Rh5CG127500

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5C
OG0013500
Physical Location & Seq
Forward (+)
10619509 .. 10620750
1242 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5CG127500.1

Sequence Viewer

Length: 1242 bp
ATGTCTGAGAGAGACCTGGTGGCTTGGAACTCTGTGATTAATGGGTTTTCTTTGAATGGAAGGCCCAATGAGGCTCTGACTATATTTAGGGAGATGAGTTTGGAGGGTGTTGAGCCGGATGGGTTCACCATGGTTAGCTTGTTGTGCGCTTGTGCCGAGCTTGGAGCTTTGGCTTTGGGTGGGAGGGTTCATGTGTATATGTTGAAGGCGGGTTTGACAAGGAATGCGCATGCTAGTAATGCGCTTCTGGATGTTTATGCAAAGTGTGGAAGCATAAGGGAGGCGCAGAAGGTGTTTGAAGAAATGGAGGAGAGGAGTGTGGTTTCGTGGACTGCTTTGGTTGTTGGGTTGGCTGTTAATGGGTTTGGTAAGGAAGCATTGGAGCTTTTTAAAGAGTTTAAAAGAGAGGGATTGGTGCCAACTGAGATAACTTTTGTTGGGGTTCTGTATGCCTGTAGTCATTGCGGGATGGTTGATGAAGGGTTTGAGTACTTTAGAGTGATGAAAGAGGAGTATCGGATTGTGCCCAGAATAGAACATTATGGTTGCATGGTTGATTTGTTAGCTAGAGCAGGCTTGGTGAAAGAAGCGTATGAATACATTAAGGACATGCCTGTTCACCCCAATGCTGTTATTTGGAGGACCTTATTAGGAGCATGCACCATACATGGGCAATCGGCTCTAGGGGAGATTGCAAGAGGCCACATCCTGCAGTTAGAACCTAGACATAGTGGGGATTATGTGCTGATCTCCAATCTCTACGCATCTGAGCGTCGATGGTCGGATGTGCAAAAGGTGAGGAGGACAATGCTTAGTGAAGGTGTGAAGAAAACTCCGGGCTATAGTATTGTTGAGTTAAGGAACAGAGTTTTCGAGTTTACTATGGGTGACAGATCTCATGCACAAAGTGATGAGATATATGCAAAGCTGGTAGAGATTACAAAATTACTGAAACAGAAAGGTTATGTGCCTCATACGGAGAATGTTCTTGCAGACATAGAGGAGGAAGAAAAAGAAAATGCTTTGTCCTATCACAGTGAAAAAATTGCAATTGCATTCATGCTCCTAGTTACCGCACCAGGCATACCAATTAGGATTTGGAAGAATTTGAGAGTTTGTGCAGATTGTCATCTTGCATTTAAGCTCATCTCAAAAGTTTATGATCGGGAGATTGTTGTGAGGGATCGTAGCCGATTTCACCATTTTAGAGATGGTTCTTGTTCTTGTAGTGATTACTGGTAA
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
DYW_deaminase PPR PPR_2 X8

Protein Analysis

413

Amino Acids

46.74

Weight (kDa)

6.3

Isoelectric Point (pI)

45.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 5 - 52 5.1e-11 PPR repeat family
PPR PF01535 7 - 37 2.6e-07 PPR repeat
PPR PF01535 80 - 106 7.1e-06 PPR repeat
PPR_2 PF13041 106 - 153 1.9e-06 PPR repeat family
PPR PF01535 108 - 138 7.8e-06 PPR repeat
E_motif PF20431 226 - 285 1.8e-17 E motif
Eplus_motif PF20430 291 - 315 6.4e-06 E+ motif
DYW_deaminase PF14432 321 - 413 3.6e-40 DYW family of nucleic acid deaminases
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: OG0013500)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G21065 AT4G21065
fragaria_vesca FvH4_3g09500
malus_domestica MD05G1277300.v1.1 MD10G1256200.v1.1
prunus_persica Prupe.4G087400_v2.0.a1
pyrus_communis pycom05g25840 pycom10g21200
rosa_chinensis RchiOBHm_Chr5g0015081
rosa_laevigata RLG00000032168
rosa_multiflora Rmu_co8160296.1_g000001 Rmu_sc0002209.1_g000002 Rmu_sc0009777.1_g000014 Rmu_sc0036572.1_g000001
rosa_roxburghii Rroxscaffold_1G00061450
rosa_rugosa Rorug05G0024200
rosa_samantha Rh5CG127500
rosa_wichuraiana Rw5G010250

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 228
AccB1I GGYRCC 1 cut(s) 415
AciI CCGC 3 cut(s) 209, 465, 1074
AclWI GGATC 1 cut(s) 1191
AcsI RAATTY 1 cut(s) 1105
AdeI CACNNNGTG 1 cut(s) 908
AfaI GTAC 1 cut(s) 491
AfiI CCNNNNNNNGG 1 cut(s) 669
AgsI TTSAA 3 cut(s) 55, 205, 299
AjnI CCWGG 2 cut(s) 15, 1078
AluBI AGCT 7 cut(s) 138, 160, 167, 385, 566, 928, 1144
AluI AGCT 7 cut(s) 138, 160, 167, 385, 566, 928, 1144
Alw26I GTCTC 1 cut(s) 6
AlwI GGATC 1 cut(s) 1191
AoxI GGCC 2 cut(s) 62, 700
ApoI RAATTY 1 cut(s) 1105
AseI ATTAAT 1 cut(s) 39
AspLEI GCGC 4 cut(s) 149, 229, 244, 286
AspS9I GGNCC 2 cut(s) 63, 642
AsuC2I CCSGG 1 cut(s) 837
AsuHPI GGTGA 6 cut(s) 118, 592, 611, 808, 899, 1190
AvaII GGWCC 1 cut(s) 642
BaeGI GKGCMC 1 cut(s) 528
BanI GGYRCC 1 cut(s) 415
BccI CCATC 4 cut(s) 113, 463, 771, 1205
BciT130I CCWGG 2 cut(s) 17, 1080
BcnI CCSGG 1 cut(s) 837
BcoDI GTCTC 1 cut(s) 6
BfaI CTAG 5 cut(s) 234, 567, 683, 723, 1067
BfmI CTRYAG 3 cut(s) 454, 710, 841
BglII AGATCT 1 cut(s) 893
BmcAI AGTACT 1 cut(s) 491
Bme1390I CCNGG 3 cut(s) 17, 837, 1080
Bme18I GGWCC 1 cut(s) 642
BmgT120I GGNCC 2 cut(s) 63, 642
BmiI GGNNCC 1 cut(s) 417
BmrFI CCNGG 3 cut(s) 17, 837, 1080
BmsI GCATC 1 cut(s) 773
BpuMI CCSGG 1 cut(s) 837
BsaBI GATNNNNATC 1 cut(s) 1128
BsaI GGTCTC 1 cut(s) 6
BsaJI CCNNGG 1 cut(s) 129
Bsc4I CCNNNNNNNGG 1 cut(s) 669
Bse1I ACTGG 1 cut(s) 1241
Bse3DI GCAATG 1 cut(s) 460
Bse8I GATNNNNATC 1 cut(s) 1128
BseBI CCWGG 2 cut(s) 17, 1080
BseDI CCNNGG 1 cut(s) 129
BseGI GGATG 5 cut(s) 124, 256, 474, 705, 790
BseJI GATNNNNATC 1 cut(s) 1128
BseLI CCNNNNNNNGG 1 cut(s) 669
BseMI GCAATG 1 cut(s) 460
BseMII CTCAG 2 cut(s) 414, 759
BseNI ACTGG 1 cut(s) 1241
BseRI GAGGAG 5 cut(s) 323, 328, 524, 814, 1016
BseSI GKGCMC 1 cut(s) 528
BsgI GTGCAG 1 cut(s) 1140
BshFI GGCC 2 cut(s) 64, 702
BshNI GGYRCC 1 cut(s) 415
BsiSI CCGG 2 cut(s) 116, 836
BslI CCNNNNNNNGG 1 cut(s) 669
BsmAI GTCTC 1 cut(s) 6
BsmI GAATGC 2 cut(s) 229, 1055
BsnI GGCC 2 cut(s) 64, 702
Bso31I GGTCTC 1 cut(s) 6
Bsp1286I GDGCHC 1 cut(s) 528
Bsp143I GATC 4 cut(s) 747, 893, 1162, 1183
Bsp19I CCATGG 1 cut(s) 129
BspACI CCGC 3 cut(s) 209, 465, 1074
BspANI GGCC 2 cut(s) 64, 702
BspCNI CTCAG 2 cut(s) 415, 760
BspLI GGNNCC 1 cut(s) 417
BspMAI CTGCAG 1 cut(s) 714
BspPI GGATC 1 cut(s) 1191
BspT107I GGYRCC 1 cut(s) 415
BspTNI GGTCTC 1 cut(s) 6
BsrDI GCAATG 1 cut(s) 460
BsrI ACTGG 1 cut(s) 1241
BssECI CCNNGG 1 cut(s) 129
BssMI GATC 4 cut(s) 747, 893, 1162, 1183
BssT1I CCWWGG 1 cut(s) 129
Bst2UI CCWGG 2 cut(s) 17, 1080
Bst4CI ACNGT 1 cut(s) 1037
BstC8I GCNNGC 3 cut(s) 231, 574, 658
BstDEI CTNAG 4 cut(s) 6, 423, 768, 812
BstDSI CCRYGG 1 cut(s) 129
BstF5I GGATG 5 cut(s) 124, 256, 474, 705, 790
BstHHI GCGC 4 cut(s) 149, 229, 244, 286
BstKTI GATC 4 cut(s) 750, 896, 1165, 1186
BstMAI GTCTC 1 cut(s) 6
BstMBI GATC 4 cut(s) 747, 893, 1162, 1183
BstMWI GCNNNNNNNGC 2 cut(s) 144, 239
BstNI CCWGG 2 cut(s) 17, 1080
BstNSI RCATGY 3 cut(s) 233, 613, 660
BstSCI CCNGG 3 cut(s) 15, 835, 1078
BstSFI CTRYAG 3 cut(s) 454, 710, 841
BstSLI GKGCMC 1 cut(s) 528
BstX2I RGATCY 1 cut(s) 893
BstYI RGATCY 1 cut(s) 893
BsuRI GGCC 2 cut(s) 64, 702
BtgI CCRYGG 1 cut(s) 129
BtsCI GGATG 5 cut(s) 124, 256, 474, 705, 790
BtsIMutI CAGTG 1 cut(s) 1042
Cac8I GCNNGC 3 cut(s) 231, 574, 658
CfoI GCGC 4 cut(s) 149, 229, 244, 286
Cfr13I GGNCC 2 cut(s) 63, 642
CseI GACGC 1 cut(s) 761
CsiI ACCWGGT 1 cut(s) 15
Csp6I GTAC 1 cut(s) 490
CviAII CATG 9 cut(s) 130, 191, 230, 550, 610, 657, 668, 899, 1060
CviQI GTAC 1 cut(s) 490
DdeI CTNAG 4 cut(s) 6, 423, 768, 812
DpnI GATC 4 cut(s) 749, 895, 1164, 1185
DpnII GATC 4 cut(s) 747, 893, 1162, 1183
DraI TTTAAA 2 cut(s) 391, 400
DraIII CACNNNGTG 1 cut(s) 908
Eco130I CCWWGG 1 cut(s) 129
Eco31I GGTCTC 1 cut(s) 6
Eco47I GGWCC 1 cut(s) 642
EcoO109I RGGNCCY 1 cut(s) 642
EcoRII CCWGG 2 cut(s) 15, 1078
EcoT14I CCWWGG 1 cut(s) 129
ErhI CCWWGG 1 cut(s) 129
FaeI CATG 9 cut(s) 133, 194, 233, 553, 613, 660, 671, 902, 1063
FatI CATG 9 cut(s) 129, 190, 229, 549, 609, 656, 667, 898, 1059
FauI CCCGC 2 cut(s) 202, 458
FokI GGATG 5 cut(s) 131, 263, 481, 692, 797
FspAI RTGCGCAY 1 cut(s) 228
FspBI CTAG 5 cut(s) 234, 567, 683, 723, 1067
FspI TGCGCA 1 cut(s) 228
GlaI GCGC 4 cut(s) 148, 228, 243, 285
HaeIII GGCC 2 cut(s) 64, 702
HapII CCGG 2 cut(s) 116, 836
HgaI GACGC 1 cut(s) 761
HhaI GCGC 4 cut(s) 149, 229, 244, 286
Hin1II CATG 9 cut(s) 133, 194, 233, 553, 613, 660, 671, 902, 1063
Hin6I GCGC 4 cut(s) 147, 227, 242, 284
HinP1I GCGC 4 cut(s) 147, 227, 242, 284
HpaII CCGG 2 cut(s) 116, 836
HphI GGTGA 6 cut(s) 118, 592, 611, 808, 899, 1190
Hpy166II GTNNAC 4 cut(s) 126, 330, 619, 879
Hpy188I TCNGA 5 cut(s) 7, 78, 519, 769, 784
Hpy188III TCNNGA 2 cut(s) 248, 1166
Hpy8I GTNNAC 4 cut(s) 126, 330, 619, 879
Hpy99I CGWCG 1 cut(s) 777
HpyAV CCTTC 5 cut(s) 54, 199, 283, 473, 812
HpyCH4III ACNGT 1 cut(s) 1037
HpyF10VI GCNNNNNNNGC 2 cut(s) 144, 239
HpyF3I CTNAG 4 cut(s) 6, 423, 768, 812
Hsp92II CATG 9 cut(s) 133, 194, 233, 553, 613, 660, 671, 902, 1063
HspAI GCGC 4 cut(s) 147, 227, 242, 284
Kzo9I GATC 4 cut(s) 747, 893, 1162, 1183
LmnI GCTCC 4 cut(s) 164, 382, 653, 1068
LweI GCATC 1 cut(s) 773
MabI ACCWGGT 1 cut(s) 15
MaeI CTAG 5 cut(s) 234, 567, 683, 723, 1067
MaeIII GTNAC 2 cut(s) 887, 1069
MalI GATC 4 cut(s) 749, 895, 1164, 1185
MboI GATC 4 cut(s) 747, 893, 1162, 1183
MboII GAAGA 4 cut(s) 311, 838, 1019, 1114
MfeI CAATTG 1 cut(s) 1050
MflI RGATCY 1 cut(s) 893
MhlI GDGCHC 1 cut(s) 528
MluCI AATT 5 cut(s) 944, 1044, 1050, 1089, 1105
MmeI TCCRAC 1 cut(s) 762
MseI TTAA 7 cut(s) 39, 357, 390, 399, 603, 857, 1140
MslI CAYNNNNRTG 1 cut(s) 624
MspI CCGG 2 cut(s) 116, 836
MspR9I CCNGG 3 cut(s) 17, 837, 1080
MunI CAATTG 1 cut(s) 1050
Mva1269I GAATGC 2 cut(s) 229, 1055
MvaI CCWGG 2 cut(s) 17, 1080
MwoI GCNNNNNNNGC 2 cut(s) 144, 239
NciI CCSGG 1 cut(s) 837
NcoI CCATGG 1 cut(s) 129
NdeII GATC 4 cut(s) 747, 893, 1162, 1183
NlaIII CATG 9 cut(s) 133, 194, 233, 553, 613, 660, 671, 902, 1063
NlaIV GGNNCC 1 cut(s) 417
NmeAIII GCCGAG 1 cut(s) 181
NmuCI GTSAC 1 cut(s) 887
NsbI TGCGCA 1 cut(s) 228
NspI RCATGY 3 cut(s) 233, 613, 660
PaeI GCATGC 2 cut(s) 233, 660
PctI GAATGC 2 cut(s) 229, 1055
PpuMI RGGWCCY 1 cut(s) 642
PshBI ATTAAT 1 cut(s) 39
Psp5II RGGWCCY 1 cut(s) 642
Psp6I CCWGG 2 cut(s) 15, 1078
PspGI CCWGG 2 cut(s) 15, 1078
PspN4I GGNNCC 1 cut(s) 417
PspPI GGNCC 2 cut(s) 63, 642
PspPPI RGGWCCY 1 cut(s) 642
PstI CTGCAG 1 cut(s) 714
PsuI RGATCY 1 cut(s) 893
RsaI GTAC 1 cut(s) 491
RsaNI GTAC 1 cut(s) 490
RseI CAYNNNNRTG 1 cut(s) 624
SaqAI TTAA 7 cut(s) 39, 357, 390, 399, 603, 857, 1140
Sau3AI GATC 4 cut(s) 747, 893, 1162, 1183
Sau96I GGNCC 2 cut(s) 63, 642
ScaI AGTACT 1 cut(s) 491
ScrFI CCNGG 3 cut(s) 17, 837, 1080
SduI GDGCHC 1 cut(s) 528
SexAI ACCWGGT 1 cut(s) 15
SfaNI GCATC 1 cut(s) 773
SfcI CTRYAG 3 cut(s) 454, 710, 841
SinI GGWCC 1 cut(s) 642
SmiMI CAYNNNNRTG 1 cut(s) 624
SphI GCATGC 2 cut(s) 233, 660
Sse9I AATT 5 cut(s) 944, 1044, 1050, 1089, 1105
SsiI CCGC 3 cut(s) 209, 465, 1074
SspMI CTAG 5 cut(s) 234, 567, 683, 723, 1067
StyD4I CCNGG 3 cut(s) 15, 835, 1078
StyI CCWWGG 1 cut(s) 129
TaaI ACNGT 1 cut(s) 1037
TaqI TCGA 2 cut(s) 775, 873
TasI AATT 5 cut(s) 944, 1044, 1050, 1089, 1105
TatI WGTACW 1 cut(s) 489
Tru1I TTAA 7 cut(s) 39, 357, 390, 399, 603, 857, 1140
Tru9I TTAA 7 cut(s) 39, 357, 390, 399, 603, 857, 1140
TscAI CASTG 1 cut(s) 1042
TseFI GTSAC 1 cut(s) 887
Tsp45I GTSAC 1 cut(s) 887
TspDTI ATGAA 5 cut(s) 179, 492, 518, 609, 1048
TspGWI ACGGA 1 cut(s) 992
TspRI CASTG 1 cut(s) 1042
VpaK11BI GGWCC 1 cut(s) 642
VspI ATTAAT 1 cut(s) 39
XapI RAATTY 1 cut(s) 1105
XceI RCATGY 3 cut(s) 233, 613, 660
XcmI CCANNNNNNNNNTGG 2 cut(s) 1095, 1208
XspI CTAG 5 cut(s) 234, 567, 683, 723, 1067
ZrmI AGTACT 1 cut(s) 491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.