Rh4DG052400

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0016054
Physical Location & Seq
Forward (+)
8243660 .. 8245024
1365 bp
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UTR
Exon/CDS
Intron
Rh4DG052400.1

Sequence Viewer

Length: 1071 bp
ATGCTTGACATTCTCGGTAAGTACTTCGAGTTTGAGCTTTCTTGGGACTTGGTTCACAAAATGAAACAGAACCCAAGTTATGTTCCTGACCATACTACATTTCGTATAATGTTTAAGAGATATGTGTCTGCACATCTTGTAAAGGAAGCTATAGATACTTATAATAAGTTGGATGAGTTTAGTTTGAAGGATGAGACTTCTTATTGCAATCTTATTGATGCTCTTTGTGAGCATAAGCATGTGATTGAGGCCCAAGAGCTTTGCTCTTGGAAGAACAAAGAGTTGGGTTTTGATAAGAGTACTAAGCTGCATAATATAATTCTTCGGGGGTGGTCGAAAATGGGGTGGTGGGGAAAGTGTAGGGATTTTTGGGAAGAGATGGATAGGAGAGGTGTTTGTAAAGATTTGCATTCGTATTCGATATATATGGATATAATGTGTAAGAGTGGGAAGGCGTGGAAGGCTGTGAAGTTGTATAAGGAGGTGAAGAGGAAAGGGATCAAGCTGGATGTGGTGGCGTATAATACGGTTATTCGTGCCGTTGGTGATTCTGAGGGTGTTGATTTTGCAACTCGGATCTTGAGGGAGATGAAGGAATTGGGATGTGAACCTAATGCTGCGACGTATAATACAATTATAAAGCTTTTGTGTGAGAATATGAGATTCAGGGAGGCATTTTCAATGCTTCGAATAATGTCTAAGAACAGTTGTGGCCCGGATGTTATTACGTACCAAATCCTTTTTAAGTATCTGGAGAAGCCGAATGAGATTCTTAGGCTGTTTGATAGGATGATTGAAAGTGGGGTTCAGCCAAGGATGGACACATATGTGATGATTATGAGGAAGTTTGGGAGATGGGGCTTCCTTAGACCGATGTTTATTGTGTGGCAGAAGATGGAAAAACTTGGGTGTAGTCCTAATGAGTCTGCTTACAATGCTTTAATAGATGCTCTGGTTGAAAAGGCTGAAAACTTGGTTACAATGATGAAAGAGTTTGGGGTAGCTGCCAATAGTTTTGATGACCTTTTGTGCTGGACTTGTTACGATGGATGCACGGCAGCATGGGCATAG

Protein Analysis

356

Amino Acids

41.71

Weight (kDa)

8.3

Isoelectric Point (pI)

34.29

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 135 - 180 3.2e-09 PPR repeat family
PPR_long PF17177 141 - 252 2.2e-09 Pentacotripeptide-repeat region of PRORP
PPR_3 PF13812 158 - 216 6.6e-15 Pentatricopeptide repeat domain
PPR_2 PF13041 170 - 217 1e-12 PPR repeat family
TPR_24 PF23276 187 - 260 1e-05 Fungal tetratrico peptide repeats
PPR_1 PF12854 201 - 232 2.4e-09 PPR repeat
PPR_2 PF13041 205 - 250 1.1e-12 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: OG0016054)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G80550
fragaria_vesca FvH4_4g04420 FvH4_4g04420
malus_domestica MD16G1225100.v1.1
prunus_persica Prupe.1G046400_v2.0.a1
rosa_chinensis RchiOBHm_Chr4g0394981
rosa_laevigata RLG00000009653
rosa_multiflora Rmu_sc0005802.1_g000031
rosa_roxburghii Rroxscaffold_5G00339960
rosa_rugosa Rorug03G0360300.1
rosa_samantha Rh4AG056200 Rh4BG054900 Rh4CG060800 Rh4DG052400
rosa_wichuraiana Rw4G004500

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 162, 638
AclWI GGATC 2 cut(s) 506, 584
AfaI GTAC 3 cut(s) 23, 301, 731
AgsI TTSAA 4 cut(s) 187, 681, 797, 959
AjuI GAANNNNNNNTTGG 2 cut(s) 266, 298
AleI CACNNNNGTG 1 cut(s) 827
AluBI AGCT 7 cut(s) 37, 149, 259, 307, 505, 643, 1004
AluI AGCT 7 cut(s) 37, 149, 259, 307, 505, 643, 1004
Alw26I GTCTC 1 cut(s) 188
AlwI GGATC 2 cut(s) 506, 584
AoxI GGCC 2 cut(s) 249, 712
ApeKI GCWGC 4 cut(s) 307, 617, 1004, 1058
AspS9I GGNCC 2 cut(s) 250, 713
AsuC2I CCSGG 1 cut(s) 716
AsuHPI GGTGA 2 cut(s) 496, 557
AsuII TTCGAA 1 cut(s) 688
BbvI GCAGC 3 cut(s) 294, 604, 991
BccI CCATC 5 cut(s) 373, 811, 849, 889, 1040
BceAI ACGGC 1 cut(s) 524
BcnI CCSGG 1 cut(s) 716
BcoDI GTCTC 1 cut(s) 188
BfmI CTRYAG 1 cut(s) 150
BisI GCNGC 4 cut(s) 308, 618, 1005, 1059
BlsI GCNGC 4 cut(s) 309, 619, 1006, 1060
BmcAI AGTACT 2 cut(s) 23, 301
Bme1390I CCNGG 1 cut(s) 716
BmgT120I GGNCC 2 cut(s) 250, 713
BmrFI CCNGG 1 cut(s) 716
BmsI GCATC 3 cut(s) 208, 937, 1040
BplI GAGNNNNNCTC 2 cut(s) 248, 280
BpmI CTGGAG 1 cut(s) 773
Bpu14I TTCGAA 1 cut(s) 688
BpuEI CTTGAG 1 cut(s) 601
BpuMI CCSGG 1 cut(s) 716
BsaAI YACGTR 1 cut(s) 729
BsaJI CCNNGG 1 cut(s) 812
BseDI CCNNGG 1 cut(s) 812
BseGI GGATG 8 cut(s) 178, 196, 514, 608, 724, 795, 822, 1055
BseMII CTCAG 1 cut(s) 543
BseXI GCAGC 3 cut(s) 294, 604, 991
BsgI GTGCAG 1 cut(s) 114
BshFI GGCC 2 cut(s) 251, 714
BsiSI CCGG 1 cut(s) 716
BslFI GGGAC 1 cut(s) 59
BsmAI GTCTC 1 cut(s) 188
BsmFI GGGAC 1 cut(s) 59
BsmI GAATGC 1 cut(s) 409
BsnI GGCC 2 cut(s) 251, 714
Bsp119I TTCGAA 1 cut(s) 688
Bsp143I GATC 2 cut(s) 498, 576
BspANI GGCC 2 cut(s) 251, 714
BspCNI CTCAG 1 cut(s) 544
BspPI GGATC 2 cut(s) 506, 584
BspT104I TTCGAA 1 cut(s) 688
BssECI CCNNGG 1 cut(s) 812
BssMI GATC 2 cut(s) 498, 576
BssT1I CCWWGG 1 cut(s) 812
Bst4CI ACNGT 2 cut(s) 529, 707
Bst6I CTCTTC 2 cut(s) 369, 482
BstBAI YACGTR 1 cut(s) 729
BstBI TTCGAA 1 cut(s) 688
BstDEI CTNAG 5 cut(s) 303, 552, 699, 773, 866
BstF5I GGATG 8 cut(s) 178, 196, 514, 608, 724, 795, 822, 1055
BstKTI GATC 2 cut(s) 501, 579
BstMAI GTCTC 1 cut(s) 188
BstMBI GATC 2 cut(s) 498, 576
BstMWI GCNNNNNNNGC 3 cut(s) 461, 935, 1064
BstNSI RCATGY 1 cut(s) 242
BstSCI CCNGG 1 cut(s) 714
BstSFI CTRYAG 1 cut(s) 150
BstSNI TACGTA 1 cut(s) 729
BstV1I GCAGC 3 cut(s) 294, 604, 991
BstX2I RGATCY 1 cut(s) 576
BstYI RGATCY 1 cut(s) 576
BsuRI GGCC 2 cut(s) 251, 714
BtsCI GGATG 8 cut(s) 178, 196, 514, 608, 724, 795, 822, 1055
Cfr13I GGNCC 2 cut(s) 250, 713
Csp6I GTAC 3 cut(s) 22, 300, 730
CviAII CATG 2 cut(s) 239, 1062
CviQI GTAC 3 cut(s) 22, 300, 730
DdeI CTNAG 5 cut(s) 303, 552, 699, 773, 866
DpnI GATC 2 cut(s) 500, 578
DpnII GATC 2 cut(s) 498, 576
Eam1104I CTCTTC 2 cut(s) 369, 482
EarI CTCTTC 2 cut(s) 369, 482
Eco105I TACGTA 1 cut(s) 729
Eco130I CCWWGG 1 cut(s) 812
EcoT14I CCWWGG 1 cut(s) 812
ErhI CCWWGG 1 cut(s) 812
FaeI CATG 2 cut(s) 242, 1065
FaqI GGGAC 1 cut(s) 59
FatI CATG 2 cut(s) 238, 1061
FauNDI CATATG 1 cut(s) 826
Fnu4HI GCNGC 4 cut(s) 308, 618, 1005, 1059
FokI GGATG 8 cut(s) 185, 203, 521, 615, 731, 802, 829, 1062
Fsp4HI GCNGC 4 cut(s) 308, 618, 1005, 1059
GluI GCNGC 4 cut(s) 308, 618, 1005, 1059
GsuI CTGGAG 1 cut(s) 773
HaeIII GGCC 2 cut(s) 251, 714
HapII CCGG 1 cut(s) 716
Hin1II CATG 2 cut(s) 242, 1065
HindIII AAGCTT 1 cut(s) 641
HinfI GANTC 4 cut(s) 548, 663, 769, 923
HpaII CCGG 1 cut(s) 716
HphI GGTGA 2 cut(s) 496, 557
Hpy166II GTNNAC 2 cut(s) 55, 608
Hpy188I TCNGA 2 cut(s) 553, 576
Hpy188III TCNNGA 3 cut(s) 86, 580, 752
Hpy8I GTNNAC 2 cut(s) 55, 608
Hpy99I CGWCG 1 cut(s) 625
HpyAV CCTTC 4 cut(s) 181, 445, 454, 586
HpyCH4III ACNGT 2 cut(s) 529, 707
HpyCH4IV ACGT 2 cut(s) 623, 728
HpyCH4V TGCA 6 cut(s) 131, 207, 310, 409, 569, 1053
HpyF10VI GCNNNNNNNGC 3 cut(s) 461, 935, 1064
HpyF3I CTNAG 5 cut(s) 303, 552, 699, 773, 866
HpySE526I ACGT 2 cut(s) 623, 728
Hsp92II CATG 2 cut(s) 242, 1065
Kzo9I GATC 2 cut(s) 498, 576
LpnPI CCDG 7 cut(s) 99, 491, 652, 729, 737, 938, 1018
Lsp1109I GCAGC 3 cut(s) 294, 604, 991
LweI GCATC 3 cut(s) 208, 937, 1040
MaeII ACGT 2 cut(s) 623, 728
MaeIII GTNAC 2 cut(s) 976, 1040
MalI GATC 2 cut(s) 500, 578
MboI GATC 2 cut(s) 498, 576
MboII GAAGA 5 cut(s) 283, 314, 386, 499, 904
MflI RGATCY 1 cut(s) 576
MluCI AATT 3 cut(s) 318, 596, 633
MlyI GAGTC 1 cut(s) 932
MmeI TCCRAC 1 cut(s) 150
MnlI CCTC 8 cut(s) 241, 383, 475, 483, 547, 576, 664, 834
MseI TTAA 3 cut(s) 114, 744, 941
MslI CAYNNNNRTG 2 cut(s) 237, 827
MspI CCGG 1 cut(s) 716
MspR9I CCNGG 1 cut(s) 716
Mva1269I GAATGC 1 cut(s) 409
MwoI GCNNNNNNNGC 3 cut(s) 461, 935, 1064
NciI CCSGG 1 cut(s) 716
NdeI CATATG 1 cut(s) 826
NdeII GATC 2 cut(s) 498, 576
NlaIII CATG 2 cut(s) 242, 1065
NspI RCATGY 1 cut(s) 242
NspV TTCGAA 1 cut(s) 688
OliI CACNNNNGTG 1 cut(s) 827
PctI GAATGC 1 cut(s) 409
PfeI GAWTC 3 cut(s) 548, 663, 769
PkrI GCNGC 4 cut(s) 309, 619, 1006, 1060
PleI GAGTC 1 cut(s) 931
PpsI GAGTC 1 cut(s) 931
Ppu21I YACGTR 1 cut(s) 729
PsiI TTATAA 2 cut(s) 162, 638
PspPI GGNCC 2 cut(s) 250, 713
PsuI RGATCY 1 cut(s) 576
RsaI GTAC 3 cut(s) 23, 301, 731
RsaNI GTAC 3 cut(s) 22, 300, 730
RseI CAYNNNNRTG 2 cut(s) 237, 827
SaqAI TTAA 3 cut(s) 114, 744, 941
SatI GCNGC 4 cut(s) 308, 618, 1005, 1059
Sau3AI GATC 2 cut(s) 498, 576
Sau96I GGNCC 2 cut(s) 250, 713
ScaI AGTACT 2 cut(s) 23, 301
SchI GAGTC 1 cut(s) 932
ScrFI CCNGG 1 cut(s) 716
SfaNI GCATC 3 cut(s) 208, 937, 1040
SfcI CTRYAG 1 cut(s) 150
SfuI TTCGAA 1 cut(s) 688
SmiMI CAYNNNNRTG 2 cut(s) 237, 827
SmlI CTYRAG 1 cut(s) 580
SmoI CTYRAG 1 cut(s) 580
SnaBI TACGTA 1 cut(s) 729
Sse9I AATT 3 cut(s) 318, 596, 633
StyD4I CCNGG 1 cut(s) 714
StyI CCWWGG 1 cut(s) 812
TaaI ACNGT 2 cut(s) 529, 707
TaiI ACGT 2 cut(s) 626, 731
TaqI TCGA 4 cut(s) 27, 335, 419, 688
TaqII GACCGA 1 cut(s) 886
TasI AATT 3 cut(s) 318, 596, 633
TatI WGTACW 2 cut(s) 21, 299
TfiI GAWTC 3 cut(s) 548, 663, 769
Tru1I TTAA 3 cut(s) 114, 744, 941
Tru9I TTAA 3 cut(s) 114, 744, 941
TseI GCWGC 4 cut(s) 307, 617, 1004, 1058
TspDTI ATGAA 3 cut(s) 77, 605, 1001
XceI RCATGY 1 cut(s) 242
ZrmI AGTACT 2 cut(s) 23, 301
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.