Rh5DG355200

Cleavage site for pathogenic type III effector avirulence factor Avr

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0012034
Physical Location & Seq
Forward (+)
52408706 .. 52411741
3036 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG355200.1

Sequence Viewer

Length: 438 bp
ATGGGACACCGGGAGGAGGGAAATGGTCGGAAGTCAATTCCTCAATTTGGAGGATGGGAACAAAACGCCACTGTAGAGCCTACCAGCTATACTGTGGTGTTTAGTCAAGCTCGTGCTAACCGGAAGCAAAATAAGACTGACTTGACCGAGTTCAAGCGCAACAGCCTTGGAAATGAACAGGAATTAATGGCTGCTCAAGGCCATCATGATCATCGTCATCATTCTGATGATTCTGTTACGGTAACACTATCTGTTTCGATCTCCAATTATTCCTTACATATCATCTTGGTAGTTGATTTAATTTTTCTTTTTTCTCTCTTTTCATGCAGACGAAAAAGACATCATCTCCATTTAATTTTCTTTTGTCTCTCTTTTCATGCAGAGGAAAAAGACAATTCTGACCTACATAAATTGTTGTATCAGGCCTTGATTTCTTGA
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

145

Amino Acids

16.71

Weight (kDa)

7.22

Isoelectric Point (pI)

45.05

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
AvrRpt-cleavage PF05627 9 - 42 2.6e-09 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
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AfiI CCNNNNNNNGG 2 cut(s) 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) 371
AoxI GGCC 2 cut(s) 199, 423
ApeKI GCWGC 1 cut(s) 191
AseI ATTAAT 1 cut(s) 185
AspLEI GCGC 1 cut(s) 159
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) 371
BfmI CTRYAG 1 cut(s) 72
BisI GCNGC 1 cut(s) 192
BlsI GCNGC 1 cut(s) 193
Bme1390I CCNGG 1 cut(s) 11
BmrFI CCNGG 1 cut(s) 11
BpuEI CTTGAG 1 cut(s) 180
BpuMI CCSGG 1 cut(s) 11
BsaJI CCNNGG 1 cut(s) 166
BsaWI WCCGGW 1 cut(s) 120
BsaXI ACNNNNNCTCC 2 cut(s) 330, 360
Bsc4I CCNNNNNNNGG 2 cut(s) 16, 47
BseDI CCNNGG 1 cut(s) 166
BseGI GGATG 1 cut(s) 59
BseLI CCNNNNNNNGG 2 cut(s) 16, 47
BseRI GAGGAG 1 cut(s) 29
BseXI GCAGC 1 cut(s) 178
BshFI GGCC 2 cut(s) 201, 425
BsiSI CCGG 2 cut(s) 10, 121
BslFI GGGAC 1 cut(s) 18
BslI CCNNNNNNNGG 2 cut(s) 16, 47
BsmAI GTCTC 1 cut(s) 371
BsmFI GGGAC 1 cut(s) 18
BsnI GGCC 2 cut(s) 201, 425
Bsp143I GATC 2 cut(s) 208, 258
BspANI GGCC 2 cut(s) 201, 425
BspHI TCATGA 1 cut(s) 205
BssECI CCNNGG 1 cut(s) 166
BssMI GATC 2 cut(s) 208, 258
BssSI CACGAG 1 cut(s) 111
BssT1I CCWWGG 1 cut(s) 166
Bst2BI CACGAG 1 cut(s) 111
Bst4CI ACNGT 3 cut(s) 73, 94, 241
BstF5I GGATG 1 cut(s) 59
BstHHI GCGC 1 cut(s) 159
BstKTI GATC 2 cut(s) 211, 261
BstMAI GTCTC 1 cut(s) 371
BstMBI GATC 2 cut(s) 208, 258
BstSCI CCNGG 1 cut(s) 9
BstSFI CTRYAG 1 cut(s) 72
BstV1I GCAGC 1 cut(s) 178
BsuRI GGCC 2 cut(s) 201, 425
BtsCI GGATG 1 cut(s) 59
BtsIMutI CAGTG 1 cut(s) 69
CciI TCATGA 1 cut(s) 205
CfoI GCGC 1 cut(s) 159
CviAII CATG 3 cut(s) 206, 324, 377
CviJI RGCY 7 cut(s) 79, 87, 110, 165, 191, 201, 425
CviKI_1 RGCY 7 cut(s) 79, 87, 110, 165, 191, 201, 425
DpnI GATC 2 cut(s) 210, 260
DpnII GATC 2 cut(s) 208, 258
Eco130I CCWWGG 1 cut(s) 166
Eco147I AGGCCT 1 cut(s) 425
EcoT14I CCWWGG 1 cut(s) 166
ErhI CCWWGG 1 cut(s) 166
FaeI CATG 3 cut(s) 209, 327, 380
FaiI YATR 6 cut(s) 90, 207, 279, 325, 378, 408
FalI AAGNNNNNCTT 2 cut(s) 125, 157
FaqI GGGAC 1 cut(s) 18
FatI CATG 3 cut(s) 205, 323, 376
FbaI TGATCA 1 cut(s) 208
Fnu4HI GCNGC 1 cut(s) 192
FokI GGATG 1 cut(s) 66
Fsp4HI GCNGC 1 cut(s) 192
GlaI GCGC 1 cut(s) 158
GluI GCNGC 1 cut(s) 192
HaeIII GGCC 2 cut(s) 201, 425
HapII CCGG 2 cut(s) 10, 121
HhaI GCGC 1 cut(s) 159
Hin1II CATG 3 cut(s) 209, 327, 380
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, 400
Hpy188III TCNNGA 2 cut(s) 206, 435
HpyCH4III ACNGT 3 cut(s) 73, 94, 241
HpyCH4V TGCA 2 cut(s) 327, 380
Hsp92II CATG 3 cut(s) 209, 327, 380
HspAI GCGC 1 cut(s) 157
Ksp22I TGATCA 1 cut(s) 208
Kzo9I GATC 2 cut(s) 208, 258
LpnPI CCDG 5 cut(s) 23, 97, 134, 164, 407
Lsp1109I GCAGC 1 cut(s) 178
MaeIII GTNAC 2 cut(s) 235, 241
MalI GATC 2 cut(s) 210, 260
MboI GATC 2 cut(s) 208, 258
MluCI AATT 8 cut(s) 36, 44, 182, 265, 300, 354, 394, 410
MmeI TCCRAC 1 cut(s) 8
MnlI CCTC 5 cut(s) 7, 10, 44, 51, 376
MseI TTAA 3 cut(s) 185, 299, 353
MslI CAYNNNNRTG 1 cut(s) 225
MspI CCGG 2 cut(s) 10, 121
MspR9I CCNGG 1 cut(s) 11
NciI CCSGG 1 cut(s) 11
NdeII GATC 2 cut(s) 208, 258
NlaIII CATG 3 cut(s) 209, 327, 380
PagI TCATGA 1 cut(s) 205
PceI AGGCCT 1 cut(s) 425
PfeI GAWTC 1 cut(s) 230
PkrI GCNGC 1 cut(s) 193
PshBI ATTAAT 1 cut(s) 185
RseI CAYNNNNRTG 1 cut(s) 225
SaqAI TTAA 3 cut(s) 185, 299, 353
SatI GCNGC 1 cut(s) 192
Sau3AI GATC 2 cut(s) 208, 258
ScrFI CCNGG 1 cut(s) 11
SetI ASST 3 cut(s) 89, 112, 405
SfcI CTRYAG 1 cut(s) 72
SmiMI CAYNNNNRTG 1 cut(s) 225
SmlI CTYRAG 1 cut(s) 195
SmoI CTYRAG 1 cut(s) 195
Sse9I AATT 8 cut(s) 36, 44, 182, 265, 300, 354, 394, 410
SseBI AGGCCT 1 cut(s) 425
StuI AGGCCT 1 cut(s) 425
StyD4I CCNGG 1 cut(s) 9
StyI CCWWGG 1 cut(s) 166
TaaI ACNGT 3 cut(s) 73, 94, 241
TaqI TCGA 1 cut(s) 257
TaqII GACCGA 1 cut(s) 161
TasI AATT 8 cut(s) 36, 44, 182, 265, 300, 354, 394, 410
TfiI GAWTC 1 cut(s) 230
Tru1I TTAA 3 cut(s) 185, 299, 353
Tru9I TTAA 3 cut(s) 185, 299, 353
TscAI CASTG 1 cut(s) 76
TseI GCWGC 1 cut(s) 191
TspDTI ATGAA 3 cut(s) 189, 312, 365
TspRI CASTG 1 cut(s) 76
VspI ATTAAT 1 cut(s) 185
XcmI CCANNNNNNNNNTGG 1 cut(s) 91
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.