Rh3DG106300

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0015649
Physical Location & Seq
Forward (+)
8544019 .. 8544765
747 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG106300.1

Sequence Viewer

Length: 747 bp
ATGGATGGTTTTTGTAAAGTGGGTCGCACAGATGAGGCGATGGAACTGCTTAATGAAGCTGTGGAGTTGGGATTAACACCAGATGTGGTTGCTTTCAATACTCTGTTTGATGGGTACTGCAGGGAGGGTAGGGCAATGGAGGGACTTAATGTGTTGAAGCAGATGAAGGAGAGAAACTGCATCCCTGATTATATTACTTATAGCACATTGTTACATGGATTGTTGAAATGGGGTAAGACCCGTAATGCGCTAAGGATTTACAAAGAGATGGTGGAAATTGGTTTCGAAGTGGATGAGAGATTGACGAATGCTCTTGTGAGAGGGTTATGCAGGAGATCATCGAAGGAAAAAGACCTGTTGGAAGATGCCTGTGAACTGTTTGAAAAATTGCAGAATGGGGTTTCTGACATAGAAGCTAGTACATATGGGCTTATGATCCAAAGTCTTTGCATGGAAAAGAAGATTGATGACGCTATGATCAATTTGAAGCAGATGATGGCAGTGGGTTATTCACCATGGATGATCACCTTTAACAAAGTGATTCAAACCCTCTGTTCTGACGACAAGATGATTGATGCATTAGTAGTTTTAGGTACTGCGTATGAATGTGATAGAGTAGCAAGTAGAGCAACTTATAACCTTTTGATTCAAAAGTTGAATCAACATGGCAATATGCTAGAAGCTTGTAGTGTATATGGTGCGGCATTGAAGAGAGGTTTAATTCCGAATAAAAGGCCTCAACAATGA
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

248

Amino Acids

28.05

Weight (kDa)

5.61

Isoelectric Point (pI)

32.14

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_3 PF13812 16 - 71 2e-08 Pentatricopeptide repeat domain
PPR_1 PF12854 24 - 56 3.3e-09 PPR repeat
PPR_2 PF13041 27 - 76 2e-16 PPR repeat family
PPR PF01535 30 - 60 2.4e-07 PPR repeat
PPR_2 PF13041 62 - 111 1.5e-08 PPR repeat family
PPR PF01535 65 - 95 3e-06 PPR repeat
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: 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)
AanI TTATAA 1 cut(s) 636
AciI CCGC 1 cut(s) 701
AclWI GGATC 1 cut(s) 430
AfaI GTAC 3 cut(s) 116, 421, 595
AgsI TTSAA 9 cut(s) 97, 157, 226, 383, 487, 545, 650, 658, 709
AluBI AGCT 3 cut(s) 59, 416, 683
AluI AGCT 3 cut(s) 59, 416, 683
AlwI GGATC 1 cut(s) 430
AoxI GGCC 1 cut(s) 734
AspLEI GCGC 1 cut(s) 250
AsuHPI GGTGA 2 cut(s) 504, 517
AsuII TTCGAA 1 cut(s) 285
BccI CCATC 4 cut(s) 34, 104, 262, 490
BcgI CGANNNNNNTGC 2 cut(s) 28, 62
BclI TGATCA 2 cut(s) 477, 522
BfaI CTAG 2 cut(s) 417, 677
BfmI CTRYAG 1 cut(s) 118
BisI GCNGC 1 cut(s) 702
BlsI GCNGC 1 cut(s) 703
BmsI GCATC 3 cut(s) 189, 355, 565
Bpu10I CCTNAGC 1 cut(s) 251
Bpu14I TTCGAA 1 cut(s) 285
BsaJI CCNNGG 1 cut(s) 515
Bse3DI GCAATG 1 cut(s) 141
BseDI CCNNGG 1 cut(s) 515
BseGI GGATG 4 cut(s) 10, 180, 298, 525
BseMI GCAATG 1 cut(s) 141
BshFI GGCC 1 cut(s) 736
BslFI GGGAC 1 cut(s) 156
BsmFI GGGAC 1 cut(s) 156
BsmI GAATGC 1 cut(s) 313
BsnI GGCC 1 cut(s) 736
Bsp119I TTCGAA 1 cut(s) 285
Bsp143I GATC 4 cut(s) 335, 435, 477, 522
Bsp19I CCATGG 1 cut(s) 515
BspACI CCGC 1 cut(s) 701
BspANI GGCC 1 cut(s) 736
BspMAI CTGCAG 1 cut(s) 122
BspPI GGATC 1 cut(s) 430
BspT104I TTCGAA 1 cut(s) 285
BsrDI GCAATG 1 cut(s) 141
BssECI CCNNGG 1 cut(s) 515
BssMI GATC 4 cut(s) 335, 435, 477, 522
BssT1I CCWWGG 1 cut(s) 515
Bst4CI ACNGT 1 cut(s) 378
Bst6I CTCTTC 1 cut(s) 704
BstBI TTCGAA 1 cut(s) 285
BstDEI CTNAG 1 cut(s) 251
BstDSI CCRYGG 1 cut(s) 515
BstF5I GGATG 4 cut(s) 10, 180, 298, 525
BstHHI GCGC 1 cut(s) 250
BstKTI GATC 4 cut(s) 338, 438, 480, 525
BstMBI GATC 4 cut(s) 335, 435, 477, 522
BstMWI GCNNNNNNNGC 1 cut(s) 626
BstSFI CTRYAG 1 cut(s) 118
BsuRI GGCC 1 cut(s) 736
BtgI CCRYGG 1 cut(s) 515
BtgZI GCGATG 1 cut(s) 53
BtsCI GGATG 4 cut(s) 10, 180, 298, 525
BtsI GCAGTG 1 cut(s) 507
BtsIMutI CAGTG 1 cut(s) 507
CfoI GCGC 1 cut(s) 250
CseI GACGC 1 cut(s) 479
Csp6I GTAC 3 cut(s) 115, 420, 594
CviAII CATG 4 cut(s) 215, 451, 516, 665
CviJI RGCY 5 cut(s) 59, 416, 430, 683, 736
CviKI_1 RGCY 5 cut(s) 59, 416, 430, 683, 736
CviQI GTAC 3 cut(s) 115, 420, 594
DdeI CTNAG 1 cut(s) 251
DpnI GATC 4 cut(s) 337, 437, 479, 524
DpnII GATC 4 cut(s) 335, 435, 477, 522
Eam1104I CTCTTC 1 cut(s) 704
EarI CTCTTC 1 cut(s) 704
Eco130I CCWWGG 1 cut(s) 515
Eco147I AGGCCT 1 cut(s) 736
EcoT14I CCWWGG 1 cut(s) 515
EcoT22I ATGCAT 1 cut(s) 580
ErhI CCWWGG 1 cut(s) 515
FaeI CATG 4 cut(s) 218, 454, 519, 668
FaqI GGGAC 1 cut(s) 156
FatI CATG 4 cut(s) 214, 450, 515, 664
FauNDI CATATG 1 cut(s) 424
FbaI TGATCA 2 cut(s) 477, 522
Fnu4HI GCNGC 1 cut(s) 702
FokI GGATG 4 cut(s) 17, 167, 305, 532
Fsp4HI GCNGC 1 cut(s) 702
FspBI CTAG 2 cut(s) 417, 677
GlaI GCGC 1 cut(s) 249
GluI GCNGC 1 cut(s) 702
HaeIII GGCC 1 cut(s) 736
HgaI GACGC 1 cut(s) 479
HhaI GCGC 1 cut(s) 250
Hin1II CATG 4 cut(s) 218, 454, 519, 668
Hin6I GCGC 1 cut(s) 248
HinP1I GCGC 1 cut(s) 248
HindIII AAGCTT 1 cut(s) 681
HinfI GANTC 3 cut(s) 541, 646, 658
HphI GGTGA 2 cut(s) 504, 517
Hpy166II GTNNAC 1 cut(s) 374
Hpy188I TCNGA 3 cut(s) 406, 559, 726
Hpy8I GTNNAC 1 cut(s) 374
HpyAV CCTTC 2 cut(s) 160, 337
HpyCH4III ACNGT 1 cut(s) 378
HpyCH4V TGCA 6 cut(s) 120, 180, 330, 391, 450, 578
HpyF10VI GCNNNNNNNGC 1 cut(s) 626
HpyF3I CTNAG 1 cut(s) 251
Hsp92II CATG 4 cut(s) 218, 454, 519, 668
HspAI GCGC 1 cut(s) 248
Ksp22I TGATCA 2 cut(s) 477, 522
Kzo9I GATC 4 cut(s) 335, 435, 477, 522
LpnPI CCDG 6 cut(s) 93, 106, 198, 316, 368, 382
LweI GCATC 3 cut(s) 189, 355, 565
MaeI CTAG 2 cut(s) 417, 677
MaeIII GTNAC 1 cut(s) 210
MalI GATC 4 cut(s) 337, 437, 479, 524
MboI GATC 4 cut(s) 335, 435, 477, 522
MboII GAAGA 3 cut(s) 374, 472, 721
MluCI AATT 4 cut(s) 276, 386, 481, 720
MmeI TCCRAC 1 cut(s) 339
MnlI CCTC 7 cut(s) 28, 118, 133, 314, 560, 707, 747
Mph1103I ATGCAT 1 cut(s) 580
MseI TTAA 5 cut(s) 51, 74, 147, 531, 719
Mva1269I GAATGC 1 cut(s) 313
MwoI GCNNNNNNNGC 1 cut(s) 626
NcoI CCATGG 1 cut(s) 515
NdeI CATATG 1 cut(s) 424
NdeII GATC 4 cut(s) 335, 435, 477, 522
NlaIII CATG 4 cut(s) 218, 454, 519, 668
NsiI ATGCAT 1 cut(s) 580
NspV TTCGAA 1 cut(s) 285
PceI AGGCCT 1 cut(s) 736
PctI GAATGC 1 cut(s) 313
PfeI GAWTC 3 cut(s) 541, 646, 658
PkrI GCNGC 1 cut(s) 703
PsiI TTATAA 1 cut(s) 636
PstI CTGCAG 1 cut(s) 122
RsaI GTAC 3 cut(s) 116, 421, 595
RsaNI GTAC 3 cut(s) 115, 420, 594
SaqAI TTAA 5 cut(s) 51, 74, 147, 531, 719
SatI GCNGC 1 cut(s) 702
Sau3AI GATC 4 cut(s) 335, 435, 477, 522
SetI ASST 8 cut(s) 61, 357, 418, 530, 595, 642, 685, 718
SfaNI GCATC 3 cut(s) 189, 355, 565
SfcI CTRYAG 1 cut(s) 118
SfuI TTCGAA 1 cut(s) 285
Sse9I AATT 4 cut(s) 276, 386, 481, 720
SseBI AGGCCT 1 cut(s) 736
SsiI CCGC 1 cut(s) 701
SspMI CTAG 2 cut(s) 417, 677
StuI AGGCCT 1 cut(s) 736
StyI CCWWGG 1 cut(s) 515
TaaI ACNGT 1 cut(s) 378
TaqI TCGA 2 cut(s) 285, 341
TasI AATT 4 cut(s) 276, 386, 481, 720
TatI WGTACW 1 cut(s) 419
TauI GCSGC 1 cut(s) 704
TfiI GAWTC 3 cut(s) 541, 646, 658
Tru1I TTAA 5 cut(s) 51, 74, 147, 531, 719
Tru9I TTAA 5 cut(s) 51, 74, 147, 531, 719
TscAI CASTG 1 cut(s) 507
TspDTI ATGAA 3 cut(s) 69, 179, 618
TspRI CASTG 1 cut(s) 507
XspI CTAG 2 cut(s) 417, 677
Zsp2I ATGCAT 1 cut(s) 580
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.