Rorug03G0042900

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000003
OG0015649
Physical Location & Seq
Forward (+)
3310481 .. 3317178
6698 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug03G0042900.1

Sequence Viewer

Length: 522 bp
ATGGTTGAGAGGATTTATGAATTGTTTCATTATGAAACCACTGGCCCAGAGATCTGGAGAGACTCCGCAGGGAAAGTTGATATCTTGGTTTCAGGGATAGGAACCGGTGGCACAGTAACCGGTATAGGGAAATTTCTTAAAGAGCAAAATCCAGAGATCAAGGTTTGCGGTGTAGAACCAGTTGAGAGTGCAGTCTTGAATGGAGGTCCACCTGGAAGGCATCTGATCCAAGGAATCGGTGTTGGCTTCATACCTCAAGTTCTCGATGTTAGCCTGCTAGACGAAGTTATTCCAGTATCCAGTGAGGAATCTATTGAGACTGCTAAGCTACTTGCCTTGAAAGAAGGTCTTTTGGTGGGATTCTCATCTGGTGCTGCAACAGCAGCAGCAATAAAGTTGGCAAAAAGGCCAGAAAATGCCGGAAAACTAATAGTTGTCGTGTTCCCCTGTTGTGGAGAGCGGTATCTGTCTACTGAACTCTTTGATACCATTAGGCATGAGGCAGAAAACATGACACTTTGA
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
PPR PPR_1 PPR_2 PPR_3

Protein Analysis

173

Amino Acids

18.45

Weight (kDa)

4.91

Isoelectric Point (pI)

28.05

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PALP PF00291 11 - 149 7.6e-33 Pyridoxal-phosphate dependent enzyme
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0015649)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g09870
malus_domestica MD04G1174700.v1.1
prunus_persica Prupe.6G293600_v2.0.a1
pyrus_communis pycom04g15410
rosa_chinensis RchiOBHm_Chr3g0460471
rosa_laevigata RLG00000025002 RLG00000025008
rosa_multiflora Rmu_co8379257.1_g000001 Rmu_sc0004267.1_g000007
rosa_roxburghii Rroxscaffold_6G00419450
rosa_rugosa Rorug03G0042900
rosa_samantha Rh3AG101000 Rh3BG105000 Rh3CG106800 Rh3DG106300
rosa_wichuraiana Rw3G008590

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 460
AccI GTMKAC 1 cut(s) 470
AciI CCGC 3 cut(s) 66, 168, 460
AclWI GGATC 1 cut(s) 220
AcsI RAATTY 1 cut(s) 131
AfiI CCNNNNNNNGG 2 cut(s) 126, 452
AgeI ACCGGT 2 cut(s) 104, 119
AgsI TTSAA 2 cut(s) 199, 340
AjnI CCWGG 1 cut(s) 211
AluBI AGCT 1 cut(s) 328
AluI AGCT 1 cut(s) 328
Alw26I GTCTC 2 cut(s) 54, 311
AlwI GGATC 1 cut(s) 220
AoxI GGCC 2 cut(s) 43, 407
ApeKI GCWGC 3 cut(s) 374, 383, 386
ApoI RAATTY 1 cut(s) 131
AsiGI ACCGGT 2 cut(s) 104, 119
Asp700I GAANNNNTTC 2 cut(s) 24, 288
AspS9I GGNCC 2 cut(s) 44, 206
AvaII GGWCC 1 cut(s) 206
BbvI GCAGC 3 cut(s) 361, 395, 398
BciT130I CCWGG 1 cut(s) 213
BciVI GTATCC 1 cut(s) 307
BcoDI GTCTC 2 cut(s) 54, 311
BfaI CTAG 1 cut(s) 278
BfuI GTATCC 1 cut(s) 307
BglII AGATCT 1 cut(s) 51
BisI GCNGC 3 cut(s) 375, 384, 387
BlpI GCTNAGC 1 cut(s) 324
BlsI GCNGC 3 cut(s) 376, 385, 388
Bme1390I CCNGG 1 cut(s) 213
Bme18I GGWCC 1 cut(s) 206
BmgT120I GGNCC 2 cut(s) 44, 206
BmiI GGNNCC 1 cut(s) 103
BmrFI CCNGG 1 cut(s) 213
BmsI GCATC 1 cut(s) 229
BpmI CTGGAG 1 cut(s) 76
Bpu1102I GCTNAGC 1 cut(s) 324
BpuEI CTTGAG 1 cut(s) 240
BsaBI GATNNNNATC 1 cut(s) 364
BsaJI CCNNGG 1 cut(s) 229
BsaWI WCCGGW 2 cut(s) 104, 119
Bsc4I CCNNNNNNNGG 2 cut(s) 126, 452
Bse118I RCCGGY 2 cut(s) 104, 119
Bse1I ACTGG 4 cut(s) 46, 179, 293, 300
Bse8I GATNNNNATC 1 cut(s) 364
BseBI CCWGG 1 cut(s) 213
BseDI CCNNGG 1 cut(s) 229
BseJI GATNNNNATC 1 cut(s) 364
BseLI CCNNNNNNNGG 2 cut(s) 126, 452
BseNI ACTGG 4 cut(s) 46, 179, 293, 300
BseXI GCAGC 3 cut(s) 361, 395, 398
BsgI GTGCAG 1 cut(s) 210
BshFI GGCC 2 cut(s) 45, 409
BshTI ACCGGT 2 cut(s) 104, 119
BsiSI CCGG 3 cut(s) 105, 120, 420
BslI CCNNNNNNNGG 2 cut(s) 126, 452
BsmAI GTCTC 2 cut(s) 54, 311
BsnI GGCC 2 cut(s) 45, 409
Bsp143I GATC 3 cut(s) 51, 156, 225
Bsp1720I GCTNAGC 1 cut(s) 324
BspACI CCGC 3 cut(s) 66, 168, 460
BspANI GGCC 2 cut(s) 45, 409
BspLI GGNNCC 1 cut(s) 103
BspPI GGATC 1 cut(s) 220
BsrBI CCGCTC 1 cut(s) 460
BsrFI RCCGGY 2 cut(s) 104, 119
BsrI ACTGG 4 cut(s) 46, 179, 293, 300
BssAI RCCGGY 2 cut(s) 104, 119
BssECI CCNNGG 1 cut(s) 229
BssMI GATC 3 cut(s) 51, 156, 225
BssT1I CCWWGG 1 cut(s) 229
Bst2UI CCWGG 1 cut(s) 213
Bst4CI ACNGT 1 cut(s) 115
BstC8I GCNNGC 1 cut(s) 275
BstDEI CTNAG 1 cut(s) 324
BstKTI GATC 3 cut(s) 54, 159, 228
BstMAI GTCTC 2 cut(s) 54, 311
BstMBI GATC 3 cut(s) 51, 156, 225
BstMWI GCNNNNNNNGC 2 cut(s) 380, 383
BstNI CCWGG 1 cut(s) 213
BstSCI CCNGG 1 cut(s) 211
BstV1I GCAGC 3 cut(s) 361, 395, 398
BstX2I RGATCY 1 cut(s) 51
BstXI CCANNNNNNTGG 1 cut(s) 54
BstYI RGATCY 1 cut(s) 51
BsuI GTATCC 1 cut(s) 307
BsuRI GGCC 2 cut(s) 45, 409
BtsIMutI CAGTG 2 cut(s) 39, 307
Cac8I GCNNGC 1 cut(s) 275
Cfr10I RCCGGY 2 cut(s) 104, 119
Cfr13I GGNCC 2 cut(s) 44, 206
CspAI ACCGGT 2 cut(s) 104, 119
CviAII CATG 2 cut(s) 497, 511
CviJI RGCY 5 cut(s) 45, 246, 273, 328, 409
CviKI_1 RGCY 5 cut(s) 45, 246, 273, 328, 409
DdeI CTNAG 1 cut(s) 324
DpnI GATC 3 cut(s) 53, 158, 227
DpnII GATC 3 cut(s) 51, 156, 225
Eco130I CCWWGG 1 cut(s) 229
Eco32I GATATC 1 cut(s) 82
Eco47I GGWCC 1 cut(s) 206
EcoRII CCWGG 1 cut(s) 211
EcoRV GATATC 1 cut(s) 82
EcoT14I CCWWGG 1 cut(s) 229
ErhI CCWWGG 1 cut(s) 229
FaeI CATG 2 cut(s) 500, 514
FaiI YATR 6 cut(s) 18, 33, 125, 251, 498, 512
FalI AAGNNNNNCTT 2 cut(s) 333, 365
FatI CATG 2 cut(s) 496, 510
FblI GTMKAC 1 cut(s) 470
Fnu4HI GCNGC 3 cut(s) 375, 384, 387
Fsp4HI GCNGC 3 cut(s) 375, 384, 387
FspBI CTAG 1 cut(s) 278
GluI GCNGC 3 cut(s) 375, 384, 387
GsuI CTGGAG 1 cut(s) 76
HaeIII GGCC 2 cut(s) 45, 409
HapII CCGG 3 cut(s) 105, 120, 420
Hin1II CATG 2 cut(s) 500, 514
HinfI GANTC 4 cut(s) 62, 234, 308, 360
HpaII CCGG 3 cut(s) 105, 120, 420
Hpy166II GTNNAC 2 cut(s) 209, 471
Hpy188I TCNGA 1 cut(s) 225
Hpy188III TCNNGA 4 cut(s) 55, 152, 196, 263
Hpy8I GTNNAC 2 cut(s) 209, 471
HpyAV CCTTC 2 cut(s) 210, 338
HpyCH4III ACNGT 1 cut(s) 115
HpyCH4V TGCA 2 cut(s) 191, 377
HpyF10VI GCNNNNNNNGC 2 cut(s) 380, 383
HpyF3I CTNAG 1 cut(s) 324
Hsp92II CATG 2 cut(s) 500, 514
Kzo9I GATC 3 cut(s) 51, 156, 225
Lsp1109I GCAGC 3 cut(s) 361, 395, 398
LweI GCATC 1 cut(s) 229
MaeI CTAG 1 cut(s) 278
MaeIII GTNAC 1 cut(s) 115
MalI GATC 3 cut(s) 53, 158, 227
MbiI CCGCTC 1 cut(s) 460
MboI GATC 3 cut(s) 51, 156, 225
MflI RGATCY 1 cut(s) 51
MluCI AATT 2 cut(s) 20, 131
MlyI GAGTC 1 cut(s) 56
MnlI CCTC 5 cut(s) 3, 197, 264, 298, 493
MroXI GAANNNNTTC 2 cut(s) 24, 288
MseI TTAA 1 cut(s) 138
MspI CCGG 3 cut(s) 105, 120, 420
MspR9I CCNGG 1 cut(s) 213
MvaI CCWGG 1 cut(s) 213
MwoI GCNNNNNNNGC 2 cut(s) 380, 383
NdeII GATC 3 cut(s) 51, 156, 225
NlaIII CATG 2 cut(s) 500, 514
NlaIV GGNNCC 1 cut(s) 103
PdmI GAANNNNTTC 2 cut(s) 24, 288
PfeI GAWTC 3 cut(s) 234, 308, 360
PinAI ACCGGT 2 cut(s) 104, 119
PkrI GCNGC 3 cut(s) 376, 385, 388
PleI GAGTC 1 cut(s) 56
PpsI GAGTC 1 cut(s) 56
Psp6I CCWGG 1 cut(s) 211
PspGI CCWGG 1 cut(s) 211
PspN4I GGNNCC 1 cut(s) 103
PspPI GGNCC 2 cut(s) 44, 206
PsuI RGATCY 1 cut(s) 51
SaqAI TTAA 1 cut(s) 138
SatI GCNGC 3 cut(s) 375, 384, 387
Sau3AI GATC 3 cut(s) 51, 156, 225
Sau96I GGNCC 2 cut(s) 44, 206
SchI GAGTC 1 cut(s) 56
ScrFI CCNGG 1 cut(s) 213
SetI ASST 6 cut(s) 165, 208, 214, 256, 330, 349
SfaNI GCATC 1 cut(s) 229
SinI GGWCC 1 cut(s) 206
SmlI CTYRAG 1 cut(s) 255
SmoI CTYRAG 1 cut(s) 255
Sse9I AATT 2 cut(s) 20, 131
SsiI CCGC 3 cut(s) 66, 168, 460
SspMI CTAG 1 cut(s) 278
StyD4I CCNGG 1 cut(s) 211
StyI CCWWGG 1 cut(s) 229
TaaI ACNGT 1 cut(s) 115
TaqI TCGA 1 cut(s) 264
TasI AATT 2 cut(s) 20, 131
TfiI GAWTC 3 cut(s) 234, 308, 360
Tru1I TTAA 1 cut(s) 138
Tru9I TTAA 1 cut(s) 138
TscAI CASTG 2 cut(s) 46, 307
TseI GCWGC 3 cut(s) 374, 383, 386
TspDTI ATGAA 4 cut(s) 17, 33, 48, 238
TspRI CASTG 2 cut(s) 46, 307
VpaK11BI GGWCC 1 cut(s) 206
XapI RAATTY 1 cut(s) 131
XmiI GTMKAC 1 cut(s) 470
XmnI GAANNNNTTC 2 cut(s) 24, 288
XspI CTAG 1 cut(s) 278
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.