Rroxscaffold_7G00162420

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000007
OG0016771
Physical Location & Seq
Reverse (-)
4929773 .. 4931601
1829 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_7G00162420.1

Sequence Viewer

Length: 1224 bp
ATGGCATCAGTCTTAAGAGTTCTATCAGCGACGAAAATTCCGAGTAGCTCTCAGTCTCAGCGTTGTTGGCTAAGTAACCAAGCGTGCTTGCTTCGGAGGTTGATGGAGGAACCCAAATCGCGAATCAAAACCCTTCTTGCTTCTGCAGCGGAGAAAGACTCTGCCTCTGATTTTTCTTGGGAATCACTCGTTAGTTCTCTCGCTTCTTCTTCCTCTCCTGACAAAACCCACTTGGTTCTGGAATGGAAATTGGAGAAGTTGCTAAAGGAGAATGAGAGAGATCATGATCGTTACTGTGAGCTGATATCTCTATGTGGAAAAGTTCGGAATCTCCCACTTGCAATGCAAGTCTTTTCTTCTATGGAGGCCAATGGAGTTCAACCCACTTCTGCAGTTTTCAATTCCCTTATTCATGTTTGCTTCTCTTCCGGGAATTTGTTGACTGCTATCAGCCTGTTTGAGATTATGGAAAGCTCAGAGGGACTTAAACCCAATTCCGACACTTATGATGCATTCATGTTTGCTTTCTTAAAGTCGGGCAAAATTGATATGATGCAAGCTTGGTACTCTGCCAAGAAGTCTGCTGGCTTTAATTCTGATATTCAAACCTATCAGTCTTTGATTTCGGGTTGTATCAAATTGAAAAATTACGAGCTTGGTGATATGTTTTACAAAGAAATGGTATTGTCGGGAATCATGCCTAACTTGCCCATATTGGAGTATATGCTGGAAGGGCTTTGTAGGAGGAGAAGCTCCAGCCAAGTCAAAGAATTCTTGGAGATGGTGTGTGGTTATGGGTGGAAGATGAGTGGGAAAATGGCTGAGATGGTTGTGGGGTTGCATATTGAACTTGGGAAGGTGGAGCGATTGGAGGAGCTACTTGTGACTTTAATGGAGAGTGATCAGACTTCAGAAGTTTTGTTGCCGGTCCATTGTGGGATTGTAAGGACGTACGCCATGATGGATAGATTGGATGATGTAGAGTACTCTGTTGGTAGAATGTTGAAACAAGGATTGTCATTTAAACATCCGGATGATGTAGAAAAGGTGATATGCTCGTACTTCAGGCTCTCGGAGTATGATAGGCTGGAGTTGTTCTTGGAATGTATCAAGGGTTCTCATGAACTTACAGGATCGACTTATGATTTATTGGTTGCTGGCTATCGAAGAGCCGGGTTATCTGACAAGTTGAGTGATATGAAACTAGATGGTGGATCTTCATAG
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_2 PPR_3

Protein Analysis

407

Amino Acids

45.75

Weight (kDa)

5.67

Isoelectric Point (pI)

41.31

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_3 PF13812 97 - 140 5.3e-08 Pentatricopeptide repeat domain
TPR_24 PF23276 102 - 226 7.1e-07 Fungal tetratrico peptide repeats
PPR_long PF17177 111 - 207 7e-08 Pentacotripeptide-repeat region of PRORP
PPR_2 PF13041 128 - 176 4e-07 PPR repeat family
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: OG0016771)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g36160
malus_domestica MD08G1118800.v1.1
prunus_persica Prupe.1G453000_v2.0.a1
pyrus_communis pycom08g09920
rosa_chinensis RchiOBHm_Chr6g0305711
rosa_laevigata RLG00000010866
rosa_multiflora Rmu_sc0001809.1_g000036
rosa_roxburghii Rroxscaffold_7G00162420
rosa_rugosa Rorug06G0343400
rosa_samantha Rh6AG454900 Rh6BG446600 Rh6CG468800 Rh6DG455400
rosa_wichuraiana Rw6G039670

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 121
AccIII TCCGGA 1 cut(s) 1030
AciI CCGC 1 cut(s) 149
AclWI GGATC 2 cut(s) 1141, 1222
AcsI RAATTY 3 cut(s) 36, 433, 770
AcuI CTGAAG 2 cut(s) 894, 1048
AfaI GTAC 4 cut(s) 566, 953, 986, 1061
AflII CTTAAG 1 cut(s) 13
AgsI TTSAA 6 cut(s) 380, 400, 605, 643, 848, 1006
AluBI AGCT 7 cut(s) 48, 301, 474, 560, 655, 753, 877
AluI AGCT 7 cut(s) 48, 301, 474, 560, 655, 753, 877
Alw26I GTCTC 1 cut(s) 60
AlwI GGATC 2 cut(s) 1141, 1222
Aor13HI TCCGGA 1 cut(s) 1030
AoxI GGCC 1 cut(s) 366
ApeKI GCWGC 1 cut(s) 146
ApoI RAATTY 3 cut(s) 36, 433, 770
AspS9I GGNCC 1 cut(s) 928
AsuC2I CCSGG 2 cut(s) 430, 1174
AsuHPI GGTGA 2 cut(s) 671, 1060
AvaII GGWCC 1 cut(s) 928
BbvI GCAGC 1 cut(s) 158
BccI CCATC 5 cut(s) 97, 775, 820, 955, 1202
BclI TGATCA 1 cut(s) 901
BcnI CCSGG 2 cut(s) 430, 1174
BcoDI GTCTC 1 cut(s) 60
BfaI CTAG 1 cut(s) 1205
BfmI CTRYAG 2 cut(s) 144, 390
BfrI CTTAAG 1 cut(s) 13
BisI GCNGC 1 cut(s) 147
BlsI GCNGC 1 cut(s) 148
BmcAI AGTACT 1 cut(s) 986
Bme1390I CCNGG 2 cut(s) 430, 1174
Bme18I GGWCC 1 cut(s) 928
BmgT120I GGNCC 1 cut(s) 928
BmiI GGNNCC 1 cut(s) 111
BmrFI CCNGG 2 cut(s) 430, 1174
BmsI GCATC 3 cut(s) 14, 499, 543
BplI GAGNNNNNCTC 4 cut(s) 34, 66, 143, 175
BpmI CTGGAG 2 cut(s) 739, 1109
BpuMI CCSGG 2 cut(s) 430, 1174
BsaBI GATNNNNATC 1 cut(s) 285
BsaWI WCCGGW 1 cut(s) 1030
BsaXI ACNNNNNCTCC 2 cut(s) 770, 800
Bse118I RCCGGY 1 cut(s) 925
Bse3DI GCAATG 1 cut(s) 348
Bse8I GATNNNNATC 1 cut(s) 285
BseAI TCCGGA 1 cut(s) 1030
BseGI GGATG 3 cut(s) 979, 1027, 1039
BseJI GATNNNNATC 1 cut(s) 285
BseMI GCAATG 1 cut(s) 348
BseMII CTCAG 4 cut(s) 65, 71, 489, 813
BseRI GAGGAG 2 cut(s) 760, 887
BseXI GCAGC 1 cut(s) 158
Bsh1236I CGCG 1 cut(s) 121
BshFI GGCC 1 cut(s) 368
BsiSI CCGG 4 cut(s) 429, 926, 1031, 1173
BsiWI CGTACG 1 cut(s) 951
BslFI GGGAC 1 cut(s) 495
BsmAI GTCTC 1 cut(s) 60
BsmFI GGGAC 1 cut(s) 495
BsmI GAATGC 1 cut(s) 512
BsnI GGCC 1 cut(s) 368
Bsp13I TCCGGA 1 cut(s) 1030
Bsp143I GATC 5 cut(s) 280, 286, 901, 1133, 1214
Bsp68I TCGCGA 1 cut(s) 121
BspACI CCGC 1 cut(s) 149
BspANI GGCC 1 cut(s) 368
BspCNI CTCAG 4 cut(s) 64, 70, 488, 814
BspEI TCCGGA 1 cut(s) 1030
BspFNI CGCG 1 cut(s) 121
BspHI TCATGA 2 cut(s) 283, 1120
BspLI GGNNCC 1 cut(s) 111
BspMAI CTGCAG 2 cut(s) 148, 394
BspPI GGATC 2 cut(s) 1141, 1222
BspQI GCTCTTC 1 cut(s) 1162
BspTI CTTAAG 1 cut(s) 13
BsrDI GCAATG 1 cut(s) 348
BsrFI RCCGGY 1 cut(s) 925
BssAI RCCGGY 1 cut(s) 925
BssMI GATC 5 cut(s) 280, 286, 901, 1133, 1214
Bst4CI ACNGT 1 cut(s) 296
Bst6I CTCTTC 2 cut(s) 430, 1162
BstAFI CTTAAG 1 cut(s) 13
BstC8I GCNNGC 5 cut(s) 85, 89, 558, 586, 1159
BstDEI CTNAG 5 cut(s) 51, 57, 71, 475, 822
BstF5I GGATG 3 cut(s) 979, 1027, 1039
BstFNI CGCG 1 cut(s) 121
BstKTI GATC 5 cut(s) 283, 289, 904, 1136, 1217
BstMAI GTCTC 1 cut(s) 60
BstMBI GATC 5 cut(s) 280, 286, 901, 1133, 1214
BstMWI GCNNNNNNNGC 4 cut(s) 67, 146, 706, 733
BstSCI CCNGG 2 cut(s) 428, 1172
BstSFI CTRYAG 2 cut(s) 144, 390
BstUI CGCG 1 cut(s) 121
BstV1I GCAGC 1 cut(s) 158
BstX2I RGATCY 1 cut(s) 1214
BstYI RGATCY 1 cut(s) 1214
BsuRI GGCC 1 cut(s) 368
BtsCI GGATG 3 cut(s) 979, 1027, 1039
BtuMI TCGCGA 1 cut(s) 121
Cac8I GCNNGC 5 cut(s) 85, 89, 558, 586, 1159
CciI TCATGA 2 cut(s) 283, 1120
Cfr10I RCCGGY 1 cut(s) 925
Cfr13I GGNCC 1 cut(s) 928
Csp6I GTAC 4 cut(s) 565, 952, 985, 1060
CviAII CATG 6 cut(s) 284, 413, 517, 697, 958, 1121
CviQI GTAC 4 cut(s) 565, 952, 985, 1060
DdeI CTNAG 5 cut(s) 51, 57, 71, 475, 822
DpnI GATC 5 cut(s) 282, 288, 903, 1135, 1216
DpnII GATC 5 cut(s) 280, 286, 901, 1133, 1214
DraI TTTAAA 1 cut(s) 1024
Eam1104I CTCTTC 2 cut(s) 430, 1162
EarI CTCTTC 2 cut(s) 430, 1162
Eco32I GATATC 1 cut(s) 306
Eco47I GGWCC 1 cut(s) 928
Eco57I CTGAAG 2 cut(s) 894, 1048
EcoRI GAATTC 1 cut(s) 770
EcoRV GATATC 1 cut(s) 306
EcoT22I ATGCAT 1 cut(s) 514
FaeI CATG 6 cut(s) 287, 416, 520, 700, 961, 1124
FaqI GGGAC 1 cut(s) 495
FatI CATG 6 cut(s) 283, 412, 516, 696, 957, 1120
FbaI TGATCA 1 cut(s) 901
Fnu4HI GCNGC 1 cut(s) 147
FokI GGATG 3 cut(s) 986, 1014, 1046
Fsp4HI GCNGC 1 cut(s) 147
FspBI CTAG 1 cut(s) 1205
GluI GCNGC 1 cut(s) 147
GsuI CTGGAG 2 cut(s) 739, 1109
HaeIII GGCC 1 cut(s) 368
HapII CCGG 4 cut(s) 429, 926, 1031, 1173
Hin1II CATG 6 cut(s) 287, 416, 520, 700, 961, 1124
HincII GTYRAC 1 cut(s) 441
HindII GTYRAC 1 cut(s) 441
HindIII AAGCTT 1 cut(s) 558
HinfI GANTC 5 cut(s) 123, 158, 182, 328, 693
HpaII CCGG 4 cut(s) 429, 926, 1031, 1173
HphI GGTGA 2 cut(s) 671, 1060
Hpy166II GTNNAC 1 cut(s) 441
Hpy188III TCNNGA 7 cut(s) 120, 218, 239, 284, 690, 1031, 1121
Hpy8I GTNNAC 1 cut(s) 441
Hpy99I CGWCG 1 cut(s) 34
HpyAV CCTTC 3 cut(s) 143, 725, 850
HpyCH4III ACNGT 1 cut(s) 296
HpyCH4IV ACGT 1 cut(s) 950
HpyCH4V TGCA 7 cut(s) 146, 341, 346, 392, 512, 556, 841
HpyF10VI GCNNNNNNNGC 4 cut(s) 67, 146, 706, 733
HpyF3I CTNAG 5 cut(s) 51, 57, 71, 475, 822
HpySE526I ACGT 1 cut(s) 950
Hsp92II CATG 6 cut(s) 287, 416, 520, 700, 961, 1124
Kpn2I TCCGGA 1 cut(s) 1030
Ksp22I TGATCA 1 cut(s) 901
Kzo9I GATC 5 cut(s) 280, 286, 901, 1133, 1214
LguI GCTCTTC 1 cut(s) 1162
LmnI GCTCC 3 cut(s) 758, 862, 874
Lsp1109I GCAGC 1 cut(s) 158
LweI GCATC 3 cut(s) 14, 499, 543
MaeI CTAG 1 cut(s) 1205
MaeII ACGT 1 cut(s) 950
MaeIII GTNAC 3 cut(s) 74, 290, 883
MalI GATC 5 cut(s) 282, 288, 903, 1135, 1216
MboI GATC 5 cut(s) 280, 286, 901, 1133, 1214
MboII GAAGA 7 cut(s) 198, 201, 348, 417, 814, 1179, 1209
MflI RGATCY 1 cut(s) 1214
MlyI GAGTC 1 cut(s) 152
MmeI TCCRAC 1 cut(s) 522
MnlI CCTC 8 cut(s) 90, 100, 175, 223, 358, 472, 738, 865
Mph1103I ATGCAT 1 cut(s) 514
MroI TCCGGA 1 cut(s) 1030
MseI TTAA 6 cut(s) 14, 486, 530, 591, 890, 1023
MslI CAYNNNNRTG 1 cut(s) 1032
MspA1I CMGCKG 1 cut(s) 149
MspCI CTTAAG 1 cut(s) 13
MspI CCGG 4 cut(s) 429, 926, 1031, 1173
MspR9I CCNGG 2 cut(s) 430, 1174
Mva1269I GAATGC 1 cut(s) 512
MvnI CGCG 1 cut(s) 121
MwoI GCNNNNNNNGC 4 cut(s) 67, 146, 706, 733
NciI CCSGG 2 cut(s) 430, 1174
NdeII GATC 5 cut(s) 280, 286, 901, 1133, 1214
NlaIII CATG 6 cut(s) 287, 416, 520, 700, 961, 1124
NlaIV GGNNCC 1 cut(s) 111
NmuCI GTSAC 1 cut(s) 883
NruI TCGCGA 1 cut(s) 121
NsiI ATGCAT 1 cut(s) 514
PagI TCATGA 2 cut(s) 283, 1120
PciSI GCTCTTC 1 cut(s) 1162
PcsI WCGNNNNNNNCGW 1 cut(s) 38
PctI GAATGC 1 cut(s) 512
PfeI GAWTC 4 cut(s) 123, 182, 328, 693
Pfl23II CGTACG 1 cut(s) 951
PfoI TCCNGGA 1 cut(s) 428
PkrI GCNGC 1 cut(s) 148
PleI GAGTC 1 cut(s) 152
PpsI GAGTC 1 cut(s) 152
PspLI CGTACG 1 cut(s) 951
PspN4I GGNNCC 1 cut(s) 111
PspPI GGNCC 1 cut(s) 928
PsrI GAACNNNNNNTAC 2 cut(s) 1099, 1131
PstI CTGCAG 2 cut(s) 148, 394
PsuI RGATCY 1 cut(s) 1214
RruI TCGCGA 1 cut(s) 121
RsaI GTAC 4 cut(s) 566, 953, 986, 1061
RsaNI GTAC 4 cut(s) 565, 952, 985, 1060
RseI CAYNNNNRTG 1 cut(s) 1032
SapI GCTCTTC 1 cut(s) 1162
SaqAI TTAA 6 cut(s) 14, 486, 530, 591, 890, 1023
SatI GCNGC 1 cut(s) 147
Sau3AI GATC 5 cut(s) 280, 286, 901, 1133, 1214
Sau96I GGNCC 1 cut(s) 928
ScaI AGTACT 1 cut(s) 986
SchI GAGTC 1 cut(s) 152
ScrFI CCNGG 2 cut(s) 430, 1174
SfaNI GCATC 3 cut(s) 14, 499, 543
SfcI CTRYAG 2 cut(s) 144, 390
SinI GGWCC 1 cut(s) 928
SmiMI CAYNNNNRTG 1 cut(s) 1032
SmlI CTYRAG 1 cut(s) 13
SmoI CTYRAG 1 cut(s) 13
SsiI CCGC 1 cut(s) 149
SspMI CTAG 1 cut(s) 1205
StyD4I CCNGG 2 cut(s) 428, 1172
TaaI ACNGT 1 cut(s) 296
TaiI ACGT 1 cut(s) 953
TaqI TCGA 2 cut(s) 1136, 1165
TatI WGTACW 1 cut(s) 984
TfiI GAWTC 4 cut(s) 123, 182, 328, 693
Tru1I TTAA 6 cut(s) 14, 486, 530, 591, 890, 1023
Tru9I TTAA 6 cut(s) 14, 486, 530, 591, 890, 1023
TseFI GTSAC 1 cut(s) 883
TseI GCWGC 1 cut(s) 146
Tsp45I GTSAC 1 cut(s) 883
TspDTI ATGAA 5 cut(s) 401, 505, 1137, 1209, 1214
Vha464I CTTAAG 1 cut(s) 13
VpaK11BI GGWCC 1 cut(s) 928
XapI RAATTY 3 cut(s) 36, 433, 770
XspI CTAG 1 cut(s) 1205
ZrmI AGTACT 1 cut(s) 986
Zsp2I ATGCAT 1 cut(s) 514
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.