AT4G28830

Putative RNA methylase family UPF0020

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
4
OG0008537
Physical Location & Seq
Forward (+)
14232422 .. 14234334
1913 bp
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UTR
Exon/CDS
Intron
AT4G28830.3

Sequence Viewer

Length: 627 bp
ATGAAGCTGAAGCAATTAGAAGGCTTGTTGGGTGATCTTGAACAGTTCTCCAATCCTAAAGTGGAATTCGAGCAATACCCAACTGGTCCTCACATTGCTTCTCGTATGCTTTTCACTGCAGAGAATTCATATGGAGATATAACTGATAAGGTCGTTGCGGATTTTGGTTGTGGCTGTGGTACTTTAAGTGCTGCTGCTGCTCTTCTAGATGCTGCGTCTGTGATTGGATTCGATATCGACCCTGAATCTCTTGAAACAGCAACACTAAATGCAGAGGAACTTGAGGTCGAGATAGATTTCGTTCAGTGTGACATCACAAAGCTAGAGTTAAAAGGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAGGTCGCCTCAAAGGCAGTTTATTCCTTGCATAAGACATCTACCAGAGAACACATTAAAAGGGCGGCTTTGCGTGATTTCAATGCGAAAAGTGCTGAAGTTATATGTGAGCTCCGATATGACTTGCCAAAACTCTACAAGTTCCACAAGCGAAAAGAAGTTGATATTGCCGTTGATCTCTGGCGTTTTGAGCCTAGACAGAACTAG
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
MTS PrmA

Protein Analysis

208

Amino Acids

23.19

Weight (kDa)

5.22

Isoelectric Point (pI)

23.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PrmA PF06325 28 - 121 6.5e-12 Ribosomal protein L11 methyltransferase (PrmA)
MTS PF05175 44 - 139 2.5e-13 Methyltransferase small domain
Methyltransf_31 PF13847 50 - 134 1.7e-12 Methyltransferase domain
Methyltransf_25 PF13649 52 - 128 8.5e-12 Methyltransferase domain
Methyltransf_11 PF08241 54 - 121 2.5e-08 Methyltransferase domain
UPF0020 PF01170 70 - 142 7.3e-10 RMKL-like, methyltransferase domain
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)
AciI CCGC 3 cut(s) 158, 413, 485
AcsI RAATTY 2 cut(s) 65, 124
AcuI CTGAAG 2 cut(s) 29, 537
AfaI GTAC 2 cut(s) 181, 376
AfiI CCNNNNNNNGG 2 cut(s) 343, 371
AgsI TTSAA 3 cut(s) 41, 254, 502
AluBI AGCT 4 cut(s) 7, 322, 392, 532
AluI AGCT 4 cut(s) 7, 322, 392, 532
Alw21I GWGCWC 1 cut(s) 534
AoxI GGCC 1 cut(s) 334
ApeKI GCWGC 4 cut(s) 191, 194, 197, 212
ApoI RAATTY 2 cut(s) 65, 124
AspS9I GGNCC 1 cut(s) 86
AsuHPI GGTGA 1 cut(s) 44
AvaII GGWCC 1 cut(s) 86
BaeI ACNNNNGTAYC 2 cut(s) 339, 372
BanII GRGCYC 1 cut(s) 534
Bbv12I GWGCWC 1 cut(s) 534
BbvI GCAGC 4 cut(s) 178, 181, 184, 199
BceAI ACGGC 1 cut(s) 575
BciVI GTATCC 1 cut(s) 340
BfaI CTAG 4 cut(s) 206, 323, 615, 625
BfmI CTRYAG 1 cut(s) 117
BfuI GTATCC 1 cut(s) 340
BglI GCCNNNNNGGC 1 cut(s) 434
BisI GCNGC 6 cut(s) 192, 195, 198, 213, 414, 486
BlsI GCNGC 6 cut(s) 193, 196, 199, 214, 415, 487
Bme18I GGWCC 1 cut(s) 86
BmgT120I GGNCC 1 cut(s) 86
BmsI GCATC 1 cut(s) 199
BplI GAGNNNNNCTC 2 cut(s) 392, 424
BpuEI CTTGAG 1 cut(s) 302
Bsc4I CCNNNNNNNGG 2 cut(s) 343, 371
Bse1I ACTGG 1 cut(s) 88
Bse3DI GCAATG 2 cut(s) 93, 423
BseLI CCNNNNNNNGG 2 cut(s) 343, 371
BseMI GCAATG 2 cut(s) 93, 423
BseNI ACTGG 1 cut(s) 88
BseXI GCAGC 4 cut(s) 178, 181, 184, 199
BshFI GGCC 1 cut(s) 336
BsiHKAI GWGCWC 1 cut(s) 534
BslI CCNNNNNNNGG 2 cut(s) 343, 371
BsnI GGCC 1 cut(s) 336
Bsp1286I GDGCHC 1 cut(s) 534
Bsp143I GATC 2 cut(s) 34, 595
BspACI CCGC 3 cut(s) 158, 413, 485
BspANI GGCC 1 cut(s) 336
BspMAI CTGCAG 1 cut(s) 121
BspQI GCTCTTC 1 cut(s) 207
BsrDI GCAATG 2 cut(s) 93, 423
BsrI ACTGG 1 cut(s) 88
BssMI GATC 2 cut(s) 34, 595
Bst4CI ACNGT 2 cut(s) 45, 352
Bst6I CTCTTC 1 cut(s) 207
BstKTI GATC 2 cut(s) 37, 598
BstMBI GATC 2 cut(s) 34, 595
BstMWI GCNNNNNNNGC 4 cut(s) 197, 434, 512, 610
BstSFI CTRYAG 1 cut(s) 117
BstV1I GCAGC 4 cut(s) 178, 181, 184, 199
BsuI GTATCC 1 cut(s) 340
BsuRI GGCC 1 cut(s) 336
BtsI GCAGTG 1 cut(s) 114
BtsIMutI CAGTG 2 cut(s) 114, 311
Cfr13I GGNCC 1 cut(s) 86
CseI GACGC 1 cut(s) 204
Csp6I GTAC 2 cut(s) 180, 375
CviAII CATG 1 cut(s) 397
CviJI RGCY 9 cut(s) 7, 24, 174, 322, 336, 392, 488, 532, 613
CviKI_1 RGCY 9 cut(s) 7, 24, 174, 322, 336, 392, 488, 532, 613
CviQI GTAC 2 cut(s) 180, 375
DpnI GATC 2 cut(s) 36, 597
DpnII GATC 2 cut(s) 34, 595
Eam1104I CTCTTC 1 cut(s) 207
EarI CTCTTC 1 cut(s) 207
Ecl136II GAGCTC 1 cut(s) 532
Eco147I AGGCCT 1 cut(s) 336
Eco24I GRGCYC 1 cut(s) 534
Eco32I GATATC 1 cut(s) 235
Eco47I GGWCC 1 cut(s) 86
Eco53kI GAGCTC 1 cut(s) 532
Eco57I CTGAAG 2 cut(s) 29, 537
EcoICRI GAGCTC 1 cut(s) 532
EcoRI GAATTC 2 cut(s) 65, 124
EcoRV GATATC 1 cut(s) 235
EcoT38I GRGCYC 1 cut(s) 534
FaeI CATG 1 cut(s) 400
FaiI YATR 9 cut(s) 107, 130, 132, 140, 398, 453, 524, 526, 540
FalI AAGNNNNNCTT 2 cut(s) 472, 504
FatI CATG 1 cut(s) 396
FauNDI CATATG 1 cut(s) 130
Fnu4HI GCNGC 6 cut(s) 192, 195, 198, 213, 414, 486
FriOI GRGCYC 1 cut(s) 534
Fsp4HI GCNGC 6 cut(s) 192, 195, 198, 213, 414, 486
FspBI CTAG 4 cut(s) 206, 323, 615, 625
GluI GCNGC 6 cut(s) 192, 195, 198, 213, 414, 486
HaeIII GGCC 1 cut(s) 336
HgaI GACGC 1 cut(s) 204
Hin1II CATG 1 cut(s) 400
HinfI GANTC 2 cut(s) 228, 245
HphI GGTGA 1 cut(s) 44
Hpy166II GTNNAC 1 cut(s) 377
Hpy188I TCNGA 1 cut(s) 536
Hpy188III TCNNGA 4 cut(s) 38, 206, 251, 289
Hpy8I GTNNAC 1 cut(s) 377
HpyAV CCTTC 2 cut(s) 14, 415
HpyCH4III ACNGT 2 cut(s) 45, 352
HpyCH4V TGCA 3 cut(s) 119, 272, 451
HpyF10VI GCNNNNNNNGC 4 cut(s) 197, 434, 512, 610
Hsp92II CATG 1 cut(s) 400
Kzo9I GATC 2 cut(s) 34, 595
LguI GCTCTTC 1 cut(s) 207
LmnI GCTCC 2 cut(s) 389, 537
LpnPI CCDG 5 cut(s) 69, 255, 350, 478, 586
Lsp1109I GCAGC 4 cut(s) 178, 181, 184, 199
LweI GCATC 1 cut(s) 199
MaeI CTAG 4 cut(s) 206, 323, 615, 625
MaeIII GTNAC 1 cut(s) 308
MalI GATC 2 cut(s) 36, 597
MboI GATC 2 cut(s) 34, 595
MboII GAAGA 2 cut(s) 194, 394
MhlI GDGCHC 1 cut(s) 534
MluCI AATT 3 cut(s) 14, 65, 124
MnlI CCTC 5 cut(s) 99, 268, 277, 375, 439
MseI TTAA 3 cut(s) 185, 329, 477
MwoI GCNNNNNNNGC 4 cut(s) 197, 434, 512, 610
NdeI CATATG 1 cut(s) 130
NdeII GATC 2 cut(s) 34, 595
NlaIII CATG 1 cut(s) 400
NmuCI GTSAC 1 cut(s) 308
PceI AGGCCT 1 cut(s) 336
PciSI GCTCTTC 1 cut(s) 207
PfeI GAWTC 2 cut(s) 228, 245
PkrI GCNGC 6 cut(s) 193, 196, 199, 214, 415, 487
Psp124BI GAGCTC 1 cut(s) 534
PspPI GGNCC 1 cut(s) 86
PstI CTGCAG 1 cut(s) 121
RsaI GTAC 2 cut(s) 181, 376
RsaNI GTAC 2 cut(s) 180, 375
SacI GAGCTC 1 cut(s) 534
SapI GCTCTTC 1 cut(s) 207
SaqAI TTAA 3 cut(s) 185, 329, 477
SatI GCNGC 6 cut(s) 192, 195, 198, 213, 414, 486
Sau3AI GATC 2 cut(s) 34, 595
Sau96I GGNCC 1 cut(s) 86
SduI GDGCHC 1 cut(s) 534
SetI ASST 7 cut(s) 9, 153, 288, 324, 394, 426, 534
SfaNI GCATC 1 cut(s) 199
SfcI CTRYAG 1 cut(s) 117
SinI GGWCC 1 cut(s) 86
SmlI CTYRAG 1 cut(s) 281
SmoI CTYRAG 1 cut(s) 281
Sse9I AATT 3 cut(s) 14, 65, 124
SseBI AGGCCT 1 cut(s) 336
SsiI CCGC 3 cut(s) 158, 413, 485
SspMI CTAG 4 cut(s) 206, 323, 615, 625
SstI GAGCTC 1 cut(s) 534
StuI AGGCCT 1 cut(s) 336
TaaI ACNGT 2 cut(s) 45, 352
TaqI TCGA 4 cut(s) 69, 231, 237, 288
TasI AATT 3 cut(s) 14, 65, 124
TauI GCSGC 2 cut(s) 416, 488
TfiI GAWTC 2 cut(s) 228, 245
Tru1I TTAA 3 cut(s) 185, 329, 477
Tru9I TTAA 3 cut(s) 185, 329, 477
TscAI CASTG 2 cut(s) 121, 311
TseFI GTSAC 1 cut(s) 308
TseI GCWGC 4 cut(s) 191, 194, 197, 212
Tsp45I GTSAC 1 cut(s) 308
TspDTI ATGAA 4 cut(s) 17, 117, 374, 434
TspGWI ACGGA 1 cut(s) 394
TspRI CASTG 2 cut(s) 121, 311
VpaK11BI GGWCC 1 cut(s) 86
XapI RAATTY 2 cut(s) 65, 124
XbaI TCTAGA 1 cut(s) 205
XcmI CCANNNNNNNNNTGG 1 cut(s) 58
XspI CTAG 4 cut(s) 206, 323, 615, 625
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.