) 208
FspBI CTAG 1 cut(s) 96
GluI GCNGC 1 cut(s) 208
GsuI CTGGAG 1 cut(s) 186
HaeIII GGCC 3 cut(s) 163, 184, 215
Hin1II CATG 1 cut(s) 214
HinfI GANTC 1 cut(s) 128
HphI GGTGA 2 cut(s) 47, 123
Hpy166II GTNNAC 2 cut(s) 17, 75
Hpy188I TCNGA 2 cut(s) 7, 150
Hpy188III TCNNGA 1 cut(s) 234
Hpy8I GTNNAC 2 cut(s) 17, 75
HpyAV CCTTC 1 cut(s) 62
HpyCH4III ACNGT 1 cut(s) 79
HpyCH4V TGCA 1 cut(s) 210
HpyF3I CTNAG 2 cut(s) 126, 147
Hsp92II CATG 1 cut(s) 214
Kzo9I GATC 2 cut(s) 52, 172
LpnPI CCDG 9 cut(s) 69, 99, 138, 145, 150, 162, 166, 177, 189
Lsp1109I GCAGC 1 cut(s) 194
LweI GCATC 1 cut(s) 133
MaeI CTAG 1 cut(s) 96
MaeIII GTNAC 1 cut(s) 129
MalI GATC 2 cut(s) 54, 174
MboI GATC 2 cut(s) 52, 172
MflI RGATCY 1 cut(s) 172
MluCI AATT 1 cut(s) 29
MlyI GAGTC 1 cut(s) 137
MnlI CCTC 1 cut(s) 30
MseI TTAA 1 cut(s) 87
MspR9I CCNGG 2 cut(s) 165, 177
MvaI CCWGG 2 cut(s) 165, 177
NdeII GATC 2 cut(s) 52, 172
NlaIII CATG 1 cut(s) 214
NlaIV GGNNCC 1 cut(s) 174
NmuCI GTSAC 1 cut(s) 129
PceI AGGCCT 1 cut(s) 163
PflMI CCANNNNNTGG 1 cut(s) 32
PkrI GCNGC 1 cut(s) 209
PleI GAGTC 1 cut(s) 136
PpsI GAGTC 1 cut(s) 136
Psp6I CCWGG 2 cut(s) 163, 175
PspGI CCWGG 2 cut(s) 163, 175
PspN4I GGNNCC 1 cut(s) 174
PspPI GGNCC 1 cut(s) 214
PsuI RGATCY 1 cut(s) 172
SaqAI TTAA 1 cut(s) 87
SatI GCNGC 1 cut(s) 208
Sau3AI GATC 2 cut(s) 52, 172
Sau96I GGNCC 1 cut(s) 214
SchI GAGTC 1 cut(s) 137
ScrFI CCNGG 2 cut(s) 165, 177
SetI ASST 4 cut(s) 22, 118, 127, 226
SfaNI GCATC 1 cut(s) 133
Sse9I AATT 1 cut(s) 29
SseBI AGGCCT 1 cut(s) 163
SspMI CTAG 1 cut(s) 96
StuI AGGCCT 1 cut(s) 163
StyD4I CCNGG 2 cut(s) 163, 175
StyI CCWWGG 1 cut(s) 138
TaaI ACNGT 1 cut(s) 79
TasI AATT 1 cut(s) 29
Tru1I TTAA 1 cut(s) 87
Tru9I TTAA 1 cut(s) 87
TseFI GTSAC 1 cut(s) 129
TseI GCWGC 1 cut(s) 207
Tsp45I GTSAC 1 cut(s) 129
TspDTI ATGAA 1 cut(s) 117
Van91I CCANNNNNTGG 1 cut(s) 32
XapI RAATTY 1 cut(s) 29
XcmI CCANNNNNNNNNTGG 1 cut(s) 195
XmiI GTMKAC 1 cut(s) 16
XspI CTAG 1 cut(s) 96
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.