AT1G54890

Root cap

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
1
OG0006038
Physical Location & Seq
Forward (+)
20462940 .. 20464697
1758 bp
Loading structure...
UTR
Exon/CDS
Intron
AT1G54890.1

Sequence Viewer

Length: 1044 bp
ATGAAGGGAGATCTGAGAAATGGGGTTTACGTTGGATTGGTGGTGATGCTCTATGCGTGTATTGTCGTTGTACAACTCGAAGCAGCGTTGGAAACAAAGACATGTTTCCAAAGGAAGAGTCCATGTTTCCTAAAGAAGCAAACTTGCCCAAAGCAATGTCCTTCGTTTTCCCCTCCCAATGGCAGTACCAAGGCATGCGTCATCGATTGCTTTAACCCTATTTGCAAAGCCACTTGCCGAAATAGGAAGCCTAATTGCAACGGCAAAGGATCAGCATGCTTAGATCCACGTTTCATCGGCGGAGATGGCATCGTCTTCTACTTTCATGGAAAACGCGACGAGCATTTTGCACTAATCTCTGACGTTGACTTCCAAGTCAACGCACGTTTCATTGGTCTTAGACCTAATGGTCGGGCCAGAGATTTTACGTGGATACAATCCTTAGGTCTAATCTTCGGCCCCAACAGCAAAACCTTCTCACTCGAGGCTACAAAAGCCGAGAAATGGGATCACCAAGTTGACCACCTCCGTCTTTCCTACGAAGGAAAAGAGATCTCTTTACCAAAAGGAGATACATCAGTGTGGAGTCCTCCTCTAGGAGACTATATAAAGATCGAGAGAACTTCTGACATAAACTCCGTGTTGGTCACGTTACAAGACATTGCCGAGATTTGGATCAACGTGGTTCCGGTGACAAAAGAAGACGACATAATCCATAAATACGGGATACCGGAGGATGACTGTTTTGCTCATCTTGAGGTTCAGTTCCGGTTCTTGAAGTTGTCATCAAACGTGGAAGGTGTTTTAGGAAGAACGTATAAAGAAGATTTCAAGAATCCGGCGAAACCTGGCGTTGCTATGCCGGTTGTTGGTGGCGAAGATAAATACAGAACAGCGTCACTTCTTGAAACAAGTTGTAATGCATGTGTTTACTCTGGTGGCTCAAGAAGTTTGGACAAGATTGAGCCATTGTTGCTGAATCAAAACACTGTTGATTGCACCGGTGGATCCAGCAGTGGTGTTGGAATCTTTTGCAGAAAATAA
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
Root_cap

Protein Analysis

347

Amino Acids

38.39

Weight (kDa)

8.26

Isoelectric Point (pI)

34.2

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Root_cap PF06830 255 - 311 5.4e-26 Root cap
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 2 cut(s) 374, 408
AccII CGCG 1 cut(s) 336
AciI CCGC 1 cut(s) 300
AclWI GGATC 6 cut(s) 277, 278, 516, 683, 1002, 1015
AfaI GTAC 2 cut(s) 72, 187
AfiI CCNNNNNNNGG 5 cut(s) 179, 504, 596, 672, 869
AflIII ACRYGT 1 cut(s) 101
AgeI ACCGGT 1 cut(s) 1001
AgsI TTSAA 3 cut(s) 778, 832, 908
AjnI CCWGG 1 cut(s) 847
Alw26I GTCTC 1 cut(s) 594
AlwI GGATC 6 cut(s) 277, 278, 516, 683, 1002, 1015
Ama87I CYCGRG 1 cut(s) 482
AoxI GGCC 2 cut(s) 414, 457
ApeKI GCWGC 1 cut(s) 83
ArsI GACNNNNNNTTYG 4 cut(s) 103, 135, 329, 361
AsiGI ACCGGT 1 cut(s) 1001
AspS9I GGNCC 2 cut(s) 414, 458
AsuHPI GGTGA 3 cut(s) 55, 503, 703
AvaI CYCGRG 1 cut(s) 482
AxyI CCTNAGG 1 cut(s) 442
BaeI ACNNNNGTAYC 2 cut(s) 564, 597
BamHI GGATCC 1 cut(s) 1007
BbsI GAAGAC 2 cut(s) 307, 708
BbvI GCAGC 1 cut(s) 95
BccI CCATC 1 cut(s) 299
BceAI ACGGC 1 cut(s) 277
BcgI CGANNNNNNTGC 2 cut(s) 329, 363
BciT130I CCWGG 1 cut(s) 849
BciVI GTATCC 2 cut(s) 426, 720
BcoDI GTCTC 1 cut(s) 594
BfaI CTAG 1 cut(s) 596
BfuI GTATCC 2 cut(s) 426, 720
BglII AGATCT 2 cut(s) 10, 552
BisI GCNGC 1 cut(s) 84
BlsI GCNGC 1 cut(s) 85
Bme1390I CCNGG 1 cut(s) 849
BmeT110I CYCGRG 1 cut(s) 482
BmgT120I GGNCC 2 cut(s) 414, 458
BmiI GGNNCC 3 cut(s) 460, 687, 1009
BmrFI CCNGG 1 cut(s) 849
BmsI GCATC 2 cut(s) 36, 318
BpiI GAAGAC 2 cut(s) 307, 708
BplI GAGNNNNNCTC 2 cut(s) 577, 609
BpuEI CTTGAG 2 cut(s) 776, 928
Bsa29I ATCGAT 1 cut(s) 204
BsaAI YACGTR 1 cut(s) 429
BsaBI GATNNNNATC 1 cut(s) 674
BsaJI CCNNGG 1 cut(s) 189
BsaWI WCCGGW 4 cut(s) 688, 730, 768, 1001
BsaXI ACNNNNNCTCC 2 cut(s) 620, 650
Bsc4I CCNNNNNNNGG 5 cut(s) 179, 504, 596, 672, 869
Bse118I RCCGGY 2 cut(s) 862, 1001
Bse21I CCTNAGG 1 cut(s) 442
Bse3DI GCAATG 2 cut(s) 161, 660
Bse8I GATNNNNATC 1 cut(s) 674
BseBI CCWGG 1 cut(s) 849
BseCI ATCGAT 1 cut(s) 204
BseDI CCNNGG 1 cut(s) 189
BseGI GGATG 1 cut(s) 742
BseJI GATNNNNATC 1 cut(s) 674
BseLI CCNNNNNNNGG 5 cut(s) 179, 504, 596, 672, 869
BseMI GCAATG 2 cut(s) 161, 660
BseMII CTCAG 1 cut(s) 5
BseRI GAGGAG 1 cut(s) 582
BseXI GCAGC 1 cut(s) 95
Bsh1236I CGCG 1 cut(s) 336
BshFI GGCC 2 cut(s) 416, 459
BshTI ACCGGT 1 cut(s) 1001
BshVI ATCGAT 1 cut(s) 204
BsiHKCI CYCGRG 1 cut(s) 482
BsiSI CCGG 6 cut(s) 689, 731, 769, 839, 863, 1002
BslI CCNNNNNNNGG 5 cut(s) 179, 504, 596, 672, 869
BsmAI GTCTC 1 cut(s) 594
BsnI GGCC 2 cut(s) 416, 459
BsoBI CYCGRG 1 cut(s) 482
Bsp1407I TGTACA 1 cut(s) 70
Bsp143I GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
BspACI CCGC 1 cut(s) 300
BspANI GGCC 2 cut(s) 416, 459
BspCNI CTCAG 1 cut(s) 6
BspDI ATCGAT 1 cut(s) 204
BspFNI CGCG 1 cut(s) 336
BspLI GGNNCC 3 cut(s) 460, 687, 1009
BspPI GGATC 6 cut(s) 277, 278, 516, 683, 1002, 1015
BsrDI GCAATG 2 cut(s) 161, 660
BsrFI RCCGGY 2 cut(s) 862, 1001
BsrGI TGTACA 1 cut(s) 70
BssAI RCCGGY 2 cut(s) 862, 1001
BssECI CCNNGG 1 cut(s) 189
BssMI GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
BssT1I CCWWGG 1 cut(s) 189
Bst2UI CCWGG 1 cut(s) 849
Bst4CI ACNGT 2 cut(s) 743, 991
Bst6I CTCTTC 1 cut(s) 110
BstAUI TGTACA 1 cut(s) 70
BstBAI YACGTR 1 cut(s) 429
BstC8I GCNNGC 2 cut(s) 196, 277
BstDEI CTNAG 4 cut(s) 14, 280, 398, 442
BstENI CCTNNNNNAGG 1 cut(s) 594
BstF5I GGATG 1 cut(s) 742
BstFNI CGCG 1 cut(s) 336
BstKTI GATC 8 cut(s) 13, 272, 286, 511, 555, 615, 678, 1010
BstMAI GTCTC 1 cut(s) 594
BstMBI GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
BstMWI GCNNNNNNNGC 4 cut(s) 306, 465, 494, 973
BstNI CCWGG 1 cut(s) 849
BstNSI RCATGY 4 cut(s) 105, 198, 279, 927
BstSCI CCNGG 1 cut(s) 847
BstUI CGCG 1 cut(s) 336
BstV1I GCAGC 1 cut(s) 95
BstV2I GAAGAC 2 cut(s) 307, 708
BstX2I RGATCY 4 cut(s) 10, 283, 552, 1007
BstYI RGATCY 4 cut(s) 10, 283, 552, 1007
Bsu15I ATCGAT 1 cut(s) 204
Bsu36I CCTNAGG 1 cut(s) 442
BsuI GTATCC 2 cut(s) 426, 720
BsuRI GGCC 2 cut(s) 416, 459
BsuTUI ATCGAT 1 cut(s) 204
BtsCI GGATG 1 cut(s) 742
BtsI GCAGTG 1 cut(s) 1021
BtsIMutI CAGTG 3 cut(s) 585, 987, 1021
Cac8I GCNNGC 2 cut(s) 196, 277
Cfr10I RCCGGY 2 cut(s) 862, 1001
Cfr13I GGNCC 2 cut(s) 414, 458
ClaI ATCGAT 1 cut(s) 204
CseI GACGC 2 cut(s) 187, 885
Csp6I GTAC 2 cut(s) 71, 186
CspAI ACCGGT 1 cut(s) 1001
CviAII CATG 6 cut(s) 102, 123, 195, 276, 326, 924
CviJI RGCY 8 cut(s) 230, 250, 416, 459, 488, 497, 942, 967
CviKI_1 RGCY 8 cut(s) 230, 250, 416, 459, 488, 497, 942, 967
CviQI GTAC 2 cut(s) 71, 186
DdeI CTNAG 4 cut(s) 14, 280, 398, 442
DpnI GATC 8 cut(s) 12, 271, 285, 510, 554, 614, 677, 1009
DpnII GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
DrdI GACNNNNNNGTC 2 cut(s) 374, 408
DseDI GACNNNNNNGTC 2 cut(s) 374, 408
Eam1104I CTCTTC 1 cut(s) 110
EarI CTCTTC 1 cut(s) 110
EciI GGCGGA 1 cut(s) 315
Eco130I CCWWGG 1 cut(s) 189
Eco81I CCTNAGG 1 cut(s) 442
Eco88I CYCGRG 1 cut(s) 482
EcoNI CCTNNNNNAGG 1 cut(s) 594
EcoRII CCWGG 1 cut(s) 847
EcoT14I CCWWGG 1 cut(s) 189
EcoT22I ATGCAT 1 cut(s) 925
ErhI CCWWGG 1 cut(s) 189
FaeI CATG 6 cut(s) 105, 126, 198, 279, 329, 927
FatI CATG 6 cut(s) 101, 122, 194, 275, 325, 923
Fnu4HI GCNGC 1 cut(s) 84
FokI GGATG 1 cut(s) 749
Fsp4HI GCNGC 1 cut(s) 84
FspBI CTAG 1 cut(s) 596
GluI GCNGC 1 cut(s) 84
HaeIII GGCC 2 cut(s) 416, 459
HapII CCGG 6 cut(s) 689, 731, 769, 839, 863, 1002
HgaI GACGC 2 cut(s) 187, 885
Hin1II CATG 6 cut(s) 105, 126, 198, 279, 329, 927
HincII GTYRAC 3 cut(s) 367, 379, 520
HindII GTYRAC 3 cut(s) 367, 379, 520
HinfI GANTC 5 cut(s) 118, 586, 835, 979, 1026
HpaII CCGG 6 cut(s) 689, 731, 769, 839, 863, 1002
HphI GGTGA 3 cut(s) 55, 503, 703
Hpy166II GTNNAC 5 cut(s) 28, 367, 379, 520, 931
Hpy188I TCNGA 3 cut(s) 15, 361, 628
Hpy188III TCNNGA 6 cut(s) 616, 755, 775, 832, 905, 945
Hpy8I GTNNAC 5 cut(s) 28, 367, 379, 520, 931
Hpy99I CGWCG 1 cut(s) 341
HpyAV CCTTC 4 cut(s) 171, 484, 536, 791
HpyCH4III ACNGT 2 cut(s) 743, 991
HpyCH4IV ACGT 9 cut(s) 30, 289, 363, 385, 428, 650, 681, 792, 815
HpyCH4V TGCA 6 cut(s) 225, 258, 350, 923, 999, 1035
HpyF10VI GCNNNNNNNGC 4 cut(s) 306, 465, 494, 973
HpyF3I CTNAG 4 cut(s) 14, 280, 398, 442
HpySE526I ACGT 9 cut(s) 30, 289, 363, 385, 428, 650, 681, 792, 815
Hsp92II CATG 6 cut(s) 105, 126, 198, 279, 329, 927
Kzo9I GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
Lsp1109I GCAGC 1 cut(s) 95
LweI GCATC 2 cut(s) 36, 318
MaeI CTAG 1 cut(s) 596
MaeII ACGT 9 cut(s) 30, 289, 363, 385, 428, 650, 681, 792, 815
MaeIII GTNAC 4 cut(s) 646, 651, 691, 897
MalI GATC 8 cut(s) 12, 271, 285, 510, 554, 614, 677, 1009
MboI GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
MboII GAAGA 7 cut(s) 127, 307, 445, 713, 822, 836, 890
MflI RGATCY 4 cut(s) 10, 283, 552, 1007
MluCI AATT 1 cut(s) 253
MlyI GAGTC 2 cut(s) 127, 595
MmeI TCCRAC 3 cut(s) 13, 69, 1003
MnlI CCTC 7 cut(s) 183, 478, 536, 600, 603, 727, 751
Mph1103I ATGCAT 1 cut(s) 925
MseI TTAA 1 cut(s) 213
MslI CAYNNNNRTG 1 cut(s) 580
MspI CCGG 6 cut(s) 689, 731, 769, 839, 863, 1002
MspR9I CCNGG 1 cut(s) 849
MvaI CCWGG 1 cut(s) 849
MvnI CGCG 1 cut(s) 336
MwoI GCNNNNNNNGC 4 cut(s) 306, 465, 494, 973
NdeII GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
NlaIII CATG 6 cut(s) 105, 126, 198, 279, 329, 927
NlaIV GGNNCC 3 cut(s) 460, 687, 1009
NmeAIII GCCGAG 2 cut(s) 523, 691
NmuCI GTSAC 3 cut(s) 646, 691, 897
NsiI ATGCAT 1 cut(s) 925
NspI RCATGY 4 cut(s) 105, 198, 279, 927
PaeI GCATGC 2 cut(s) 198, 279
PaeR7I CTCGAG 1 cut(s) 482
PciI ACATGT 1 cut(s) 101
PfeI GAWTC 3 cut(s) 835, 979, 1026
PinAI ACCGGT 1 cut(s) 1001
PkrI GCNGC 1 cut(s) 85
PleI GAGTC 2 cut(s) 126, 594
PpsI GAGTC 2 cut(s) 126, 594
Ppu21I YACGTR 1 cut(s) 429
PscI ACATGT 1 cut(s) 101
Psp6I CCWGG 1 cut(s) 847
PspGI CCWGG 1 cut(s) 847
PspN4I GGNNCC 3 cut(s) 460, 687, 1009
PspPI GGNCC 2 cut(s) 414, 458
PspXI VCTCGAGB 1 cut(s) 482
PsuI RGATCY 4 cut(s) 10, 283, 552, 1007
RsaI GTAC 2 cut(s) 72, 187
RsaNI GTAC 2 cut(s) 71, 186
RseI CAYNNNNRTG 1 cut(s) 580
SaqAI TTAA 1 cut(s) 213
SatI GCNGC 1 cut(s) 84
Sau3AI GATC 8 cut(s) 10, 269, 283, 508, 552, 612, 675, 1007
Sau96I GGNCC 2 cut(s) 414, 458
SchI GAGTC 2 cut(s) 127, 595
ScrFI CCNGG 1 cut(s) 849
SfaNI GCATC 2 cut(s) 36, 318
Sfr274I CTCGAG 1 cut(s) 482
SgrAI CRCCGGYG 1 cut(s) 1001
SlaI CTCGAG 1 cut(s) 482
SmiMI CAYNNNNRTG 1 cut(s) 580
SmlI CTYRAG 3 cut(s) 482, 755, 943
SmoI CTYRAG 3 cut(s) 482, 755, 943
SphI GCATGC 2 cut(s) 198, 279
Sse9I AATT 1 cut(s) 253
SsiI CCGC 1 cut(s) 300
SspMI CTAG 1 cut(s) 596
StyD4I CCNGG 1 cut(s) 847
StyI CCWWGG 1 cut(s) 189
TaaI ACNGT 2 cut(s) 743, 991
TaiI ACGT 9 cut(s) 33, 292, 366, 388, 431, 653, 684, 795, 818
TaqI TCGA 4 cut(s) 78, 204, 483, 615
TasI AATT 1 cut(s) 253
TatI WGTACW 1 cut(s) 70
TfiI GAWTC 3 cut(s) 835, 979, 1026
Tru1I TTAA 1 cut(s) 213
Tru9I TTAA 1 cut(s) 213
TscAI CASTG 3 cut(s) 585, 994, 1021
TseFI GTSAC 3 cut(s) 646, 691, 897
TseI GCWGC 1 cut(s) 83
Tsp45I GTSAC 3 cut(s) 646, 691, 897
TspDTI ATGAA 4 cut(s) 17, 283, 314, 379
TspGWI ACGGA 2 cut(s) 518, 628
TspRI CASTG 3 cut(s) 585, 994, 1021
XagI CCTNNNNNAGG 1 cut(s) 594
XceI RCATGY 4 cut(s) 105, 198, 279, 927
XhoI CTCGAG 1 cut(s) 482
XspI CTAG 1 cut(s) 596
Zsp2I ATGCAT 1 cut(s) 925
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.