Rh3DG187600

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0015655
Physical Location & Seq
Reverse (-)
16714131 .. 16716263
2133 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG187600.1

Sequence Viewer

Length: 2133 bp
ATGCAGAGTGAGGGGCTGAAGCCGAATTCGCGCAGTGTCGTTGCATTGCTTTTGGCTTGTAGGGAGGTTGCGGAGTTGAGATGTGGGAAAGAGATACATGGCTATGGTTTGAGGAATGGATTGCTTGATTTGGATGCTCATGTGGGGACTGCTTTGATTGGGTTTTATATGAGATTTGATGTCAGAATGTCGCATCTTACATTTGATTCGATGGTTGTGAGGAATGTTGTTAGTTCGAATGCAATAATTACAGGATATGTTTATGTTGGGGAGTATTTGATGGCGGTGAAGCTTTTCGTGCAGTTGCTTGTGGACGGGGTTGAGTTTGACTCTGTTTCGATGTTGGTTTTGATTCAGGCTTGTGCGAAAATTGGAGCTGTTGAATTGGCTAGGCAAATTCATCAAATGGCCATAAAGTACAGCTACAGCAGTGATCTTTTCATTGTAAATGCATTGCTGAATATGTATAGTGAGTGTGGACGTATTGAATTATCGCGTGCATTATTTGAAACTGTCCCAAACCGTGATGTAGCTTTGTGGAATTCCATGCTAGCTGCATACAGTGAATATGGTTTTTATGAGGAAGCCATGAACTTATTTTTGAAAATGCGAACAGAAGGAATCGTGGAAGATCAAAGAACTGTTTATATAATGTTGTTGTTATGTGAAGAAATATCTGAAGGCTTGATAGAGGGAAAAAGCTTGCATGCTCTTGCGCGCAAGAGTGGGATGGAAATGGATGTTTCTCTCGGAAATACATTGTTAAGTATGTATGCTGAATTTAACTGTGTGCAGTCTGTTAAGAAGGTTTTTGCTGAGATGAAAGGTTCAGATGTTGTATCATGGAACATTCTGATCAGGGCATTGGCCTGCAATGGATTGCGAGATGAAGCATGGGAAACATTTGGTGTCATGCGAGAATCTGGAACCAAGCCAAACTCACACACCATAATATCTGTCCTTGCTATTTTTGAAGCTGAAACTTGTGTAAATACAGTGCGAGCGATTCATGGTTTTGTAATGAAACATGGTATTGAAGTTGACCTATCTTTGAATACTGCACTGTTAGATATATACATGAATAGCGGTGATGAAGCAGCAGCTAGGACTCTATTTGAGAACCGCCTCTATAGGGATGTGATCTCATGGAATGCTATAATTGCCAGTTACATCCGAAACAATGAAAGCAATGAAGCTCGGTTACTTTTCAACCGTATGATTTCAGAAGTGAAACCCAACTCTGTCACGATCACAAGTATTCTCTCATCATGTACCCAAGTTGCATCTCTGCCTCTAGGTCAATGCTTGCATGCTTATGCAACTAGGAGGCACTTCTCATTTGACTTTGATCTGTCTCTTGCAAATGCTTTTATATCTATGTACGCTAGAAGCGGTAGTATGCAAAATGCTGAAAAGATCTTTAAGAGTTTACCAACGAGAAATGTTATATCGTGGAATGCCTTGATAACTGGCTACAGCATGCACGGTCATGGATATGATGCTATTCTTGTGTTCCAACAAATGTTAGAGGATGGTTTCCAACCAAATGGTTCAACTTTTGTAGCTGTACTGTCTGCTTGCAGACATTCTGGTTTGATAGAGATGGGATTGAAGCTTTTCCACACTATGGTACATGATCTGGAGATAACACCCGAGCTTGTTCACTATGGTTGTGTCGTTGACCTTCTTTGTCGTGCAGGCCGCTTAGATGAAGCTAGAGAGTTCATCGAGTCAATGCCTATTGAACCAGATGCATCTGTGTGGAGGGCTTTGCTCAATGGTTGTCGAGTTAATTCTGCACCTGAGTTAGCTGGAGCAATCTTTGAGAAACTTGTGGAATTAGAACCCATGAATGCAGGGAATTATGTTCTGCTATCTAATATATATGCTGCAGCAGGTCTATGGTTAGAGGTCAGGAAGATAAGAACATTGCTGAGGGAAAAGGGTTTGAAAAAGCCTCCAGGAACAAGCTGGATTGTTATTAAAAGTCAGGTCCACTCTTTTGTTGCCTCAGACACATCACACCTTGATTCAAACAGAATTTATGCTTGTTTAAATTCTCTGTCAGCCTTAATCAAAGAAATTGGTTATACTCCTGATCTTCAATGGGTTTTGCATGAAGAAGAAAATTAA
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

Protein Analysis

710

Amino Acids

79.29

Weight (kDa)

5.63

Isoelectric Point (pI)

38.81

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 74 - 123 1.4e-06 PPR repeat family
PPR_2 PF13041 176 - 219 7.3e-06 PPR repeat family
PPR PF01535 180 - 208 5.2e-06 PPR repeat
PPR_2 PF13041 278 - 317 6.2e-09 PPR repeat family
PPR_2 PF13041 378 - 424 7.4e-09 PPR repeat family
PPR_2 PF13041 480 - 527 2.1e-09 PPR repeat family
PPR PF01535 483 - 513 7.9e-06 PPR repeat
PPR_1 PF12854 549 - 579 1.9e-06 PPR repeat
E_motif PF20431 602 - 659 3.2e-20 E motif
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: OG0015655)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g16860
malus_domestica MD12G1106700.v1.1
prunus_persica Prupe.7G125600_v2.0.a1
pyrus_communis pycom12g10720
rosa_chinensis RchiOBHm_Chr3g0470881
rosa_laevigata RLG00000024237
rosa_multiflora Rmu_sc0013860.1_g000005
rosa_roxburghii Rroxscaffold_1G00027940 Rroxscaffold_4G00331780 Rroxscaffold_6G00410450
rosa_rugosa Rorug03G0113300
rosa_samantha Rh3AG163100 Rh3BG188500 Rh3CG178500 Rh3DG187600
rosa_wichuraiana Rw3G015360

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 1886
AccB7I CCANNNNNTGG 1 cut(s) 1627
AccII CGCG 3 cut(s) 31, 496, 718
AciI CCGC 6 cut(s) 71, 284, 1086, 1123, 1392, 1702
AcoI YGGCCR 1 cut(s) 408
AcsI RAATTY 6 cut(s) 25, 396, 541, 779, 2040, 2056
AcuI CTGAAG 2 cut(s) 38, 699
AfaI GTAC 5 cut(s) 419, 1273, 1382, 1569, 1632
AfiI CCNNNNNNNGG 2 cut(s) 1132, 1627
AjnI CCWGG 1 cut(s) 1960
Alw26I GTCTC 1 cut(s) 1359
Ama87I CYCGRG 1 cut(s) 1652
AoxI GGCC 3 cut(s) 408, 867, 1699
ApeKI GCWGC 5 cut(s) 554, 1097, 1100, 1889, 1892
ApoI RAATTY 6 cut(s) 25, 396, 541, 779, 2040, 2056
Asp700I GAANNNNTTC 2 cut(s) 293, 1616
AspLEI GCGC 3 cut(s) 33, 718, 720
AspS9I GGNCC 1 cut(s) 1993
AsuHPI GGTGA 2 cut(s) 298, 1100
AsuII TTCGAA 1 cut(s) 236
AsuNHI GCTAGC 1 cut(s) 550
AvaI CYCGRG 1 cut(s) 1652
AvaII GGWCC 1 cut(s) 1993
BalI TGGCCA 1 cut(s) 410
BarI GAAGNNNNNNTAC 2 cut(s) 1185, 1217
BbvCI CCTCAGC 1 cut(s) 1934
BbvI GCAGC 5 cut(s) 541, 1109, 1112, 1876, 1904
BccI CCATC 5 cut(s) 205, 274, 724, 1526, 1597
BciT130I CCWGG 1 cut(s) 1962
BclI TGATCA 1 cut(s) 855
BcoDI GTCTC 1 cut(s) 1359
BfaI CTAG 7 cut(s) 390, 551, 1104, 1295, 1323, 1386, 1716
BfmI CTRYAG 4 cut(s) 424, 1129, 1474, 1890
BfuAI ACCTGC 1 cut(s) 1886
BglII AGATCT 1 cut(s) 1416
BisI GCNGC 6 cut(s) 555, 1098, 1101, 1702, 1890, 1893
BlsI GCNGC 6 cut(s) 556, 1099, 1102, 1703, 1891, 1894
Bme1390I CCNGG 1 cut(s) 1962
Bme18I GGWCC 1 cut(s) 1993
BmeT110I CYCGRG 1 cut(s) 1652
BmgT120I GGNCC 1 cut(s) 1993
BmiI GGNNCC 1 cut(s) 928
BmrFI CCNGG 1 cut(s) 1962
BmsI GCATC 6 cut(s) 124, 202, 1292, 1489, 1741, 1763
BmtI GCTAGC 1 cut(s) 554
BplI GAGNNNNNCTC 2 cut(s) 314, 346
BpmI CTGGAG 3 cut(s) 1661, 1833, 1944
Bpu10I CCTNAGC 1 cut(s) 1934
Bpu14I TTCGAA 1 cut(s) 236
Bsc4I CCNNNNNNNGG 2 cut(s) 1132, 1627
Bse1I ACTGG 2 cut(s) 1164, 1474
Bse3DI GCAATG 5 cut(s) 44, 452, 880, 1195, 1928
BseBI CCWGG 1 cut(s) 1962
BseGI GGATG 6 cut(s) 139, 735, 745, 1141, 1170, 1537
BseLI CCNNNNNNNGG 2 cut(s) 1132, 1627
BseMI GCAATG 5 cut(s) 44, 452, 880, 1195, 1928
BseMII CTCAG 4 cut(s) 807, 1794, 1925, 2025
BseNI ACTGG 2 cut(s) 1164, 1474
BsePI GCGCGC 1 cut(s) 716
BseXI GCAGC 5 cut(s) 541, 1109, 1112, 1876, 1904
BsgI GTGCAG 5 cut(s) 320, 812, 1044, 1716, 1782
Bsh1236I CGCG 3 cut(s) 31, 496, 718
BshFI GGCC 3 cut(s) 410, 869, 1701
BsiHKCI CYCGRG 1 cut(s) 1652
BslFI GGGAC 2 cut(s) 160, 500
BslI CCNNNNNNNGG 2 cut(s) 1132, 1627
BsmAI GTCTC 1 cut(s) 1359
BsmFI GGGAC 2 cut(s) 160, 500
BsmI GAATGC 4 cut(s) 244, 1156, 1462, 1858
BsnI GGCC 3 cut(s) 410, 869, 1701
BsoBI CYCGRG 1 cut(s) 1652
Bsp119I TTCGAA 1 cut(s) 236
Bsp143I GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
BspACI CCGC 6 cut(s) 71, 284, 1086, 1123, 1392, 1702
BspANI GGCC 3 cut(s) 410, 869, 1701
BspCNI CTCAG 4 cut(s) 808, 1795, 1926, 2024
BspFNI CGCG 3 cut(s) 31, 496, 718
BspLI GGNNCC 1 cut(s) 928
BspMAI CTGCAG 1 cut(s) 1894
BspMI ACCTGC 1 cut(s) 1886
BspOI GCTAGC 1 cut(s) 554
BspT104I TTCGAA 1 cut(s) 236
BsrDI GCAATG 5 cut(s) 44, 452, 880, 1195, 1928
BsrI ACTGG 2 cut(s) 1164, 1474
BssHII GCGCGC 1 cut(s) 716
BssMI GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
Bst2UI CCWGG 1 cut(s) 1962
BstBI TTCGAA 1 cut(s) 236
BstDEI CTNAG 5 cut(s) 816, 1705, 1803, 1934, 2011
BstF5I GGATG 6 cut(s) 139, 735, 745, 1141, 1170, 1537
BstFNI CGCG 3 cut(s) 31, 496, 718
BstHHI GCGC 3 cut(s) 33, 718, 720
BstKTI GATC 9 cut(s) 436, 634, 858, 1143, 1251, 1351, 1419, 1639, 2101
BstMAI GTCTC 1 cut(s) 1359
BstMBI GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
BstMWI GCNNNNNNNGC 3 cut(s) 28, 298, 1160
BstNI CCWGG 1 cut(s) 1962
BstNSI RCATGY 3 cut(s) 710, 1313, 1483
BstSCI CCNGG 1 cut(s) 1960
BstSFI CTRYAG 4 cut(s) 424, 1129, 1474, 1890
BstUI CGCG 3 cut(s) 31, 496, 718
BstV1I GCAGC 5 cut(s) 541, 1109, 1112, 1876, 1904
BstX2I RGATCY 1 cut(s) 1416
BstXI CCANNNNNNTGG 1 cut(s) 1547
BstYI RGATCY 1 cut(s) 1416
BsuRI GGCC 3 cut(s) 410, 869, 1701
BtsCI GGATG 6 cut(s) 139, 735, 745, 1141, 1170, 1537
BtsI GCAGTG 2 cut(s) 40, 436
BtsIMutI CAGTG 5 cut(s) 40, 436, 568, 1002, 1061
BveI ACCTGC 1 cut(s) 1886
CfoI GCGC 3 cut(s) 33, 718, 720
Cfr13I GGNCC 1 cut(s) 1993
Csp6I GTAC 5 cut(s) 418, 1272, 1381, 1568, 1631
CviQI GTAC 5 cut(s) 418, 1272, 1381, 1568, 1631
DdeI CTNAG 5 cut(s) 816, 1705, 1803, 1934, 2011
DpnI GATC 9 cut(s) 435, 633, 857, 1142, 1250, 1350, 1418, 1638, 2100
DpnII GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
DraI TTTAAA 1 cut(s) 2055
EaeI YGGCCR 1 cut(s) 408
Eco47I GGWCC 1 cut(s) 1993
Eco57I CTGAAG 2 cut(s) 38, 699
Eco88I CYCGRG 1 cut(s) 1652
EcoRI GAATTC 2 cut(s) 25, 541
EcoRII CCWGG 1 cut(s) 1960
EcoT22I ATGCAT 2 cut(s) 454, 1756
FaqI GGGAC 2 cut(s) 160, 500
FbaI TGATCA 1 cut(s) 855
Fnu4HI GCNGC 6 cut(s) 555, 1098, 1101, 1702, 1890, 1893
FokI GGATG 6 cut(s) 146, 742, 752, 1148, 1157, 1544
Fsp4HI GCNGC 6 cut(s) 555, 1098, 1101, 1702, 1890, 1893
FspBI CTAG 7 cut(s) 390, 551, 1104, 1295, 1323, 1386, 1716
GlaI GCGC 3 cut(s) 32, 717, 719
GluI GCNGC 6 cut(s) 555, 1098, 1101, 1702, 1890, 1893
GsuI CTGGAG 3 cut(s) 1661, 1833, 1944
HaeIII GGCC 3 cut(s) 410, 869, 1701
HhaI GCGC 3 cut(s) 33, 718, 720
Hin6I GCGC 3 cut(s) 31, 716, 718
HinP1I GCGC 3 cut(s) 31, 716, 718
HincII GTYRAC 2 cut(s) 1042, 1681
HindII GTYRAC 2 cut(s) 1042, 1681
HindIII AAGCTT 3 cut(s) 290, 700, 1613
HinfI GANTC 9 cut(s) 206, 329, 352, 621, 920, 1006, 1108, 1730, 2030
HphI GGTGA 2 cut(s) 298, 1100
Hpy166II GTNNAC 7 cut(s) 313, 479, 1042, 1430, 1663, 1681, 1996
Hpy188I TCNGA 8 cut(s) 185, 679, 752, 832, 855, 1175, 1225, 2014
Hpy188III TCNNGA 5 cut(s) 924, 1246, 1640, 1915, 2096
Hpy8I GTNNAC 7 cut(s) 313, 479, 1042, 1430, 1663, 1681, 1996
HpyAV CCTTC 4 cut(s) 611, 674, 799, 1694
HpyCH4IV ACGT 1 cut(s) 481
HpyF10VI GCNNNNNNNGC 3 cut(s) 28, 298, 1160
HpyF3I CTNAG 5 cut(s) 816, 1705, 1803, 1934, 2011
HpySE526I ACGT 1 cut(s) 481
HspAI GCGC 3 cut(s) 31, 716, 718
Ksp22I TGATCA 1 cut(s) 855
Kzo9I GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
LmnI GCTCC 2 cut(s) 374, 1814
Lsp1109I GCAGC 5 cut(s) 541, 1109, 1112, 1876, 1904
LweI GCATC 6 cut(s) 124, 202, 1292, 1489, 1741, 1763
MaeI CTAG 7 cut(s) 390, 551, 1104, 1295, 1323, 1386, 1716
MaeII ACGT 1 cut(s) 481
MaeIII GTNAC 3 cut(s) 1166, 1200, 1243
MalI GATC 9 cut(s) 435, 633, 857, 1142, 1250, 1350, 1418, 1638, 2100
MboI GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
MboII GAAGA 5 cut(s) 641, 680, 1930, 2093, 2132
MflI RGATCY 1 cut(s) 1416
MlsI TGGCCA 1 cut(s) 410
MluNI TGGCCA 1 cut(s) 410
MlyI GAGTC 3 cut(s) 323, 1102, 1739
MmeI TCCRAC 2 cut(s) 1540, 1564
Mox20I TGGCCA 1 cut(s) 410
Mph1103I ATGCAT 2 cut(s) 454, 1756
MroXI GAANNNNTTC 2 cut(s) 293, 1616
MscI TGGCCA 1 cut(s) 410
MseI TTAA 9 cut(s) 764, 783, 801, 1422, 1791, 1983, 2054, 2072, 2131
MslI CAYNNNNRTG 5 cut(s) 102, 1314, 1488, 1494, 1759
Msp20I TGGCCA 1 cut(s) 410
MspR9I CCNGG 1 cut(s) 1962
Mva1269I GAATGC 4 cut(s) 244, 1156, 1462, 1858
MvaI CCWGG 1 cut(s) 1962
MvnI CGCG 3 cut(s) 31, 496, 718
MwoI GCNNNNNNNGC 3 cut(s) 28, 298, 1160
NdeII GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
NheI GCTAGC 1 cut(s) 550
NlaIV GGNNCC 1 cut(s) 928
NmuCI GTSAC 1 cut(s) 1243
NsiI ATGCAT 2 cut(s) 454, 1756
NspI RCATGY 3 cut(s) 710, 1313, 1483
NspV TTCGAA 1 cut(s) 236
PaeI GCATGC 3 cut(s) 710, 1313, 1483
PauI GCGCGC 1 cut(s) 716
PctI GAATGC 4 cut(s) 244, 1156, 1462, 1858
PdmI GAANNNNTTC 2 cut(s) 293, 1616
PfeI GAWTC 6 cut(s) 206, 352, 621, 920, 1006, 2030
PflMI CCANNNNNTGG 1 cut(s) 1627
PfoI TCCNGGA 1 cut(s) 1960
PkrI GCNGC 6 cut(s) 556, 1099, 1102, 1703, 1891, 1894
PleI GAGTC 3 cut(s) 323, 1102, 1738
PpsI GAGTC 3 cut(s) 323, 1102, 1738
Psp6I CCWGG 1 cut(s) 1960
PspGI CCWGG 1 cut(s) 1960
PspN4I GGNNCC 1 cut(s) 928
PspPI GGNCC 1 cut(s) 1993
PstI CTGCAG 1 cut(s) 1894
PsuI RGATCY 1 cut(s) 1416
PteI GCGCGC 1 cut(s) 716
RsaI GTAC 5 cut(s) 419, 1273, 1382, 1569, 1632
RsaNI GTAC 5 cut(s) 418, 1272, 1381, 1568, 1631
RseI CAYNNNNRTG 5 cut(s) 102, 1314, 1488, 1494, 1759
SaqAI TTAA 9 cut(s) 764, 783, 801, 1422, 1791, 1983, 2054, 2072, 2131
SatI GCNGC 6 cut(s) 555, 1098, 1101, 1702, 1890, 1893
Sau3AI GATC 9 cut(s) 433, 631, 855, 1140, 1248, 1348, 1416, 1636, 2098
Sau96I GGNCC 1 cut(s) 1993
SchI GAGTC 3 cut(s) 323, 1102, 1739
ScrFI CCNGG 1 cut(s) 1962
SfaNI GCATC 6 cut(s) 124, 202, 1292, 1489, 1741, 1763
SfcI CTRYAG 4 cut(s) 424, 1129, 1474, 1890
SfuI TTCGAA 1 cut(s) 236
SinI GGWCC 1 cut(s) 1993
SmiMI CAYNNNNRTG 5 cut(s) 102, 1314, 1488, 1494, 1759
SphI GCATGC 3 cut(s) 710, 1313, 1483
SsiI CCGC 6 cut(s) 71, 284, 1086, 1123, 1392, 1702
SspMI CTAG 7 cut(s) 390, 551, 1104, 1295, 1323, 1386, 1716
StyD4I CCNGG 1 cut(s) 1960
TaiI ACGT 1 cut(s) 484
TaqI TCGA 5 cut(s) 209, 236, 338, 1728, 1786
TatI WGTACW 2 cut(s) 417, 1567
TauI GCSGC 1 cut(s) 1704
TfiI GAWTC 6 cut(s) 206, 352, 621, 920, 1006, 2030
Tru1I TTAA 9 cut(s) 764, 783, 801, 1422, 1791, 1983, 2054, 2072, 2131
Tru9I TTAA 9 cut(s) 764, 783, 801, 1422, 1791, 1983, 2054, 2072, 2131
TscAI CASTG 5 cut(s) 40, 436, 568, 1002, 1068
TseFI GTSAC 1 cut(s) 1243
TseI GCWGC 5 cut(s) 554, 1097, 1100, 1889, 1892
Tsp45I GTSAC 1 cut(s) 1243
TspRI CASTG 5 cut(s) 40, 436, 568, 1002, 1068
Van91I CCANNNNNTGG 1 cut(s) 1627
VpaK11BI GGWCC 1 cut(s) 1993
XapI RAATTY 6 cut(s) 25, 396, 541, 779, 2040, 2056
XceI RCATGY 3 cut(s) 710, 1313, 1483
XcmI CCANNNNNNNNNTGG 1 cut(s) 1968
XmnI GAANNNNTTC 2 cut(s) 293, 1616
XspI CTAG 7 cut(s) 390, 551, 1104, 1295, 1323, 1386, 1716
Zsp2I ATGCAT 2 cut(s) 454, 1756
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.