AT5G09920

DNA-directed RNA polymerase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
5
OG0002628
Physical Location & Seq
Forward (+)
3096183 .. 3097837
1655 bp
Loading structure...
UTR
Exon/CDS
Intron
AT5G09920.1

Sequence Viewer

Length: 417 bp
ATGTCCGGAGAAGAAGAAGAGAACGCCGCCGAACTCAAGATCGGAGATGAGTTTTTGAAGGCAAAGTGCTTAATGAACTGTGAAGTCTCTTTGATTCTTGAGCACAAGTTTGAACAGCTTCAGCAAATCTCAGAGGATCCTATGAATCAAGTTTCTCAAGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAAATACTAAGCAGACATCAACTCACTGAGTTTGAGCTATGTGTTCTTGGCAATCTCTGTCCTGAAACTGTTGAAGAAGCAGTGGCAATGGTTCCTTCTCTTAAGACAAAAGGAAGAGCTCATGATGATGAAGCTATTGAGAAGATGCTCAATGATCTCTCACTTGTCAAGAGATTCGAGTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000288 GO:0000428 GO:0000932 GO:0000956 GO:0003674 GO:0003824 GO:0003899 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0006139 GO:0006351 GO:0006352 GO:0006366 GO:0006367 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006403 GO:0006405 GO:0006406 GO:0006417 GO:0006446 GO:0006611 GO:0006725 GO:0006807 GO:0006810 GO:0006886 GO:0006913 GO:0006950 GO:0008104 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009058 GO:0009059 GO:0009266 GO:0009408 GO:0009628 GO:0009889 GO:0009891 GO:0009892 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010605 GO:0010608 GO:0010628 GO:0010629 GO:0015031 GO:0015833 GO:0015931 GO:0016043 GO:0016070 GO:0016071 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0019439 GO:0022607 GO:0022613 GO:0022618 GO:0030880 GO:0031123 GO:0031124 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031369 GO:0031503 GO:0031974 GO:0031981 GO:0031990 GO:0032268 GO:0032270 GO:0032774 GO:0032991 GO:0033036 GO:0033554 GO:0034062 GO:0034248 GO:0034250 GO:0034402 GO:0034605 GO:0034613 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0034655 GO:0035770 GO:0036464 GO:0042886 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044248 GO:0044249 GO:0044260 GO:0044265 GO:0044270 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045184 GO:0045727 GO:0045948 GO:0046483 GO:0046700 GO:0046907 GO:0048518 GO:0048519 GO:0048522 GO:0050657 GO:0050658 GO:0050789 GO:0050794 GO:0050896 GO:0051028 GO:0051168 GO:0051169 GO:0051171 GO:0051173 GO:0051179 GO:0051234 GO:0051236 GO:0051246 GO:0051247 GO:0051641 GO:0051649 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065003 GO:0065007 GO:0070013 GO:0070727 GO:0071166 GO:0071426 GO:0071427 GO:0071702 GO:0071704 GO:0071705 GO:0071826 GO:0071840 GO:0080090 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901361 GO:1901362 GO:1901575 GO:1901576 GO:1902494 GO:1990234 GO:1990904 GO:2000112
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb4

Protein Analysis

138

Amino Acids

15.93

Weight (kDa)

5.01

Isoelectric Point (pI)

53.11

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 23 - 133 1.6e-27 RNA polymerase Rpb4
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)
AccIII TCCGGA 1 cut(s) 5
AciI CCGC 2 cut(s) 27, 199
AclWI GGATC 2 cut(s) 131, 144
AcuI CTGAAG 1 cut(s) 104
AflII CTTAAG 1 cut(s) 335
AgsI TTSAA 3 cut(s) 58, 113, 308
AluBI AGCT 4 cut(s) 118, 271, 353, 368
AluI AGCT 4 cut(s) 118, 271, 353, 368
Alw21I GWGCWC 2 cut(s) 105, 355
Alw26I GTCTC 1 cut(s) 91
AlwI GGATC 2 cut(s) 131, 144
AlwNI CAGNNNCTG 1 cut(s) 218
Aor13HI TCCGGA 1 cut(s) 5
Asp700I GAANNNNTTC 2 cut(s) 117, 191
BamHI GGATCC 1 cut(s) 136
BanII GRGCYC 1 cut(s) 355
Bbv12I GWGCWC 2 cut(s) 105, 355
BcoDI GTCTC 1 cut(s) 91
BfrI CTTAAG 1 cut(s) 335
BisI GCNGC 2 cut(s) 27, 199
BlsI GCNGC 2 cut(s) 28, 200
BmiI GGNNCC 2 cut(s) 138, 327
BmsI GCATC 2 cut(s) 205, 369
BpuEI CTTGAG 3 cut(s) 20, 119, 141
BsaWI WCCGGW 1 cut(s) 5
Bse3DI GCAATG 1 cut(s) 327
BseAI TCCGGA 1 cut(s) 5
BseMI GCAATG 1 cut(s) 327
BseMII CTCAG 2 cut(s) 144, 252
BsiHKAI GWGCWC 2 cut(s) 105, 355
BsiSI CCGG 1 cut(s) 6
BsmAI GTCTC 1 cut(s) 91
Bsp1286I GDGCHC 2 cut(s) 105, 355
Bsp13I TCCGGA 1 cut(s) 5
Bsp143I GATC 3 cut(s) 39, 136, 388
BspACI CCGC 2 cut(s) 27, 199
BspCNI CTCAG 2 cut(s) 143, 253
BspEI TCCGGA 1 cut(s) 5
BspHI TCATGA 1 cut(s) 355
BspLI GGNNCC 2 cut(s) 138, 327
BspPI GGATC 2 cut(s) 131, 144
BspQI GCTCTTC 1 cut(s) 343
BspTI CTTAAG 1 cut(s) 335
BsrDI GCAATG 1 cut(s) 327
BssMI GATC 3 cut(s) 39, 136, 388
Bst4CI ACNGT 2 cut(s) 80, 304
Bst6I CTCTTC 2 cut(s) 12, 343
BstAFI CTTAAG 1 cut(s) 335
BstDEI CTNAG 3 cut(s) 130, 242, 261
BstKTI GATC 3 cut(s) 42, 139, 391
BstMAI GTCTC 1 cut(s) 91
BstMBI GATC 3 cut(s) 39, 136, 388
BstX2I RGATCY 1 cut(s) 136
BstYI RGATCY 1 cut(s) 136
BtsI GCAGTG 1 cut(s) 321
BtsIMutI CAGTG 2 cut(s) 258, 321
CaiI CAGNNNCTG 1 cut(s) 218
CciI TCATGA 1 cut(s) 355
CviAII CATG 1 cut(s) 356
CviJI RGCY 5 cut(s) 118, 198, 271, 353, 368
CviKI_1 RGCY 5 cut(s) 118, 198, 271, 353, 368
DdeI CTNAG 3 cut(s) 130, 242, 261
DpnI GATC 3 cut(s) 41, 138, 390
DpnII GATC 3 cut(s) 39, 136, 388
Eam1104I CTCTTC 2 cut(s) 12, 343
EarI CTCTTC 2 cut(s) 12, 343
Ecl136II GAGCTC 1 cut(s) 353
Eco24I GRGCYC 1 cut(s) 355
Eco53kI GAGCTC 1 cut(s) 353
Eco57I CTGAAG 1 cut(s) 104
EcoICRI GAGCTC 1 cut(s) 353
EcoT38I GRGCYC 1 cut(s) 355
FaeI CATG 1 cut(s) 359
FaiI YATR 4 cut(s) 143, 183, 274, 357
FatI CATG 1 cut(s) 355
Fnu4HI GCNGC 2 cut(s) 27, 199
FriOI GRGCYC 1 cut(s) 355
Fsp4HI GCNGC 2 cut(s) 27, 199
GluI GCNGC 2 cut(s) 27, 199
HapII CCGG 1 cut(s) 6
Hin1II CATG 1 cut(s) 359
HinfI GANTC 5 cut(s) 94, 145, 192, 208, 408
HpaII CCGG 1 cut(s) 6
Hpy188I TCNGA 2 cut(s) 44, 133
Hpy188III TCNNGA 8 cut(s) 6, 37, 98, 212, 233, 296, 356, 403
HpyAV CCTTC 2 cut(s) 52, 339
HpyCH4III ACNGT 2 cut(s) 80, 304
HpyCH4V TGCA 1 cut(s) 178
HpyF3I CTNAG 3 cut(s) 130, 242, 261
Hsp92II CATG 1 cut(s) 359
Kpn2I TCCGGA 1 cut(s) 5
Kzo9I GATC 3 cut(s) 39, 136, 388
LguI GCTCTTC 1 cut(s) 343
LpnPI CCDG 3 cut(s) 19, 225, 309
LweI GCATC 2 cut(s) 205, 369
MalI GATC 3 cut(s) 41, 138, 390
MboI GATC 3 cut(s) 39, 136, 388
MboII GAAGA 6 cut(s) 23, 26, 29, 320, 360, 388
MflI RGATCY 1 cut(s) 136
MhlI GDGCHC 2 cut(s) 105, 355
MnlI CCTC 1 cut(s) 127
MroI TCCGGA 1 cut(s) 5
MroXI GAANNNNTTC 2 cut(s) 117, 191
MseI TTAA 2 cut(s) 71, 336
MslI CAYNNNNRTG 1 cut(s) 360
MspCI CTTAAG 1 cut(s) 335
MspI CCGG 1 cut(s) 6
NdeII GATC 3 cut(s) 39, 136, 388
NlaIII CATG 1 cut(s) 359
NlaIV GGNNCC 2 cut(s) 138, 327
PagI TCATGA 1 cut(s) 355
PciSI GCTCTTC 1 cut(s) 343
PdmI GAANNNNTTC 2 cut(s) 117, 191
PfeI GAWTC 5 cut(s) 94, 145, 192, 208, 408
PkrI GCNGC 2 cut(s) 28, 200
Psp124BI GAGCTC 1 cut(s) 355
PspN4I GGNNCC 2 cut(s) 138, 327
PstNI CAGNNNCTG 1 cut(s) 218
PsuI RGATCY 1 cut(s) 136
RseI CAYNNNNRTG 1 cut(s) 360
SacI GAGCTC 1 cut(s) 355
SapI GCTCTTC 1 cut(s) 343
SaqAI TTAA 2 cut(s) 71, 336
SatI GCNGC 2 cut(s) 27, 199
Sau3AI GATC 3 cut(s) 39, 136, 388
SduI GDGCHC 2 cut(s) 105, 355
SetI ASST 4 cut(s) 120, 273, 355, 370
SfaNI GCATC 2 cut(s) 205, 369
SmiMI CAYNNNNRTG 1 cut(s) 360
SmlI CTYRAG 4 cut(s) 35, 98, 156, 335
SmoI CTYRAG 4 cut(s) 35, 98, 156, 335
SsiI CCGC 2 cut(s) 27, 199
SstI GAGCTC 1 cut(s) 355
TaaI ACNGT 2 cut(s) 80, 304
TaqI TCGA 2 cut(s) 232, 411
TauI GCSGC 2 cut(s) 29, 201
TfiI GAWTC 5 cut(s) 94, 145, 192, 208, 408
Tru1I TTAA 2 cut(s) 71, 336
Tru9I TTAA 2 cut(s) 71, 336
TscAI CASTG 2 cut(s) 265, 321
TspDTI ATGAA 3 cut(s) 89, 158, 378
TspRI CASTG 2 cut(s) 265, 321
Vha464I CTTAAG 1 cut(s) 335
XmnI GAANNNNTTC 2 cut(s) 117, 191
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.