Rh3BG105000

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3B
OG0015649
Physical Location & Seq
Forward (+)
8391888 .. 8394181
2294 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3BG105000.1

Sequence Viewer

Length: 899 bp
ATGGACCTCTCTCTGTCTCTGATGCCTTCCCCATATCCTGTAAGCTTCAAACTTGTTCAGACTCCCTCTCCATACAGAAGCAGATACATAAGAACCCAACAAGGTAAGCTACTTATTTTCACAACACTTTCATGCTCTGCTAGAAATCTTGCTGATAAAACACACCAGACATCCCCAAAAGATTATGGCTGTCACTCCCATAGTGAAGAACCCAAGTTGGGTTTTGATGAAATTACTAGTAGATTGCATGTACAGAGTTTAGTTGACAGAATTAGAGCTTTGCACACTGGAGAGACAAGTGAAATTCTTAGTATTTTTGAGCAAGATGGTTGCTTTAGAACCATTTCTGAGTTCAATGATCTGCTCATGGCTTTAGTTGTAGCGAAAGAGTTTGATATTGCTTTGAGCTTGTATGATGAAATATCATCTTACTGTTTAGTTCCTGATTCTTCCACATTTTCTATTGTGATTACCTGTTACTGTGAGAAAAATGATCTGGATGAGGCCAAGAGGGTTTTAGTCCATATGATTGAAAATGGGTTTAACCCAAGTGTTGCAACAATGACTTTTGTGATAGATTCATTATGCAAAAAGGGTAGATTGCAGAGAGCTTTGGAGGTTTTTGAGGTGATGGGTAGAGTTGGGTCCAAGCCCACTGTTCAAATGTACAATTGCTTGTTAAAGGGTTTGTGCTATGTGGGAAGAGTGGAGGATGCATATGAAATGTTGATGAAGATAAAGAAGGGTGTTGTAGAACCTGACATTTTTACATACACAGCTGTTATGGATGGTTTTTGTAAAGTGGGTCGCACAGATGAGGCGATGGAACTGCTTAATGAAGCTGTGGAGTTGGGATTAATACCAGATGTGGTTGCTTTCAATACTCTGTTTGATGGTAG
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

299

Amino Acids

33.59

Weight (kDa)

5.16

Isoelectric Point (pI)

36.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_1 PF12854 145 - 176 5.9e-08 PPR repeat
PPR_2 PF13041 148 - 197 1.5e-11 PPR repeat family
PPR_long PF17177 167 - 280 2.3e-06 Pentacotripeptide-repeat region of PRORP
PPR_3 PF13812 172 - 228 3.7e-07 Pentatricopeptide repeat domain
PPR_1 PF12854 179 - 211 4.2e-07 PPR repeat
PPR_2 PF13041 183 - 231 2.8e-11 PPR repeat family
PPR_1 PF12854 215 - 243 4.3e-07 PPR repeat
PPR_3 PF13812 215 - 262 4.2e-06 Pentatricopeptide repeat domain
PPR_2 PF13041 218 - 267 5.7e-14 PPR repeat family
PPR_1 PF12854 251 - 280 6.8e-11 PPR repeat
PPR_2 PF13041 253 - 299 7.2e-13 PPR repeat family
PPR PF01535 256 - 286 1.8e-07 PPR repeat
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)
AcsI RAATTY 1 cut(s) 303
AfaI GTAC 2 cut(s) 252, 668
AfiI CCNNNNNNNGG 1 cut(s) 218
AgsI TTSAA 5 cut(s) 49, 355, 533, 662, 880
AhlI ACTAGT 1 cut(s) 236
AluBI AGCT 7 cut(s) 45, 109, 278, 408, 611, 779, 842
AluI AGCT 7 cut(s) 45, 109, 278, 408, 611, 779, 842
Alw26I GTCTC 2 cut(s) 21, 287
AoxI GGCC 1 cut(s) 504
ApoI RAATTY 1 cut(s) 303
AseI ATTAAT 1 cut(s) 857
Asp700I GAANNNNTTC 1 cut(s) 343
AspS9I GGNCC 2 cut(s) 4, 645
AsuHPI GGTGA 1 cut(s) 640
AvaII GGWCC 2 cut(s) 4, 645
BccI CCATC 5 cut(s) 320, 625, 782, 817, 887
BcgI CGANNNNNNTGC 2 cut(s) 811, 845
BcoDI GTCTC 2 cut(s) 21, 287
BcuI ACTAGT 1 cut(s) 236
BfaI CTAG 2 cut(s) 141, 237
Bme18I GGWCC 2 cut(s) 4, 645
BmgT120I GGNCC 2 cut(s) 4, 645
BmiI GGNNCC 1 cut(s) 646
BmsI GCATC 2 cut(s) 12, 703
BpmI CTGGAG 1 cut(s) 309
BsaXI ACNNNNNCTCC 2 cut(s) 52, 82
Bsc4I CCNNNNNNNGG 1 cut(s) 218
Bse1I ACTGG 1 cut(s) 292
BseGI GGATG 4 cut(s) 170, 505, 718, 793
BseLI CCNNNNNNNGG 1 cut(s) 218
BseMII CTCAG 1 cut(s) 339
BseNI ACTGG 1 cut(s) 292
BshFI GGCC 1 cut(s) 506
BslI CCNNNNNNNGG 1 cut(s) 218
BsmAI GTCTC 2 cut(s) 21, 287
BsnI GGCC 1 cut(s) 506
Bsp1407I TGTACA 2 cut(s) 250, 666
Bsp143I GATC 2 cut(s) 358, 493
BspANI GGCC 1 cut(s) 506
BspCNI CTCAG 1 cut(s) 340
BspLI GGNNCC 1 cut(s) 646
BsrGI TGTACA 2 cut(s) 250, 666
BsrI ACTGG 1 cut(s) 292
BssMI GATC 2 cut(s) 358, 493
Bst4CI ACNGT 3 cut(s) 434, 482, 658
Bst6I CTCTTC 1 cut(s) 697
BstAUI TGTACA 2 cut(s) 250, 666
BstDEI CTNAG 2 cut(s) 308, 348
BstF5I GGATG 4 cut(s) 170, 505, 718, 793
BstKTI GATC 2 cut(s) 361, 496
BstMAI GTCTC 2 cut(s) 21, 287
BstMBI GATC 2 cut(s) 358, 493
BstNSI RCATGY 1 cut(s) 251
BsuRI GGCC 1 cut(s) 506
BtgZI GCGATG 1 cut(s) 836
BtsCI GGATG 4 cut(s) 170, 505, 718, 793
BtsIMutI CAGTG 2 cut(s) 285, 654
Cfr13I GGNCC 2 cut(s) 4, 645
Csp6I GTAC 2 cut(s) 251, 667
CviAII CATG 3 cut(s) 132, 248, 367
CviQI GTAC 2 cut(s) 251, 667
DdeI CTNAG 2 cut(s) 308, 348
DpnI GATC 2 cut(s) 360, 495
DpnII GATC 2 cut(s) 358, 493
Eam1104I CTCTTC 1 cut(s) 697
EarI CTCTTC 1 cut(s) 697
Eco47I GGWCC 2 cut(s) 4, 645
EcoT22I ATGCAT 1 cut(s) 718
FaeI CATG 3 cut(s) 135, 251, 370
FatI CATG 3 cut(s) 131, 247, 366
FauNDI CATATG 2 cut(s) 525, 718
FokI GGATG 4 cut(s) 157, 512, 725, 800
FspBI CTAG 2 cut(s) 141, 237
GsuI CTGGAG 1 cut(s) 309
HaeIII GGCC 1 cut(s) 506
Hin1II CATG 3 cut(s) 135, 251, 370
HincII GTYRAC 1 cut(s) 265
HindII GTYRAC 1 cut(s) 265
HindIII AAGCTT 1 cut(s) 43
HinfI GANTC 3 cut(s) 61, 446, 578
HphI GGTGA 1 cut(s) 640
Hpy166II GTNNAC 1 cut(s) 265
Hpy188I TCNGA 3 cut(s) 21, 60, 349
Hpy188III TCNNGA 2 cut(s) 443, 497
Hpy8I GTNNAC 1 cut(s) 265
HpyAV CCTTC 2 cut(s) 36, 736
HpyCH4III ACNGT 3 cut(s) 434, 482, 658
HpyCH4V TGCA 6 cut(s) 247, 283, 557, 588, 604, 716
HpyF3I CTNAG 2 cut(s) 308, 348
Hsp92II CATG 3 cut(s) 135, 251, 370
Kzo9I GATC 2 cut(s) 358, 493
LpnPI CCDG 8 cut(s) 51, 179, 273, 456, 482, 487, 771, 876
LweI GCATC 2 cut(s) 12, 703
MaeI CTAG 2 cut(s) 141, 237
MaeIII GTNAC 2 cut(s) 191, 476
MalI GATC 2 cut(s) 360, 495
MboI GATC 2 cut(s) 358, 493
MboII GAAGA 4 cut(s) 218, 441, 714, 745
MfeI CAATTG 1 cut(s) 670
MluCI AATT 4 cut(s) 231, 270, 303, 670
MlyI GAGTC 1 cut(s) 55
MnlI CCTC 8 cut(s) 17, 76, 496, 504, 610, 619, 703, 811
Mph1103I ATGCAT 1 cut(s) 718
MroXI GAANNNNTTC 1 cut(s) 343
MseI TTAA 4 cut(s) 543, 680, 834, 857
MslI CAYNNNNRTG 1 cut(s) 130
MspA1I CMGCKG 1 cut(s) 779
MunI CAATTG 1 cut(s) 670
NdeI CATATG 2 cut(s) 525, 718
NdeII GATC 2 cut(s) 358, 493
NlaIII CATG 3 cut(s) 135, 251, 370
NlaIV GGNNCC 1 cut(s) 646
NmuCI GTSAC 1 cut(s) 191
NsiI ATGCAT 1 cut(s) 718
NspI RCATGY 1 cut(s) 251
PdmI GAANNNNTTC 1 cut(s) 343
PfeI GAWTC 2 cut(s) 446, 578
PleI GAGTC 1 cut(s) 55
PpsI GAGTC 1 cut(s) 55
PshBI ATTAAT 1 cut(s) 857
PspN4I GGNNCC 1 cut(s) 646
PspPI GGNCC 2 cut(s) 4, 645
PvuII CAGCTG 1 cut(s) 779
RsaI GTAC 2 cut(s) 252, 668
RsaNI GTAC 2 cut(s) 251, 667
RseI CAYNNNNRTG 1 cut(s) 130
SaqAI TTAA 4 cut(s) 543, 680, 834, 857
Sau3AI GATC 2 cut(s) 358, 493
Sau96I GGNCC 2 cut(s) 4, 645
SchI GAGTC 1 cut(s) 55
SfaNI GCATC 2 cut(s) 12, 703
SinI GGWCC 2 cut(s) 4, 645
SmiMI CAYNNNNRTG 1 cut(s) 130
SpeI ACTAGT 1 cut(s) 236
Sse9I AATT 4 cut(s) 231, 270, 303, 670
SspMI CTAG 2 cut(s) 141, 237
TaaI ACNGT 3 cut(s) 434, 482, 658
TasI AATT 4 cut(s) 231, 270, 303, 670
TatI WGTACW 2 cut(s) 250, 666
TfiI GAWTC 2 cut(s) 446, 578
Tru1I TTAA 4 cut(s) 543, 680, 834, 857
Tru9I TTAA 4 cut(s) 543, 680, 834, 857
TscAI CASTG 2 cut(s) 292, 661
TseFI GTSAC 1 cut(s) 191
Tsp45I GTSAC 1 cut(s) 191
TspDTI ATGAA 7 cut(s) 120, 243, 432, 570, 735, 746, 852
TspRI CASTG 2 cut(s) 292, 661
VpaK11BI GGWCC 2 cut(s) 4, 645
VspI ATTAAT 1 cut(s) 857
XapI RAATTY 1 cut(s) 303
XceI RCATGY 1 cut(s) 251
XmnI GAANNNNTTC 1 cut(s) 343
XspI CTAG 2 cut(s) 141, 237
Zsp2I ATGCAT 1 cut(s) 718
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.