AT3G49180

root initiation defective

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0007848
Physical Location & Seq
Forward (+)
18229747 .. 18232004
2258 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G49180.1

Sequence Viewer

Length: 1317 bp
ATGGAGATTACTGTAATCGCTTCTTCCTCAATCGATGAAGGAATTGGAAGTTGGGATCTCAAAACCGGGACAGAGCAGCTTCAATTCAAGCCGTGTGCTTCTCCGGCGCATGGTCTCACCGCCGTCGGCGAAAAATTTCTCGCCTCCTCTCAGCTCTCGGCGAGAAATACTTCTGGCTCGATTTTTTACTGGTCTTGGACTAAGCCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAGGAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAAGTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGATTCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAGGCTATTTGATGATTTCCAGAGGCAGCAAGGGAACACTCTTTATGAACACAATTTTAATGAGCATACAATGTCTGTAACTGATATTGTTATAGACTATGGAGGCTGCAATGCTGTGATAATTTCCTCTTCAGAAGATCGGACTTGCAAGGTTTGGAGCTTGTCAAGAGGGAAATTGTTGAAAAATATCATTTTTCCTTCAGTCATCAATGCACTCGCATTGGACCCTGGAGGGTGTGTGTTCTATGCTGGTGCCAGAGACAGCAAAATCTATATCGGTGCCATTAATGCCACAAGTGAATACGGGACACAAGTTCTTGGTTCAGTATCTGAAAAAGGCAAAGCTATTACTTGCTTAGCATATTGTGCAGACGGAAACCTTTTGATATCTGGATCAGAAGATGGTGTGGTTTGTGTTTGGGATCCCAAATCACTTCGCCATGTTCGTACTCTCATCCATGCAAAAGGTTCTAGAAAAGGTCCTGTGAACAATATTCAAATTGTTAGAAAAACGATTGTTGCTAATTCCAACAAAACCCAAGTTTCCTGGAAAAGTCGTGGGGCTTTAATCCCACCGCCTTTGGAAAAATATGAAAGACCAGTAGAAGATACTATGGATGGTATCGTTACGGTTGATCCGCCGCCATTTTCTGATGTTCCTGTTTACTCTTCTTTCCTCAGTGCTGACCTTATTGACGAGCAAGTTAAAGAACTTCAGCAACAAGGCTCTGCAGCAACAGAGATGGAAATGGAAAGACTGAAACTTGAATACAAAAGATCTTTACAGATGAATGAACAATGGCAGAAGAACTATGAGAATTTGCTTCAAGTGGTTATGGAAGAAGAACAAATCGGTGGTACCAATTGA

Protein Analysis

438

Amino Acids

48.15

Weight (kDa)

5.53

Isoelectric Point (pI)

35.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Beta-prop_WDR5 PF25175 5 - 148 1.5e-13 WDR5 beta-propeller domain
Beta-prop_THOC3 PF25174 5 - 149 5.4e-10 THOC3 beta-propeller domain
Beta-prop_WDR3_1st PF25173 11 - 149 1.9e-16 WDR3 first beta-propeller domain
WDR55 PF24796 15 - 205 1.2e-07 WDR55
Beta-prop_EML_2 PF23414 59 - 161 5.7e-08 Echinoderm microtubule-associated protein second beta-propeller
WD40_CDC20-Fz PF24807 61 - 211 6.4e-12 CDC20/Fizzy WD40 domain
Beta-prop_CAF1B_HIR1 PF24105 75 - 213 6.5e-06 CAF1B/HIR1 beta-propeller domain
WD40_WDHD1_1st PF24817 80 - 149 1.1e-07 WDHD1 first WD40 domain
Beta-prop_THOC3 PF25174 81 - 304 1.9e-22 THOC3 beta-propeller domain
Beta-prop_EML PF23409 81 - 160 9.1e-07 Echinoderm microtubule-associated protein first beta-propeller
WD40_Prp19 PF24814 81 - 242 1.9e-18 Prp19 WD40 domain
NBCH_WD40 PF20426 98 - 247 6.2e-08 Neurobeachin beta propeller domain
WD40 PF00400 110 - 148 2.6e-10 WD domain, G-beta repeat
EIF3I PF24805 117 - 321 1e-12 EIF3I
Beta-prop_TEP1_2nd PF25047 132 - 336 5.8e-10 TEP-1 second beta-propeller
Beta-prop_WDR36-Utp21_1st PF25171 159 - 320 6.7e-07 WDR36/Utp21 first beta-propeller
Beta-prop_WDR5 PF25175 165 - 307 3e-15 WDR5 beta-propeller domain
WD40_Prp19 PF24814 165 - 316 7e-14 Prp19 WD40 domain
Beta-prop_WDR36-Utp21_2nd PF25168 169 - 295 2.5e-07 WDR36/Utp21 second beta-propeller domain
Beta-prop_WDR3_2nd PF25172 171 - 291 2.3e-06 WDR3 second beta-propeller domain
Beta-prop_EML PF23409 184 - 333 3.1e-06 Echinoderm microtubule-associated protein first beta-propeller
WDR90_beta-prop_4th PF23342 189 - 321 4.3e-06 WDR90, 4th beta-propeller
Beta-prop_EML_2 PF23414 189 - 301 1.4e-10 Echinoderm microtubule-associated protein second beta-propeller
WD40_WDHD1_1st PF24817 216 - 301 8.9e-06 WDHD1 first WD40 domain
Beta-prop_WDR3_1st PF25173 218 - 306 1.5e-07 WDR3 first beta-propeller domain
WD40_CDC20-Fz PF24807 253 - 331 7.4e-06 CDC20/Fizzy WD40 domain
WD40 PF00400 264 - 291 1.5e-07 WD domain, G-beta repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 449
Acc65I GGTACC 1 cut(s) 1307
AccB1I GGYRCC 3 cut(s) 701, 728, 1307
AciI CCGC 4 cut(s) 120, 1025, 1088, 1091
AclWI GGATC 6 cut(s) 63, 421, 850, 866, 879, 1079
AcsI RAATTY 2 cut(s) 134, 1267
AcuI CTGAAG 4 cut(s) 234, 564, 633, 1148
AfaI GTAC 2 cut(s) 898, 1309
AfiI CCNNNNNNNGG 2 cut(s) 110, 316
AflII CTTAAG 1 cut(s) 338
AflIII ACRYGT 1 cut(s) 371
AgsI TTSAA 6 cut(s) 83, 88, 631, 947, 1217, 1277
AjnI CCWGG 2 cut(s) 676, 995
AjuI GAANNNNNNNTTGG 2 cut(s) 34, 66
AluBI AGCT 6 cut(s) 79, 154, 212, 225, 609, 794
AluI AGCT 6 cut(s) 79, 154, 212, 225, 609, 794
Alw26I GTCTC 3 cut(s) 119, 447, 702
AlwI GGATC 6 cut(s) 63, 421, 850, 866, 879, 1079
AlwNI CAGNNNCTG 1 cut(s) 779
ApeKI GCWGC 5 cut(s) 76, 254, 475, 555, 1181
ApoI RAATTY 2 cut(s) 134, 1267
AseI ATTAAT 1 cut(s) 735
Asp700I GAANNNNTTC 2 cut(s) 135, 169
Asp718I GGTACC 1 cut(s) 1307
AspLEI GCGC 1 cut(s) 109
AspS9I GGNCC 2 cut(s) 673, 929
AsuC2I CCSGG 1 cut(s) 67
AsuHPI GGTGA 1 cut(s) 109
AvaII GGWCC 2 cut(s) 673, 929
BamHI GGATCC 1 cut(s) 871
BanI GGYRCC 3 cut(s) 701, 728, 1307
BbvI GCAGC 5 cut(s) 88, 266, 487, 542, 1193
BccI CCATC 4 cut(s) 416, 845, 1061, 1186
BceAI ACGGC 2 cut(s) 76, 107
BciT130I CCWGG 2 cut(s) 678, 997
BcnI CCSGG 1 cut(s) 67
BcoDI GTCTC 3 cut(s) 119, 447, 702
BfaI CTAG 1 cut(s) 921
BfmI CTRYAG 1 cut(s) 1179
BfrI CTTAAG 1 cut(s) 338
BglII AGATCT 1 cut(s) 1226
BisI GCNGC 6 cut(s) 77, 255, 476, 556, 1091, 1182
BlpI GCTNAGC 1 cut(s) 805
BlsI GCNGC 6 cut(s) 78, 256, 477, 557, 1092, 1183
Bme1390I CCNGG 3 cut(s) 67, 678, 997
Bme18I GGWCC 2 cut(s) 673, 929
BmgT120I GGNCC 2 cut(s) 673, 929
BmiI GGNNCC 6 cut(s) 237, 675, 703, 730, 873, 1309
BmrFI CCNGG 3 cut(s) 67, 678, 997
BmrI ACTGGG 2 cut(s) 224, 336
BmuI ACTGGG 2 cut(s) 224, 336
BpmI CTGGAG 3 cut(s) 318, 408, 699
Bpu1102I GCTNAGC 1 cut(s) 805
BpuEI CTTGAG 2 cut(s) 192, 402
BpuMI CCSGG 1 cut(s) 67
Bsa29I ATCGAT 1 cut(s) 33
BsaI GGTCTC 2 cut(s) 119, 447
BsaJI CCNNGG 1 cut(s) 676
BsaXI ACNNNNNCTCC 2 cut(s) 672, 702
Bsc4I CCNNNNNNNGG 2 cut(s) 110, 316
Bse1I ACTGG 4 cut(s) 194, 230, 331, 1049
Bse3DI GCAATG 1 cut(s) 565
BseBI CCWGG 2 cut(s) 678, 997
BseCI ATCGAT 1 cut(s) 33
BseDI CCNNGG 1 cut(s) 676
BseGI GGATG 2 cut(s) 903, 1072
BseLI CCNNNNNNNGG 2 cut(s) 110, 316
BseMI GCAATG 1 cut(s) 565
BseMII CTCAG 2 cut(s) 164, 1141
BseNI ACTGG 4 cut(s) 194, 230, 331, 1049
BseRI GAGGAG 1 cut(s) 136
BseXI GCAGC 5 cut(s) 88, 266, 487, 542, 1193
BsgI GTGCAG 1 cut(s) 837
BshNI GGYRCC 3 cut(s) 701, 728, 1307
BshVI ATCGAT 1 cut(s) 33
BsiSI CCGG 2 cut(s) 66, 104
BslFI GGGAC 2 cut(s) 82, 769
BslI CCNNNNNNNGG 2 cut(s) 110, 316
BsmAI GTCTC 3 cut(s) 119, 447, 702
BsmFI GGGAC 2 cut(s) 82, 769
Bso31I GGTCTC 2 cut(s) 119, 447
Bsp143I GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
Bsp1720I GCTNAGC 1 cut(s) 805
BspACI CCGC 4 cut(s) 120, 1025, 1088, 1091
BspCNI CTCAG 2 cut(s) 163, 1140
BspDI ATCGAT 1 cut(s) 33
BspLI GGNNCC 6 cut(s) 237, 675, 703, 730, 873, 1309
BspMAI CTGCAG 1 cut(s) 1183
BspPI GGATC 6 cut(s) 63, 421, 850, 866, 879, 1079
BspQI GCTCTTC 1 cut(s) 215
BspT107I GGYRCC 3 cut(s) 701, 728, 1307
BspTI CTTAAG 1 cut(s) 338
BspTNI GGTCTC 2 cut(s) 119, 447
BsrDI GCAATG 1 cut(s) 565
BsrI ACTGG 4 cut(s) 194, 230, 331, 1049
BssECI CCNNGG 1 cut(s) 676
BssMI GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
Bst2UI CCWGG 2 cut(s) 678, 997
Bst4CI ACNGT 2 cut(s) 13, 1081
Bst6I CTCTTC 3 cut(s) 215, 583, 1123
BstAFI CTTAAG 1 cut(s) 338
BstAPI GCANNNNNTGC 1 cut(s) 815
BstDEI CTNAG 5 cut(s) 150, 201, 277, 805, 1127
BstENI CCTNNNNNAGG 1 cut(s) 314
BstF5I GGATG 2 cut(s) 903, 1072
BstHHI GCGC 1 cut(s) 109
BstKTI GATC 7 cut(s) 58, 416, 589, 845, 874, 1087, 1229
BstMAI GTCTC 3 cut(s) 119, 447, 702
BstMBI GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
BstMWI GCNNNNNNNGC 4 cut(s) 104, 254, 737, 815
BstNI CCWGG 2 cut(s) 678, 997
BstNSI RCATGY 1 cut(s) 375
BstSCI CCNGG 3 cut(s) 65, 676, 995
BstSFI CTRYAG 1 cut(s) 1179
BstV1I GCAGC 5 cut(s) 88, 266, 487, 542, 1193
BstX2I RGATCY 4 cut(s) 55, 413, 871, 1226
BstYI RGATCY 4 cut(s) 55, 413, 871, 1226
Bsu15I ATCGAT 1 cut(s) 33
BsuTUI ATCGAT 1 cut(s) 33
BtsCI GGATG 2 cut(s) 903, 1072
BtsIMutI CAGTG 2 cut(s) 237, 1135
CaiI CAGNNNCTG 1 cut(s) 779
CfoI GCGC 1 cut(s) 109
Cfr13I GGNCC 2 cut(s) 673, 929
ClaI ATCGAT 1 cut(s) 33
Csp6I GTAC 2 cut(s) 897, 1308
CspCI CAANNNNNGTGG 2 cut(s) 1011, 1046
CviAII CATG 5 cut(s) 110, 350, 372, 890, 908
CviQI GTAC 2 cut(s) 897, 1308
DdeI CTNAG 5 cut(s) 150, 201, 277, 805, 1127
DpnI GATC 7 cut(s) 57, 415, 588, 844, 873, 1086, 1228
DpnII GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
Eam1104I CTCTTC 3 cut(s) 215, 583, 1123
EarI CTCTTC 3 cut(s) 215, 583, 1123
EciI GGCGGA 1 cut(s) 1077
Eco31I GGTCTC 2 cut(s) 119, 447
Eco32I GATATC 1 cut(s) 837
Eco47I GGWCC 2 cut(s) 673, 929
Eco57I CTGAAG 4 cut(s) 234, 564, 633, 1148
EcoNI CCTNNNNNAGG 1 cut(s) 314
EcoO109I RGGNCCY 1 cut(s) 929
EcoRII CCWGG 2 cut(s) 676, 995
EcoRV GATATC 1 cut(s) 837
FaeI CATG 5 cut(s) 113, 353, 375, 893, 911
FaqI GGGAC 2 cut(s) 82, 769
FatI CATG 5 cut(s) 109, 349, 371, 889, 907
Fnu4HI GCNGC 6 cut(s) 77, 255, 476, 556, 1091, 1182
FokI GGATG 2 cut(s) 890, 1079
Fsp4HI GCNGC 6 cut(s) 77, 255, 476, 556, 1091, 1182
FspBI CTAG 1 cut(s) 921
GlaI GCGC 1 cut(s) 108
GluI GCNGC 6 cut(s) 77, 255, 476, 556, 1091, 1182
GsuI CTGGAG 3 cut(s) 318, 408, 699
HapII CCGG 2 cut(s) 66, 104
HhaI GCGC 1 cut(s) 109
Hin1II CATG 5 cut(s) 113, 353, 375, 893, 911
Hin6I GCGC 1 cut(s) 107
HinP1I GCGC 1 cut(s) 107
HinfI GANTC 2 cut(s) 291, 395
HpaII CCGG 2 cut(s) 66, 104
HphI GGTGA 1 cut(s) 109
Hpy166II GTNNAC 2 cut(s) 937, 1114
Hpy188I TCNGA 5 cut(s) 583, 591, 781, 847, 1102
Hpy188III TCNNGA 8 cut(s) 297, 387, 411, 419, 469, 615, 840, 921
Hpy8I GTNNAC 2 cut(s) 937, 1114
Hpy99I CGWCG 1 cut(s) 128
HpyAV CCTTC 3 cut(s) 32, 260, 657
HpyCH4III ACNGT 2 cut(s) 13, 1081
HpyCH4V TGCA 7 cut(s) 254, 558, 597, 662, 818, 911, 1181
HpyF10VI GCNNNNNNNGC 4 cut(s) 104, 254, 737, 815
HpyF3I CTNAG 5 cut(s) 150, 201, 277, 805, 1127
Hsp92II CATG 5 cut(s) 113, 353, 375, 893, 911
HspAI GCGC 1 cut(s) 107
KpnI GGTACC 1 cut(s) 1311
Kzo9I GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
LguI GCTCTTC 1 cut(s) 215
LmnI GCTCC 1 cut(s) 606
Lsp1109I GCAGC 5 cut(s) 88, 266, 487, 542, 1193
MaeI CTAG 1 cut(s) 921
MaeIII GTNAC 3 cut(s) 367, 526, 1075
MalI GATC 7 cut(s) 57, 415, 588, 844, 873, 1086, 1228
MboI GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
MfeI CAATTG 1 cut(s) 1312
MflI RGATCY 4 cut(s) 55, 413, 871, 1226
MmeI TCCRAC 1 cut(s) 1002
MroXI GAANNNNTTC 2 cut(s) 135, 169
MseI TTAA 5 cut(s) 339, 507, 735, 1016, 1155
MspCI CTTAAG 1 cut(s) 338
MspI CCGG 2 cut(s) 66, 104
MspR9I CCNGG 3 cut(s) 67, 678, 997
MunI CAATTG 1 cut(s) 1312
MvaI CCWGG 2 cut(s) 678, 997
MwoI GCNNNNNNNGC 4 cut(s) 104, 254, 737, 815
NciI CCSGG 1 cut(s) 67
NdeII GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
NlaIII CATG 5 cut(s) 113, 353, 375, 893, 911
NlaIV GGNNCC 6 cut(s) 237, 675, 703, 730, 873, 1309
NmeAIII GCCGAG 1 cut(s) 137
NspI RCATGY 1 cut(s) 375
PciI ACATGT 1 cut(s) 371
PciSI GCTCTTC 1 cut(s) 215
PcsI WCGNNNNNNNCGW 1 cut(s) 892
PdmI GAANNNNTTC 2 cut(s) 135, 169
PfeI GAWTC 2 cut(s) 291, 395
PfoI TCCNGGA 1 cut(s) 995
PkrI GCNGC 6 cut(s) 78, 256, 477, 557, 1092, 1183
PpuMI RGGWCCY 1 cut(s) 929
PscI ACATGT 1 cut(s) 371
PshBI ATTAAT 1 cut(s) 735
PsiI TTATAA 1 cut(s) 449
Psp5II RGGWCCY 1 cut(s) 929
Psp6I CCWGG 2 cut(s) 676, 995
PspGI CCWGG 2 cut(s) 676, 995
PspN4I GGNNCC 6 cut(s) 237, 675, 703, 730, 873, 1309
PspPI GGNCC 2 cut(s) 673, 929
PspPPI RGGWCCY 1 cut(s) 929
PstI CTGCAG 1 cut(s) 1183
PstNI CAGNNNCTG 1 cut(s) 779
PsuI RGATCY 4 cut(s) 55, 413, 871, 1226
RsaI GTAC 2 cut(s) 898, 1309
RsaNI GTAC 2 cut(s) 897, 1308
SapI GCTCTTC 1 cut(s) 215
SaqAI TTAA 5 cut(s) 339, 507, 735, 1016, 1155
SatI GCNGC 6 cut(s) 77, 255, 476, 556, 1091, 1182
Sau3AI GATC 7 cut(s) 55, 413, 586, 842, 871, 1084, 1226
Sau96I GGNCC 2 cut(s) 673, 929
ScrFI CCNGG 3 cut(s) 67, 678, 997
SfcI CTRYAG 1 cut(s) 1179
SinI GGWCC 2 cut(s) 673, 929
SmlI CTYRAG 3 cut(s) 207, 338, 417
SmoI CTYRAG 3 cut(s) 207, 338, 417
SsiI CCGC 4 cut(s) 120, 1025, 1088, 1091
SspI AATATT 1 cut(s) 943
SspMI CTAG 1 cut(s) 921
StyD4I CCNGG 3 cut(s) 65, 676, 995
TaaI ACNGT 2 cut(s) 13, 1081
TaqI TCGA 2 cut(s) 33, 179
TauI GCSGC 1 cut(s) 1093
TfiI GAWTC 2 cut(s) 291, 395
Tru1I TTAA 5 cut(s) 339, 507, 735, 1016, 1155
Tru9I TTAA 5 cut(s) 339, 507, 735, 1016, 1155
TscAI CASTG 2 cut(s) 237, 1135
TseI GCWGC 5 cut(s) 76, 254, 475, 555, 1181
TspDTI ATGAA 6 cut(s) 51, 279, 510, 1056, 1253, 1257
TspGWI ACGGA 1 cut(s) 837
TspRI CASTG 2 cut(s) 237, 1135
Vha464I CTTAAG 1 cut(s) 338
VpaK11BI GGWCC 2 cut(s) 673, 929
VspI ATTAAT 1 cut(s) 735
XagI CCTNNNNNAGG 1 cut(s) 314
XapI RAATTY 2 cut(s) 134, 1267
XbaI TCTAGA 1 cut(s) 920
XceI RCATGY 1 cut(s) 375
XmnI GAANNNNTTC 2 cut(s) 135, 169
XspI CTAG 1 cut(s) 921
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.