Rroxscaffold_1G00030580

Cleavage site for pathogenic type III effector avirulence factor Avr

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0012034
Physical Location & Seq
Reverse (-)
40649437 .. 40651338
1902 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00030580.1

Sequence Viewer

Length: 312 bp
ATGGGCCACCGGGAGGAGGGAAATGGTCGGAAGTCAATTCCTCAATTTGGAGGATGGGAACAAAACGCCGCAGTAGAGCCTACCAGCTATACTGTGGTGTTTAGTCAAGCTCGTGCTAACCGGAAGCAAAATAAGACTGACTTGACCGAGTTCAAGCGCAACAGCCTTGGAAATGAACAGGAATTAATGGCTGCTAAAGCCCATCATGATCATCGTCATCATTCTGATGATTCTGTTATGACGAAAAAGACATCATCTCCATTTAATTTTCTTTTGTCTCTCTTTTCATGCAGAGGAAAAAGACAATTCTGA
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

103

Amino Acids

11.78

Weight (kDa)

9.72

Isoelectric Point (pI)

47.31

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AvrRpt-cleavage PF05627 9 - 42 6.2e-10 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

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0012034)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G19473 AT5G19473
fragaria_vesca FvH4_3g27760 FvH4_3g27760
malus_domestica MD03G1164700.v1.1
prunus_persica Prupe.4G264200_v2.0.a1
rosa_chinensis RchiOBHm_Chr5g0050361
rosa_laevigata RLG00000034699
rosa_multiflora Rmu_sc0005060.1_g000015
rosa_roxburghii Rroxscaffold_1G00030580
rosa_rugosa Rorug05G0260100 Rorug05G0260200 Rorug05G0260300 Rorug05G0260400
rosa_samantha Rh5AG332100 Rh5BG342400 Rh5CG369600 Rh5DG355200
rosa_wichuraiana Rw5G031390

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 69
AfiI CCNNNNNNNGG 3 cut(s) 13, 16, 47
AgsI TTSAA 1 cut(s) 154
AluBI AGCT 2 cut(s) 87, 110
AluI AGCT 2 cut(s) 87, 110
Alw26I GTCTC 1 cut(s) 282
AoxI GGCC 1 cut(s) 4
ApeKI GCWGC 1 cut(s) 191
AseI ATTAAT 1 cut(s) 185
AspLEI GCGC 1 cut(s) 159
AspS9I GGNCC 1 cut(s) 4
AsuC2I CCSGG 1 cut(s) 11
BauI CACGAG 1 cut(s) 111
BbvI GCAGC 1 cut(s) 178
BccI CCATC 2 cut(s) 48, 210
BclI TGATCA 1 cut(s) 208
BcnI CCSGG 1 cut(s) 11
BcoDI GTCTC 1 cut(s) 282
BisI GCNGC 2 cut(s) 69, 192
BlsI GCNGC 2 cut(s) 70, 193
Bme1390I CCNGG 1 cut(s) 11
BmgT120I GGNCC 1 cut(s) 4
BmrFI CCNGG 1 cut(s) 11
BpuMI CCSGG 1 cut(s) 11
BsaJI CCNNGG 1 cut(s) 166
BsaWI WCCGGW 1 cut(s) 120
BsaXI ACNNNNNCTCC 2 cut(s) 241, 271
Bsc4I CCNNNNNNNGG 3 cut(s) 13, 16, 47
BseDI CCNNGG 1 cut(s) 166
BseGI GGATG 1 cut(s) 59
BseLI CCNNNNNNNGG 3 cut(s) 13, 16, 47
BseRI GAGGAG 1 cut(s) 29
BseXI GCAGC 1 cut(s) 178
BshFI GGCC 1 cut(s) 6
BsiSI CCGG 2 cut(s) 10, 121
BslI CCNNNNNNNGG 3 cut(s) 13, 16, 47
BsmAI GTCTC 1 cut(s) 282
BsnI GGCC 1 cut(s) 6
Bsp143I GATC 1 cut(s) 208
BspACI CCGC 1 cut(s) 69
BspANI GGCC 1 cut(s) 6
BspHI TCATGA 1 cut(s) 205
BssECI CCNNGG 1 cut(s) 166
BssMI GATC 1 cut(s) 208
BssSI CACGAG 1 cut(s) 111
BssT1I CCWWGG 1 cut(s) 166
Bst2BI CACGAG 1 cut(s) 111
Bst4CI ACNGT 1 cut(s) 94
BstF5I GGATG 1 cut(s) 59
BstHHI GCGC 1 cut(s) 159
BstKTI GATC 1 cut(s) 211
BstMAI GTCTC 1 cut(s) 282
BstMBI GATC 1 cut(s) 208
BstMWI GCNNNNNNNGC 1 cut(s) 197
BstSCI CCNGG 1 cut(s) 9
BstV1I GCAGC 1 cut(s) 178
BsuRI GGCC 1 cut(s) 6
BtsCI GGATG 1 cut(s) 59
CciI TCATGA 1 cut(s) 205
CfoI GCGC 1 cut(s) 159
Cfr13I GGNCC 1 cut(s) 4
CviAII CATG 2 cut(s) 206, 288
CviJI RGCY 7 cut(s) 6, 79, 87, 110, 165, 191, 200
CviKI_1 RGCY 7 cut(s) 6, 79, 87, 110, 165, 191, 200
DpnI GATC 1 cut(s) 210
DpnII GATC 1 cut(s) 208
Eco130I CCWWGG 1 cut(s) 166
EcoT14I CCWWGG 1 cut(s) 166
ErhI CCWWGG 1 cut(s) 166
FaeI CATG 2 cut(s) 209, 291
FaiI YATR 4 cut(s) 90, 207, 239, 289
FalI AAGNNNNNCTT 2 cut(s) 125, 157
FatI CATG 2 cut(s) 205, 287
FbaI TGATCA 1 cut(s) 208
Fnu4HI GCNGC 2 cut(s) 69, 192
FokI GGATG 1 cut(s) 66
Fsp4HI GCNGC 2 cut(s) 69, 192
GlaI GCGC 1 cut(s) 158
GluI GCNGC 2 cut(s) 69, 192
HaeIII GGCC 1 cut(s) 6
HapII CCGG 2 cut(s) 10, 121
HhaI GCGC 1 cut(s) 159
Hin1II CATG 2 cut(s) 209, 291
Hin6I GCGC 1 cut(s) 157
HinP1I GCGC 1 cut(s) 157
HinfI GANTC 1 cut(s) 230
HpaII CCGG 2 cut(s) 10, 121
Hpy188I TCNGA 3 cut(s) 30, 226, 311
Hpy188III TCNNGA 1 cut(s) 206
HpyCH4III ACNGT 1 cut(s) 94
HpyCH4V TGCA 1 cut(s) 291
HpyF10VI GCNNNNNNNGC 1 cut(s) 197
Hsp92II CATG 2 cut(s) 209, 291
HspAI GCGC 1 cut(s) 157
Ksp22I TGATCA 1 cut(s) 208
Kzo9I GATC 1 cut(s) 208
LpnPI CCDG 4 cut(s) 23, 97, 134, 164
Lsp1109I GCAGC 1 cut(s) 178
MalI GATC 1 cut(s) 210
MboI GATC 1 cut(s) 208
MluCI AATT 5 cut(s) 36, 44, 182, 265, 305
MmeI TCCRAC 1 cut(s) 8
MnlI CCTC 5 cut(s) 7, 10, 44, 51, 287
MseI TTAA 2 cut(s) 185, 264
MslI CAYNNNNRTG 1 cut(s) 225
MspI CCGG 2 cut(s) 10, 121
MspR9I CCNGG 1 cut(s) 11
MwoI GCNNNNNNNGC 1 cut(s) 197
NciI CCSGG 1 cut(s) 11
NdeII GATC 1 cut(s) 208
NlaIII CATG 2 cut(s) 209, 291
PagI TCATGA 1 cut(s) 205
PfeI GAWTC 1 cut(s) 230
PkrI GCNGC 2 cut(s) 70, 193
PshBI ATTAAT 1 cut(s) 185
PspPI GGNCC 1 cut(s) 4
RseI CAYNNNNRTG 1 cut(s) 225
SaqAI TTAA 2 cut(s) 185, 264
SatI GCNGC 2 cut(s) 69, 192
Sau3AI GATC 1 cut(s) 208
Sau96I GGNCC 1 cut(s) 4
ScrFI CCNGG 1 cut(s) 11
SetI ASST 2 cut(s) 89, 112
SmiMI CAYNNNNRTG 1 cut(s) 225
Sse9I AATT 5 cut(s) 36, 44, 182, 265, 305
SsiI CCGC 1 cut(s) 69
StyD4I CCNGG 1 cut(s) 9
StyI CCWWGG 1 cut(s) 166
TaaI ACNGT 1 cut(s) 94
TaqII GACCGA 1 cut(s) 161
TasI AATT 5 cut(s) 36, 44, 182, 265, 305
TauI GCSGC 1 cut(s) 71
TfiI GAWTC 1 cut(s) 230
Tru1I TTAA 2 cut(s) 185, 264
Tru9I TTAA 2 cut(s) 185, 264
TseI GCWGC 1 cut(s) 191
TspDTI ATGAA 2 cut(s) 189, 276
VspI ATTAAT 1 cut(s) 185
XcmI CCANNNNNNNNNTGG 1 cut(s) 91
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.