FvH4_2g23842

Protein ROOT PRIMORDIUM DEFECTIVE 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb2
OG0014611
Physical Location & Seq
Reverse (-)
19489584 .. 19493083
3500 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_2g23842.t1

Sequence Viewer

Length: 1185 bp
ATGCTCTCCAAGTCTCGAACCACCCTCTCCTCCTATCTCCACAGCTACGTGAGAGTATCCCACACGAACCCAGAACTCCACCTCCACATCAAACCCATTTCCAGCCTCAAAGTCGCGTGGCGCAAAGACCCGAAGCTAGACCAGGCCATAGAGCACGACAAGCCGTACAAGCTCTGCGCCCGCGTCGTCAAGGAGGTCCTAAACGAGCCCGGCCAGAAAATCCCGCTCCGCTACCTCGAAAAACGCCGCGAAAGACTGCGCCTCAGAACCAAAGCAACAACCTTCATCGCCCAAAACCCAGGTTTGTTTGAGGTTTATTACGATAGAATCAAACCCAAGACAGAAAAGGTTCAGTTTATTAGGGTTGGTGATAAACTTAGGGAGTTTCTTGATGAAGAGAAGAGGATTTGTGTGGAGAATGAGGGTTTGATTGTGGCTAAGTTGTGTAAATTGTTGATGATTGCGAAGAATAAGGTGGTTAGTGCTGAGAAATTGGTTGATGTGAAGAGGGAATTCGGGTTTCCTAATGATTTTATGGTGACATTGGTGCCGAAATATCCGGAGTATTTCCGGGTAGTTGGGGGTTCCGGTCAGGGGAAATCATTCTTGGAGTTGGTTGATTGGAACCCGGAGTTTGCAAAATCGGTTATTGAGAGGAGAGCAGAGGAGGAGTCAAGCTTGACAGGGATCCGGGTCCGGCCTAACTTTTATTACAAGCTTCCACAGGGGTGTGTGTTGAAGAAGGAAATGAGGGAGTGGGTTAGGGATTGGATGGAGTTGGAGCATATATCGCCGTATGAGGATGTGTCGAAGTTGGATCAAGCGTCACCGGAGATGGAGAAGAGGACGGTTGGGGTTTTCCATGAGTTGTTGTCTTTGTCTTTGTTGAAGAGGATGCCTGTGCCCATATTGGGGAAATTCTGTGATGAGTATAGGTTTTCAAATGCGTTTCCGAATGTATTTACAAGGCATTCGGGGTTGTTCTATGTGTCGCAGAAAGGAGGGATCAAGACGGCTGTGCTGAGGGAAGCTTACAAGGATGACCAGTTGATTGATCGGGATCCGCTGCTACAGATTAAGGATAAGTTTGTTGAGCTGTTGGAGGAGGGATGGCGGGAGAGTGCAGAGCAGTTGCGGTTGCAACGGGAAGAAGTTAAGGAAATGGCTGTGAGGAATGATGAATAG
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

395

Amino Acids

46.23

Weight (kDa)

9.12

Isoelectric Point (pI)

39.42

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 42 - 371 2.2e-106 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
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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)
AccB1I GGYRCC 1 cut(s) 547
AccBSI CCGCTC 1 cut(s) 226
AccII CGCG 3 cut(s) 116, 183, 249
AccIII TCCGGA 1 cut(s) 559
AciI CCGC 7 cut(s) 181, 224, 229, 247, 1064, 1114, 1135
AclWI GGATC 6 cut(s) 682, 695, 825, 1013, 1055, 1068
AcoI YGGCCR 1 cut(s) 211
AcsI RAATTY 2 cut(s) 512, 917
AfaI GTAC 1 cut(s) 167
AfiI CCNNNNNNNGG 3 cut(s) 594, 911, 912
AgsI TTSAA 3 cut(s) 739, 889, 942
AjnI CCWGG 2 cut(s) 141, 298
AjuI GAANNNNNNNTTGG 2 cut(s) 590, 622
AleI CACNNNNGTG 1 cut(s) 727
AloI GAACNNNNNNTCC 2 cut(s) 66, 98
AluBI AGCT 7 cut(s) 45, 136, 172, 678, 718, 1031, 1096
AluI AGCT 7 cut(s) 45, 136, 172, 678, 718, 1031, 1096
Alw21I GWGCWC 1 cut(s) 156
Alw26I GTCTC 1 cut(s) 18
AlwI GGATC 6 cut(s) 682, 695, 825, 1013, 1055, 1068
Aor13HI TCCGGA 1 cut(s) 559
AoxI GGCC 3 cut(s) 144, 211, 698
ApeKI GCWGC 1 cut(s) 1066
ApoI RAATTY 2 cut(s) 512, 917
Asp700I GAANNNNTTC 2 cut(s) 348, 602
AspLEI GCGC 3 cut(s) 123, 179, 261
AspS9I GGNCC 2 cut(s) 196, 694
AsuC2I CCSGG 4 cut(s) 210, 572, 629, 692
AsuHPI GGTGA 3 cut(s) 380, 550, 819
AvaII GGWCC 2 cut(s) 196, 694
BaeGI GKGCMC 1 cut(s) 906
BamHI GGATCC 2 cut(s) 687, 1060
BanI GGYRCC 1 cut(s) 547
BanII GRGCYC 1 cut(s) 210
Bbv12I GWGCWC 1 cut(s) 156
BbvCI CCTCAGC 1 cut(s) 1022
BbvI GCAGC 1 cut(s) 1053
BccI CCATC 3 cut(s) 766, 829, 1104
BceAI ACGGC 3 cut(s) 148, 778, 1029
BciT130I CCWGG 2 cut(s) 143, 300
BciVI GTATCC 1 cut(s) 67
BcnI CCSGG 4 cut(s) 210, 572, 629, 692
BcoDI GTCTC 1 cut(s) 18
BfaI CTAG 1 cut(s) 137
BfmI CTRYAG 1 cut(s) 1070
BfuI GTATCC 1 cut(s) 67
BisI GCNGC 2 cut(s) 247, 1067
BlsI GCNGC 2 cut(s) 248, 1068
Bme1390I CCNGG 6 cut(s) 143, 210, 300, 572, 629, 692
Bme18I GGWCC 2 cut(s) 196, 694
BmgT120I GGNCC 2 cut(s) 196, 694
BmiI GGNNCC 6 cut(s) 549, 586, 626, 689, 695, 1062
BmrFI CCNGG 6 cut(s) 143, 210, 300, 572, 629, 692
BmsI GCATC 1 cut(s) 885
Bpu10I CCTNAGC 1 cut(s) 1022
BpuMI CCSGG 4 cut(s) 210, 572, 629, 692
BsaAI YACGTR 1 cut(s) 49
BsaBI GATNNNNATC 1 cut(s) 1059
BsaJI CCNNGG 1 cut(s) 298
BsaWI WCCGGW 3 cut(s) 559, 587, 829
BsaXI ACNNNNNCTCC 2 cut(s) 66, 96
Bsc4I CCNNNNNNNGG 3 cut(s) 594, 911, 912
Bse1I ACTGG 1 cut(s) 1045
Bse8I GATNNNNATC 1 cut(s) 1059
BseAI TCCGGA 1 cut(s) 559
BseBI CCWGG 2 cut(s) 143, 300
BseDI CCNNGG 1 cut(s) 298
BseGI GGATG 5 cut(s) 777, 808, 900, 1045, 1115
BseJI GATNNNNATC 1 cut(s) 1059
BseLI CCNNNNNNNGG 3 cut(s) 594, 911, 912
BseMII CTCAG 3 cut(s) 277, 477, 1013
BseNI ACTGG 1 cut(s) 1045
BseRI GAGGAG 5 cut(s) 19, 670, 680, 683, 1118
BseSI GKGCMC 1 cut(s) 906
BseXI GCAGC 1 cut(s) 1053
BsgI GTGCAG 1 cut(s) 1143
Bsh1236I CGCG 3 cut(s) 116, 183, 249
BshFI GGCC 3 cut(s) 146, 213, 700
BshNI GGYRCC 1 cut(s) 547
BsiHKAI GWGCWC 1 cut(s) 156
BsiSI CCGG 8 cut(s) 210, 560, 571, 588, 629, 691, 697, 830
BslI CCNNNNNNNGG 3 cut(s) 594, 911, 912
BsmAI GTCTC 1 cut(s) 18
BsmI GAATGC 1 cut(s) 970
BsnI GGCC 3 cut(s) 146, 213, 700
Bsp1286I GDGCHC 3 cut(s) 156, 210, 906
Bsp13I TCCGGA 1 cut(s) 559
Bsp143I GATC 5 cut(s) 687, 817, 1005, 1054, 1060
BspACI CCGC 7 cut(s) 181, 224, 229, 247, 1064, 1114, 1135
BspANI GGCC 3 cut(s) 146, 213, 700
BspCNI CTCAG 3 cut(s) 276, 478, 1014
BspEI TCCGGA 1 cut(s) 559
BspFNI CGCG 3 cut(s) 116, 183, 249
BspLI GGNNCC 6 cut(s) 549, 586, 626, 689, 695, 1062
BspPI GGATC 6 cut(s) 682, 695, 825, 1013, 1055, 1068
BspT107I GGYRCC 1 cut(s) 547
BsrBI CCGCTC 1 cut(s) 226
BsrI ACTGG 1 cut(s) 1045
BssECI CCNNGG 1 cut(s) 298
BssMI GATC 5 cut(s) 687, 817, 1005, 1054, 1060
Bst2UI CCWGG 2 cut(s) 143, 300
Bst4CI ACNGT 1 cut(s) 850
Bst6I CTCTTC 5 cut(s) 390, 395, 500, 836, 884
BstBAI YACGTR 1 cut(s) 49
BstC8I GCNNGC 1 cut(s) 181
BstDEI CTNAG 5 cut(s) 263, 377, 438, 486, 1022
BstF5I GGATG 5 cut(s) 777, 808, 900, 1045, 1115
BstFNI CGCG 3 cut(s) 116, 183, 249
BstHHI GCGC 3 cut(s) 123, 179, 261
BstKTI GATC 5 cut(s) 690, 820, 1008, 1057, 1063
BstMAI GTCTC 1 cut(s) 18
BstMBI GATC 5 cut(s) 687, 817, 1005, 1054, 1060
BstMWI GCNNNNNNNGC 3 cut(s) 160, 169, 790
BstNI CCWGG 2 cut(s) 143, 300
BstSCI CCNGG 6 cut(s) 141, 208, 298, 570, 627, 690
BstSFI CTRYAG 1 cut(s) 1070
BstSLI GKGCMC 1 cut(s) 906
BstUI CGCG 3 cut(s) 116, 183, 249
BstV1I GCAGC 1 cut(s) 1053
BstX2I RGATCY 2 cut(s) 687, 1060
BstYI RGATCY 2 cut(s) 687, 1060
BsuI GTATCC 1 cut(s) 67
BsuRI GGCC 3 cut(s) 146, 213, 700
BtgZI GCGATG 1 cut(s) 271
BtsCI GGATG 5 cut(s) 777, 808, 900, 1045, 1115
Cac8I GCNNGC 1 cut(s) 181
CfoI GCGC 3 cut(s) 123, 179, 261
Cfr13I GGNCC 2 cut(s) 196, 694
CseI GACGC 2 cut(s) 172, 813
Csp6I GTAC 1 cut(s) 166
CviAII CATG 1 cut(s) 863
CviQI GTAC 1 cut(s) 166
DdeI CTNAG 5 cut(s) 263, 377, 438, 486, 1022
DpnI GATC 5 cut(s) 689, 819, 1007, 1056, 1062
DpnII GATC 5 cut(s) 687, 817, 1005, 1054, 1060
EaeI YGGCCR 1 cut(s) 211
Eam1104I CTCTTC 5 cut(s) 390, 395, 500, 836, 884
EarI CTCTTC 5 cut(s) 390, 395, 500, 836, 884
Eco24I GRGCYC 1 cut(s) 210
Eco47I GGWCC 2 cut(s) 196, 694
EcoO109I RGGNCCY 1 cut(s) 196
EcoRI GAATTC 1 cut(s) 512
EcoRII CCWGG 2 cut(s) 141, 298
EcoT38I GRGCYC 1 cut(s) 210
FaeI CATG 1 cut(s) 866
FaiI YATR 9 cut(s) 149, 536, 786, 788, 798, 864, 908, 933, 987
FatI CATG 1 cut(s) 862
FauI CCCGC 3 cut(s) 188, 231, 1107
Fnu4HI GCNGC 2 cut(s) 247, 1067
FokI GGATG 5 cut(s) 784, 815, 907, 1052, 1122
FriOI GRGCYC 1 cut(s) 210
Fsp4HI GCNGC 2 cut(s) 247, 1067
FspBI CTAG 1 cut(s) 137
GlaI GCGC 3 cut(s) 122, 178, 260
GluI GCNGC 2 cut(s) 247, 1067
HaeIII GGCC 3 cut(s) 146, 213, 700
HapII CCGG 8 cut(s) 210, 560, 571, 588, 629, 691, 697, 830
HgaI GACGC 2 cut(s) 172, 813
HhaI GCGC 3 cut(s) 123, 179, 261
Hin1II CATG 1 cut(s) 866
Hin6I GCGC 3 cut(s) 121, 177, 259
HinP1I GCGC 3 cut(s) 121, 177, 259
HindIII AAGCTT 3 cut(s) 676, 716, 1029
HinfI GANTC 2 cut(s) 327, 671
HpaII CCGG 8 cut(s) 210, 560, 571, 588, 629, 691, 697, 830
HphI GGTGA 3 cut(s) 380, 550, 819
Hpy188I TCNGA 2 cut(s) 266, 954
Hpy188III TCNNGA 5 cut(s) 15, 389, 560, 1009, 1058
Hpy99I CGWCG 1 cut(s) 188
HpyAV CCTTC 2 cut(s) 292, 736
HpyCH4III ACNGT 1 cut(s) 850
HpyCH4IV ACGT 1 cut(s) 48
HpyCH4V TGCA 3 cut(s) 638, 1124, 1141
HpyF10VI GCNNNNNNNGC 3 cut(s) 160, 169, 790
HpyF3I CTNAG 5 cut(s) 263, 377, 438, 486, 1022
HpySE526I ACGT 1 cut(s) 48
Hsp92II CATG 1 cut(s) 866
HspAI GCGC 3 cut(s) 121, 177, 259
Kpn2I TCCGGA 1 cut(s) 559
Kzo9I GATC 5 cut(s) 687, 817, 1005, 1054, 1060
LmnI GCTCC 2 cut(s) 231, 781
Lsp1109I GCAGC 1 cut(s) 1053
LweI GCATC 1 cut(s) 885
MaeI CTAG 1 cut(s) 137
MaeII ACGT 1 cut(s) 48
MaeIII GTNAC 2 cut(s) 538, 825
MalI GATC 5 cut(s) 689, 819, 1007, 1056, 1062
MbiI CCGCTC 1 cut(s) 226
MboI GATC 5 cut(s) 687, 817, 1005, 1054, 1060
MboII GAAGA 8 cut(s) 407, 412, 478, 517, 751, 853, 901, 1160
MflI RGATCY 2 cut(s) 687, 1060
MhlI GDGCHC 3 cut(s) 156, 210, 906
MluCI AATT 4 cut(s) 449, 491, 512, 917
MlyI GAGTC 1 cut(s) 680
MmeI TCCRAC 3 cut(s) 759, 795, 1080
MroI TCCGGA 1 cut(s) 559
MroXI GAANNNNTTC 2 cut(s) 348, 602
MseI TTAA 2 cut(s) 1077, 1155
MslI CAYNNNNRTG 1 cut(s) 727
MspA1I CMGCKG 1 cut(s) 1066
MspI CCGG 8 cut(s) 210, 560, 571, 588, 629, 691, 697, 830
MspR9I CCNGG 6 cut(s) 143, 210, 300, 572, 629, 692
Mva1269I GAATGC 1 cut(s) 970
MvaI CCWGG 2 cut(s) 143, 300
MvnI CGCG 3 cut(s) 116, 183, 249
MwoI GCNNNNNNNGC 3 cut(s) 160, 169, 790
NciI CCSGG 4 cut(s) 210, 572, 629, 692
NdeII GATC 5 cut(s) 687, 817, 1005, 1054, 1060
NlaIII CATG 1 cut(s) 866
NlaIV GGNNCC 6 cut(s) 549, 586, 626, 689, 695, 1062
NmuCI GTSAC 2 cut(s) 538, 825
OliI CACNNNNGTG 1 cut(s) 727
PctI GAATGC 1 cut(s) 970
PdmI GAANNNNTTC 2 cut(s) 348, 602
PfeI GAWTC 1 cut(s) 327
PkrI GCNGC 2 cut(s) 248, 1068
PleI GAGTC 1 cut(s) 679
PpsI GAGTC 1 cut(s) 679
Ppu21I YACGTR 1 cut(s) 49
PpuMI RGGWCCY 1 cut(s) 196
Psp5II RGGWCCY 1 cut(s) 196
Psp6I CCWGG 2 cut(s) 141, 298
PspGI CCWGG 2 cut(s) 141, 298
PspN4I GGNNCC 6 cut(s) 549, 586, 626, 689, 695, 1062
PspPI GGNCC 2 cut(s) 196, 694
PspPPI RGGWCCY 1 cut(s) 196
PsuI RGATCY 2 cut(s) 687, 1060
RsaI GTAC 1 cut(s) 167
RsaNI GTAC 1 cut(s) 166
RseI CAYNNNNRTG 1 cut(s) 727
SaqAI TTAA 2 cut(s) 1077, 1155
SatI GCNGC 2 cut(s) 247, 1067
Sau3AI GATC 5 cut(s) 687, 817, 1005, 1054, 1060
Sau96I GGNCC 2 cut(s) 196, 694
SchI GAGTC 1 cut(s) 680
ScrFI CCNGG 6 cut(s) 143, 210, 300, 572, 629, 692
SduI GDGCHC 3 cut(s) 156, 210, 906
SfaNI GCATC 1 cut(s) 885
SfcI CTRYAG 1 cut(s) 1070
SinI GGWCC 2 cut(s) 196, 694
SmiMI CAYNNNNRTG 1 cut(s) 727
Sse9I AATT 4 cut(s) 449, 491, 512, 917
SsiI CCGC 7 cut(s) 181, 224, 229, 247, 1064, 1114, 1135
SspMI CTAG 1 cut(s) 137
StyD4I CCNGG 6 cut(s) 141, 208, 298, 570, 627, 690
TaaI ACNGT 1 cut(s) 850
TaiI ACGT 1 cut(s) 51
TaqI TCGA 3 cut(s) 16, 237, 809
TasI AATT 4 cut(s) 449, 491, 512, 917
TauI GCSGC 1 cut(s) 249
TfiI GAWTC 1 cut(s) 327
Tru1I TTAA 2 cut(s) 1077, 1155
Tru9I TTAA 2 cut(s) 1077, 1155
TseFI GTSAC 2 cut(s) 538, 825
TseI GCWGC 1 cut(s) 1066
Tsp45I GTSAC 2 cut(s) 538, 825
TspDTI ATGAA 2 cut(s) 274, 408
VpaK11BI GGWCC 2 cut(s) 196, 694
XapI RAATTY 2 cut(s) 512, 917
XmnI GAANNNNTTC 2 cut(s) 348, 602
XspI CTAG 1 cut(s) 137
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.