MD03G1268200.v1.1

Protein ROOT PRIMORDIUM DEFECTIVE 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr03
OG0014611
Physical Location & Seq
Reverse (-)
35298276 .. 35300440
2165 bp
Loading structure...
UTR
Exon/CDS
Intron
MD03G1268200.v1.1.491

Sequence Viewer

Length: 1200 bp
ATGCTCTCCAAAACCCGACCAATCTCCTCCTATATGCGCACCCACAAGCCCGCTCTCACACCCAGCACGCGCCCAGCGACCCACCTCCAATCCCAATCAATCTCGAGCCTCAAAGTCGTCTGGCGCAAGGACCAGAAGCTCGACCGGGCAATCGAAAACGACAAGTCGTACAAGCTCTGCGCCCGCGTCGTCAAGGAGGTGCACAACGAACCGGGTCGGGTGATCCCGCTTCGATACTTCGAAAAACGGCGCGAAAGGCTGCGGCTCAATATCAAAGTCGAAACCTTTCTTAGCAGAAACCCAGGTTTGTTCGATGTTTACTATGATAGAATTAAACCCAAATCGGAACCGGTTCAGTTTCTTCGATTTAGCGATAGATTAAGGATGTTTCTGGAGGAGGAAGAGAGGATTTTTAAGGAAAATGAGCCGTTGATTGTGTCTAAATTGTGTAAATTGCTGATGATGTGTAAGGATAGGGTTGTTAGTGTTGATAAATTGGTTCATGTGAAGAGGGAATTCGGGTTTCCGAACGATTTCTTGGTTAGCTTGGTGCCCAAGTATCCGCAGTATTTTCGGATACTTGGGTGCCCCGGAGAGGAGAATTGTTATCTGGAATTGGTTTCATGGAACCCCGAGTTTGCGAAATCAGTGATTGAGAGGAGGGCAGAAGAGGAGTCGAATTTGACAGGGATTCGGGTTCGGCCTAATTTTAACTATAGGCTGCCATCAGGGTTTTTCTTGAAGAAGGAAATGAGAGAGTGGGTAAGGGATTGGGTGGAAATGGATTATATTTCTCCGTATGAAGATGCGTCGAAATTGGATCAAGCTTCGCAGGAAATGGAGAAGAGGACGGTTGGAGTTTTTCATGAACTGTTATCGTTGTCTTTGTTTAAAAGGATTCCTGTGCCGATATTGGGTAAATTTAGTGATGAGTATAGGTTTTCAAATGCGTTCTCGAATGTGTTCACAAGGCATGCTGGGATATTCTATCTGTCGTTGAAGGGAGGGATTAAGACGGCGGTGCTGAGGGAAGCGTACAAGGATGATCAGTTGATTGACCGGGATCCACTGCTAGAGATAAAGTACAAGTTTGCGGAGCTATTGGAGGAGGGATGGAGGGAGAGACGAGAGCATTTGCGGTTGCAAAGGGAAGAGGTTGAGAAGAACAAGGAAATGATGGCTATGAGGAACGAAGAATAG
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
PORR

Protein Analysis

400

Amino Acids

47.57

Weight (kDa)

9.28

Isoelectric Point (pI)

46.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 43 - 372 2.8e-110 Plant organelle RNA recognition domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0014611)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G63090
fragaria_vesca FvH4_2g23842
malus_domestica MD03G1268200.v1.1 MD11G1289000.v1.1
prunus_persica Prupe.8G243800_v2.0.a1
pyrus_communis pycom03g21410 pycom11g25640
rosa_chinensis RchiOBHm_Chr6g0291451
rosa_laevigata RLG00000012113
rosa_multiflora Rmu_sc0003296.1_g000003
rosa_roxburghii Rroxscaffold_7G00176040
rosa_rugosa Rorug06G0219500
rosa_samantha Rh6AG331800 Rh6BG338700 Rh6CG344900 Rh6DG332000
rosa_wichuraiana Rw6G028800

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 38
AccB1I GGYRCC 2 cut(s) 550, 585
AccBSI CCGCTC 1 cut(s) 53
AccII CGCG 3 cut(s) 70, 186, 252
AciI CCGC 8 cut(s) 51, 184, 227, 262, 563, 1019, 1094, 1138
AclWI GGATC 4 cut(s) 217, 828, 1058, 1071
AcsI RAATTY 3 cut(s) 515, 679, 920
AfaI GTAC 3 cut(s) 170, 1037, 1085
AfiI CCNNNNNNNGG 2 cut(s) 595, 914
AgeI ACCGGT 1 cut(s) 349
AgsI TTSAA 3 cut(s) 742, 945, 1000
AjnI CCWGG 1 cut(s) 301
AjuI GAANNNNNNNTTGG 2 cut(s) 521, 553
AluBI AGCT 5 cut(s) 139, 175, 546, 827, 1099
AluI AGCT 5 cut(s) 139, 175, 546, 827, 1099
Alw21I GWGCWC 1 cut(s) 204
Alw26I GTCTC 1 cut(s) 1117
Alw44I GTGCAC 1 cut(s) 200
AlwI GGATC 4 cut(s) 217, 828, 1058, 1071
Ama87I CYCGRG 2 cut(s) 103, 632
AoxI GGCC 1 cut(s) 701
ApaLI GTGCAC 1 cut(s) 200
ApeKI GCWGC 2 cut(s) 259, 721
ApoI RAATTY 3 cut(s) 515, 679, 920
AsiGI ACCGGT 1 cut(s) 349
Asp700I GAANNNNTTC 4 cut(s) 285, 351, 533, 962
AspLEI GCGC 5 cut(s) 39, 72, 126, 182, 252
AspS9I GGNCC 1 cut(s) 130
AsuC2I CCSGG 4 cut(s) 146, 213, 591, 1061
AsuHPI GGTGA 1 cut(s) 232
AsuII TTCGAA 1 cut(s) 240
AvaI CYCGRG 2 cut(s) 103, 632
AvaII GGWCC 1 cut(s) 130
BaeGI GKGCMC 3 cut(s) 204, 555, 590
BaeI ACNNNNGTAYC 2 cut(s) 569, 602
BamHI GGATCC 1 cut(s) 1063
BanI GGYRCC 2 cut(s) 550, 585
Bbv12I GWGCWC 1 cut(s) 204
BbvCI CCTCAGC 1 cut(s) 1025
BbvI GCAGC 2 cut(s) 246, 708
BccI CCATC 3 cut(s) 733, 1107, 1171
BceAI ACGGC 3 cut(s) 263, 412, 1032
BcgI CGANNNNNNTGC 2 cut(s) 554, 588
BciT130I CCWGG 1 cut(s) 303
BciVI GTATCC 2 cut(s) 570, 570
BclI TGATCA 1 cut(s) 1045
BcnI CCSGG 4 cut(s) 146, 213, 591, 1061
BcoDI GTCTC 1 cut(s) 1117
BfaI CTAG 1 cut(s) 1073
BfmI CTRYAG 1 cut(s) 715
BfuI GTATCC 2 cut(s) 570, 570
BisI GCNGC 3 cut(s) 260, 263, 722
BlsI GCNGC 3 cut(s) 261, 264, 723
Bme1390I CCNGG 5 cut(s) 146, 213, 303, 591, 1061
Bme18I GGWCC 1 cut(s) 130
BmeT110I CYCGRG 2 cut(s) 103, 632
BmgT120I GGNCC 1 cut(s) 130
BmiI GGNNCC 5 cut(s) 348, 552, 587, 629, 1065
BmrFI CCNGG 5 cut(s) 146, 213, 303, 591, 1061
BmsI GCATC 1 cut(s) 796
BpmI CTGGAG 1 cut(s) 413
Bpu10I CCTNAGC 1 cut(s) 1025
Bpu14I TTCGAA 1 cut(s) 240
BpuMI CCSGG 4 cut(s) 146, 213, 591, 1061
BsaJI CCNNGG 2 cut(s) 301, 589
BsaWI WCCGGW 1 cut(s) 349
Bsc4I CCNNNNNNNGG 2 cut(s) 595, 914
Bse118I RCCGGY 1 cut(s) 349
BseBI CCWGG 1 cut(s) 303
BseDI CCNNGG 2 cut(s) 301, 589
BseGI GGATG 3 cut(s) 390, 1048, 1118
BseLI CCNNNNNNNGG 2 cut(s) 595, 914
BseMII CTCAG 1 cut(s) 1016
BseRI GAGGAG 6 cut(s) 16, 410, 611, 673, 686, 1121
BseSI GKGCMC 3 cut(s) 204, 555, 590
BseXI GCAGC 2 cut(s) 246, 708
BseYI CCCAGC 3 cut(s) 62, 73, 977
Bsh1236I CGCG 3 cut(s) 70, 186, 252
Bsh1285I CGRYCG 1 cut(s) 145
BshFI GGCC 1 cut(s) 703
BshNI GGYRCC 2 cut(s) 550, 585
BshTI ACCGGT 1 cut(s) 349
BsiEI CGRYCG 1 cut(s) 145
BsiHKAI GWGCWC 1 cut(s) 204
BsiHKCI CYCGRG 2 cut(s) 103, 632
BsiSI CCGG 5 cut(s) 145, 212, 350, 591, 1060
BslI CCNNNNNNNGG 2 cut(s) 595, 914
BsmAI GTCTC 1 cut(s) 1117
BsmBI CGTCTC 1 cut(s) 1117
BsnI GGCC 1 cut(s) 703
BsoBI CYCGRG 2 cut(s) 103, 632
Bsp119I TTCGAA 1 cut(s) 240
Bsp1286I GDGCHC 3 cut(s) 204, 555, 590
Bsp143I GATC 4 cut(s) 222, 820, 1045, 1063
BspACI CCGC 8 cut(s) 51, 184, 227, 262, 563, 1019, 1094, 1138
BspANI GGCC 1 cut(s) 703
BspCNI CTCAG 1 cut(s) 1017
BspFNI CGCG 3 cut(s) 70, 186, 252
BspHI TCATGA 1 cut(s) 865
BspLI GGNNCC 5 cut(s) 348, 552, 587, 629, 1065
BspPI GGATC 4 cut(s) 217, 828, 1058, 1071
BspT104I TTCGAA 1 cut(s) 240
BspT107I GGYRCC 2 cut(s) 550, 585
BsrBI CCGCTC 1 cut(s) 53
BsrFI RCCGGY 1 cut(s) 349
BssAI RCCGGY 1 cut(s) 349
BssECI CCNNGG 2 cut(s) 301, 589
BssMI GATC 4 cut(s) 222, 820, 1045, 1063
Bst2UI CCWGG 1 cut(s) 303
Bst4CI ACNGT 2 cut(s) 853, 873
Bst6I CTCTTC 5 cut(s) 396, 503, 663, 839, 1146
BstBI TTCGAA 1 cut(s) 240
BstC8I GCNNGC 4 cut(s) 51, 68, 184, 975
BstDEI CTNAG 2 cut(s) 290, 1025
BstF5I GGATG 3 cut(s) 390, 1048, 1118
BstFNI CGCG 3 cut(s) 70, 186, 252
BstHHI GCGC 5 cut(s) 39, 72, 126, 182, 252
BstKTI GATC 4 cut(s) 225, 823, 1048, 1066
BstMAI GTCTC 1 cut(s) 1117
BstMBI GATC 4 cut(s) 222, 820, 1045, 1063
BstMCI CGRYCG 1 cut(s) 145
BstMWI GCNNNNNNNGC 1 cut(s) 256
BstNI CCWGG 1 cut(s) 303
BstNSI RCATGY 1 cut(s) 977
BstSCI CCNGG 5 cut(s) 144, 211, 301, 589, 1059
BstSFI CTRYAG 1 cut(s) 715
BstSLI GKGCMC 3 cut(s) 204, 555, 590
BstUI CGCG 3 cut(s) 70, 186, 252
BstV1I GCAGC 2 cut(s) 246, 708
BstX2I RGATCY 1 cut(s) 1063
BstYI RGATCY 1 cut(s) 1063
BsuI GTATCC 2 cut(s) 570, 570
BsuRI GGCC 1 cut(s) 703
BtsCI GGATG 3 cut(s) 390, 1048, 1118
BtsI GCAGTG 1 cut(s) 1067
BtsIMutI CAGTG 2 cut(s) 654, 1067
Cac8I GCNNGC 4 cut(s) 51, 68, 184, 975
CciI TCATGA 1 cut(s) 865
CfoI GCGC 5 cut(s) 39, 72, 126, 182, 252
Cfr10I RCCGGY 1 cut(s) 349
Cfr13I GGNCC 1 cut(s) 130
CseI GACGC 2 cut(s) 175, 798
Csp6I GTAC 3 cut(s) 169, 1036, 1084
CspAI ACCGGT 1 cut(s) 349
CviAII CATG 4 cut(s) 503, 624, 866, 974
CviQI GTAC 3 cut(s) 169, 1036, 1084
DdeI CTNAG 2 cut(s) 290, 1025
DpnI GATC 4 cut(s) 224, 822, 1047, 1065
DpnII GATC 4 cut(s) 222, 820, 1045, 1063
DraI TTTAAA 1 cut(s) 892
Eam1104I CTCTTC 5 cut(s) 396, 503, 663, 839, 1146
EarI CTCTTC 5 cut(s) 396, 503, 663, 839, 1146
Eco47I GGWCC 1 cut(s) 130
Eco88I CYCGRG 2 cut(s) 103, 632
EcoRI GAATTC 1 cut(s) 515
EcoRII CCWGG 1 cut(s) 301
Esp3I CGTCTC 1 cut(s) 1117
FaeI CATG 4 cut(s) 506, 627, 869, 977
FatI CATG 4 cut(s) 502, 623, 865, 973
FauI CCCGC 3 cut(s) 58, 191, 234
FbaI TGATCA 1 cut(s) 1045
Fnu4HI GCNGC 3 cut(s) 260, 263, 722
FokI GGATG 3 cut(s) 397, 1055, 1125
Fsp4HI GCNGC 3 cut(s) 260, 263, 722
FspAI RTGCGCAY 1 cut(s) 38
FspBI CTAG 1 cut(s) 1073
FspI TGCGCA 1 cut(s) 38
GlaI GCGC 5 cut(s) 38, 71, 125, 181, 251
GluI GCNGC 3 cut(s) 260, 263, 722
GsaI CCCAGC 3 cut(s) 66, 77, 981
GsuI CTGGAG 1 cut(s) 413
HaeIII GGCC 1 cut(s) 703
HapII CCGG 5 cut(s) 145, 212, 350, 591, 1060
HgaI GACGC 2 cut(s) 175, 798
HhaI GCGC 5 cut(s) 39, 72, 126, 182, 252
Hin1II CATG 4 cut(s) 506, 627, 869, 977
Hin6I GCGC 5 cut(s) 37, 70, 124, 180, 250
HinP1I GCGC 5 cut(s) 37, 70, 124, 180, 250
HindIII AAGCTT 1 cut(s) 825
HinfI GANTC 3 cut(s) 674, 691, 898
HpaII CCGG 5 cut(s) 145, 212, 350, 591, 1060
HphI GGTGA 1 cut(s) 232
Hpy166II GTNNAC 3 cut(s) 202, 319, 966
Hpy188I TCNGA 3 cut(s) 346, 528, 576
Hpy188III TCNNGA 6 cut(s) 103, 392, 611, 739, 866, 955
Hpy8I GTNNAC 3 cut(s) 202, 319, 966
Hpy99I CGWCG 2 cut(s) 191, 814
HpyAV CCTTC 2 cut(s) 739, 994
HpyCH4III ACNGT 2 cut(s) 853, 873
HpyCH4V TGCA 2 cut(s) 202, 1144
HpyF10VI GCNNNNNNNGC 1 cut(s) 256
HpyF3I CTNAG 2 cut(s) 290, 1025
Hsp92II CATG 4 cut(s) 506, 627, 869, 977
HspAI GCGC 5 cut(s) 37, 70, 124, 180, 250
Ksp22I TGATCA 1 cut(s) 1045
Kzo9I GATC 4 cut(s) 222, 820, 1045, 1063
LmnI GCTCC 1 cut(s) 1096
Lsp1109I GCAGC 2 cut(s) 246, 708
LweI GCATC 1 cut(s) 796
MaeI CTAG 1 cut(s) 1073
MalI GATC 4 cut(s) 224, 822, 1047, 1065
MbiI CCGCTC 1 cut(s) 53
MboI GATC 4 cut(s) 222, 820, 1045, 1063
MboII GAAGA 9 cut(s) 353, 413, 520, 680, 754, 815, 856, 1163, 1174
MflI RGATCY 1 cut(s) 1063
MhlI GDGCHC 3 cut(s) 204, 555, 590
MlyI GAGTC 1 cut(s) 683
MmeI TCCRAC 1 cut(s) 835
MroXI GAANNNNTTC 4 cut(s) 285, 351, 533, 962
MseI TTAA 6 cut(s) 333, 380, 414, 711, 891, 1011
MspI CCGG 5 cut(s) 145, 212, 350, 591, 1060
MspR9I CCNGG 5 cut(s) 146, 213, 303, 591, 1061
MvaI CCWGG 1 cut(s) 303
MvnI CGCG 3 cut(s) 70, 186, 252
MwoI GCNNNNNNNGC 1 cut(s) 256
NciI CCSGG 4 cut(s) 146, 213, 591, 1061
NdeII GATC 4 cut(s) 222, 820, 1045, 1063
NlaIII CATG 4 cut(s) 506, 627, 869, 977
NlaIV GGNNCC 5 cut(s) 348, 552, 587, 629, 1065
NsbI TGCGCA 1 cut(s) 38
NspI RCATGY 1 cut(s) 977
NspV TTCGAA 1 cut(s) 240
PaeI GCATGC 1 cut(s) 977
PaeR7I CTCGAG 1 cut(s) 103
PagI TCATGA 1 cut(s) 865
PcsI WCGNNNNNNNCGW 1 cut(s) 74
PdmI GAANNNNTTC 4 cut(s) 285, 351, 533, 962
PfeI GAWTC 2 cut(s) 691, 898
PinAI ACCGGT 1 cut(s) 349
PkrI GCNGC 3 cut(s) 261, 264, 723
PleI GAGTC 1 cut(s) 682
PpsI GAGTC 1 cut(s) 682
Psp6I CCWGG 1 cut(s) 301
PspFI CCCAGC 3 cut(s) 62, 73, 977
PspGI CCWGG 1 cut(s) 301
PspN4I GGNNCC 5 cut(s) 348, 552, 587, 629, 1065
PspPI GGNCC 1 cut(s) 130
PsuI RGATCY 1 cut(s) 1063
RsaI GTAC 3 cut(s) 170, 1037, 1085
RsaNI GTAC 3 cut(s) 169, 1036, 1084
SaqAI TTAA 6 cut(s) 333, 380, 414, 711, 891, 1011
SatI GCNGC 3 cut(s) 260, 263, 722
Sau3AI GATC 4 cut(s) 222, 820, 1045, 1063
Sau96I GGNCC 1 cut(s) 130
SchI GAGTC 1 cut(s) 683
ScrFI CCNGG 5 cut(s) 146, 213, 303, 591, 1061
SduI GDGCHC 3 cut(s) 204, 555, 590
SfaNI GCATC 1 cut(s) 796
SfcI CTRYAG 1 cut(s) 715
Sfr274I CTCGAG 1 cut(s) 103
SfuI TTCGAA 1 cut(s) 240
SinI GGWCC 1 cut(s) 130
SlaI CTCGAG 1 cut(s) 103
SmlI CTYRAG 1 cut(s) 103
SmoI CTYRAG 1 cut(s) 103
SphI GCATGC 1 cut(s) 977
SsiI CCGC 8 cut(s) 51, 184, 227, 262, 563, 1019, 1094, 1138
SspMI CTAG 1 cut(s) 1073
StyD4I CCNGG 5 cut(s) 144, 211, 301, 589, 1059
TaaI ACNGT 2 cut(s) 853, 873
TatI WGTACW 1 cut(s) 1083
TauI GCSGC 1 cut(s) 265
TfiI GAWTC 2 cut(s) 691, 898
Tru1I TTAA 6 cut(s) 333, 380, 414, 711, 891, 1011
Tru9I TTAA 6 cut(s) 333, 380, 414, 711, 891, 1011
TscAI CASTG 2 cut(s) 654, 1074
TseI GCWGC 2 cut(s) 259, 721
TspDTI ATGAA 5 cut(s) 491, 612, 816, 854, 882
TspGWI ACGGA 1 cut(s) 786
TspRI CASTG 2 cut(s) 654, 1074
VneI GTGCAC 1 cut(s) 200
VpaK11BI GGWCC 1 cut(s) 130
XapI RAATTY 3 cut(s) 515, 679, 920
XceI RCATGY 1 cut(s) 977
XhoI CTCGAG 1 cut(s) 103
XmnI GAANNNNTTC 4 cut(s) 285, 351, 533, 962
XspI CTAG 1 cut(s) 1073
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.