AT5G51940

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. Component of RNA

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
5
OG0012428
Physical Location & Seq
Forward (+)
21104551 .. 21105947
1397 bp
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UTR
Exon/CDS
Intron
AT5G51940.1

Sequence Viewer

Length: 435 bp
ATGGCTGACGAAGATTACAACGACGTCGATGACTTGGGATATGAGGATGAGCCAGCAGAGCCTGAGATTGAAGAAGGAGTAGAGGAAGATGTTGAAATGAAGGAGAATGATGATGTCAATGGTGAGCCTATTGAAGCTGAAGATAAAGTCGAAACAGAACCTGTGCAACGTCCACGCAAAACGTCAAAGTTTATGACCAAGTATGAGCGTGCTCGTATCCTCGGCACTCGCGCTTTGCAGATTAGCATGAATGCTCCTGTCATGGTTGAGCTAGAGGGTGAGACTGATCCACTTGAGATTGCGATGAAGGAGCTTAGGCAGCGGAAGATACCATTCACTATTAGACGCTATCTACCTGATGGGAGTTTCGAGGAATGGGGAGTTGATGAACTGATCGTGGAAGACTCATGGAAACGTCAAGTTGGTGGTGATTGA

Protein Analysis

144

Amino Acids

16.65

Weight (kDa)

4.22

Isoelectric Point (pI)

52.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb6 PF01192 61 - 112 4.2e-12 RNA polymerase Rpb6
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0012428)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G04630 AT5G51940
fragaria_vesca FvH4_2g14180
malus_domestica MD09G1242800.v1.1 MD12G1011200.v1.1 MD17G1234800.v1.1
prunus_persica Prupe.3G134400_v2.0.a1 Prupe.7G013200_v2.0.a1
pyrus_communis pycom09g16110 pycom12g00870 pycom17g23820
rosa_chinensis RchiOBHm_Chr6g0276321
rosa_laevigata RLG00000013404
rosa_multiflora Rmu_sc0003665.1_g000006
rosa_roxburghii Rroxscaffold_7G00192390
rosa_rugosa Rorug06G0099900 Rorug06G0100000
rosa_samantha Rh6DG207900
rosa_wichuraiana Rw6G018430

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 27
AccII CGCG 1 cut(s) 231
AciI CCGC 1 cut(s) 322
AclWI GGATC 1 cut(s) 281
AcuI CTGAAG 1 cut(s) 159
AcyI GRCGYC 1 cut(s) 24
AgsI TTSAA 3 cut(s) 71, 95, 134
AluBI AGCT 3 cut(s) 137, 271, 313
AluI AGCT 3 cut(s) 137, 271, 313
Alw21I GWGCWC 1 cut(s) 214
Alw26I GTCTC 1 cut(s) 275
AlwI GGATC 1 cut(s) 281
AlwNI CAGNNNCTG 2 cut(s) 62, 161
ApeKI GCWGC 1 cut(s) 319
AspLEI GCGC 1 cut(s) 233
AsuHPI GGTGA 2 cut(s) 134, 290
BbsI GAAGAC 1 cut(s) 408
Bbv12I GWGCWC 1 cut(s) 214
BbvI GCAGC 1 cut(s) 331
BccI CCATC 1 cut(s) 353
BciVI GTATCC 1 cut(s) 227
BcoDI GTCTC 1 cut(s) 275
BfaI CTAG 1 cut(s) 272
BfuI GTATCC 1 cut(s) 227
BisI GCNGC 1 cut(s) 320
BlsI GCNGC 1 cut(s) 321
BpiI GAAGAC 1 cut(s) 408
Bpu10I CCTNAGC 1 cut(s) 314
BpuEI CTTGAG 1 cut(s) 314
BsaHI GRCGYC 1 cut(s) 24
BsaJI CCNNGG 1 cut(s) 220
BseDI CCNNGG 1 cut(s) 220
BseGI GGATG 1 cut(s) 52
BseMII CTCAG 1 cut(s) 54
BseXI GCAGC 1 cut(s) 331
Bsh1236I CGCG 1 cut(s) 231
BsiHKAI GWGCWC 1 cut(s) 214
BsmAI GTCTC 1 cut(s) 275
BsmI GAATGC 1 cut(s) 256
Bsp1286I GDGCHC 1 cut(s) 214
Bsp143I GATC 2 cut(s) 286, 393
BspACI CCGC 1 cut(s) 322
BspCNI CTCAG 1 cut(s) 55
BspFNI CGCG 1 cut(s) 231
BspPI GGATC 1 cut(s) 281
BssECI CCNNGG 1 cut(s) 220
BssMI GATC 2 cut(s) 286, 393
BssNI GRCGYC 1 cut(s) 24
BstACI GRCGYC 1 cut(s) 24
BstC8I GCNNGC 2 cut(s) 54, 210
BstDEI CTNAG 2 cut(s) 63, 314
BstF5I GGATG 1 cut(s) 52
BstFNI CGCG 1 cut(s) 231
BstHHI GCGC 1 cut(s) 233
BstKTI GATC 2 cut(s) 289, 396
BstMAI GTCTC 1 cut(s) 275
BstMBI GATC 2 cut(s) 286, 393
BstMWI GCNNNNNNNGC 2 cut(s) 58, 319
BstUI CGCG 1 cut(s) 231
BstV1I GCAGC 1 cut(s) 331
BstV2I GAAGAC 1 cut(s) 408
BsuI GTATCC 1 cut(s) 227
BtgZI GCGATG 1 cut(s) 317
BtsCI GGATG 1 cut(s) 52
Cac8I GCNNGC 2 cut(s) 54, 210
CaiI CAGNNNCTG 2 cut(s) 62, 161
CfoI GCGC 1 cut(s) 233
CseI GACGC 1 cut(s) 354
CviAII CATG 3 cut(s) 247, 262, 408
CviJI RGCY 7 cut(s) 5, 52, 61, 127, 137, 271, 313
CviKI_1 RGCY 7 cut(s) 5, 52, 61, 127, 137, 271, 313
DdeI CTNAG 2 cut(s) 63, 314
DpnI GATC 2 cut(s) 288, 395
DpnII GATC 2 cut(s) 286, 393
Eco57I CTGAAG 1 cut(s) 159
FaeI CATG 3 cut(s) 250, 265, 411
FaiI YATR 6 cut(s) 42, 194, 204, 248, 263, 409
FatI CATG 3 cut(s) 246, 261, 407
Fnu4HI GCNGC 1 cut(s) 320
FokI GGATG 1 cut(s) 59
Fsp4HI GCNGC 1 cut(s) 320
FspBI CTAG 1 cut(s) 272
GlaI GCGC 1 cut(s) 232
GluI GCNGC 1 cut(s) 320
HgaI GACGC 1 cut(s) 354
HhaI GCGC 1 cut(s) 233
Hin1I GRCGYC 1 cut(s) 24
Hin1II CATG 3 cut(s) 250, 265, 411
Hin6I GCGC 1 cut(s) 231
HinP1I GCGC 1 cut(s) 231
HinfI GANTC 1 cut(s) 404
HphI GGTGA 2 cut(s) 134, 290
Hpy166II GTNNAC 1 cut(s) 173
Hpy8I GTNNAC 1 cut(s) 173
Hpy99I CGWCG 2 cut(s) 26, 29
HpyAV CCTTC 3 cut(s) 68, 94, 301
HpyCH4IV ACGT 4 cut(s) 24, 169, 182, 415
HpyCH4V TGCA 2 cut(s) 166, 238
HpyF10VI GCNNNNNNNGC 2 cut(s) 58, 319
HpyF3I CTNAG 2 cut(s) 63, 314
HpySE526I ACGT 4 cut(s) 24, 169, 182, 415
Hsp92I GRCGYC 1 cut(s) 24
Hsp92II CATG 3 cut(s) 250, 265, 411
HspAI GCGC 1 cut(s) 231
Kzo9I GATC 2 cut(s) 286, 393
LmnI GCTCC 2 cut(s) 259, 310
LpnPI CCDG 5 cut(s) 66, 75, 174, 270, 369
Lsp1109I GCAGC 1 cut(s) 331
MaeI CTAG 1 cut(s) 272
MaeII ACGT 4 cut(s) 24, 169, 182, 415
MalI GATC 2 cut(s) 288, 395
MboI GATC 2 cut(s) 286, 393
MboII GAAGA 6 cut(s) 23, 83, 98, 152, 337, 413
MhlI GDGCHC 1 cut(s) 214
MlyI GAGTC 1 cut(s) 398
MnlI CCTC 5 cut(s) 37, 76, 230, 268, 364
MspA1I CMGCKG 1 cut(s) 322
Mva1269I GAATGC 1 cut(s) 256
MvnI CGCG 1 cut(s) 231
MwoI GCNNNNNNNGC 2 cut(s) 58, 319
NdeII GATC 2 cut(s) 286, 393
NlaIII CATG 3 cut(s) 250, 265, 411
NmeAIII GCCGAG 1 cut(s) 201
PctI GAATGC 1 cut(s) 256
PkrI GCNGC 1 cut(s) 321
PleI GAGTC 1 cut(s) 398
PpsI GAGTC 1 cut(s) 398
PstNI CAGNNNCTG 2 cut(s) 62, 161
SatI GCNGC 1 cut(s) 320
Sau3AI GATC 2 cut(s) 286, 393
SchI GAGTC 1 cut(s) 398
SduI GDGCHC 1 cut(s) 214
SetI ASST 9 cut(s) 27, 139, 163, 172, 185, 273, 315, 358, 418
SmlI CTYRAG 1 cut(s) 293
SmoI CTYRAG 1 cut(s) 293
SsiI CCGC 1 cut(s) 322
SspMI CTAG 1 cut(s) 272
TaiI ACGT 4 cut(s) 27, 172, 185, 418
TaqI TCGA 3 cut(s) 27, 150, 369
TseI GCWGC 1 cut(s) 319
TspDTI ATGAA 4 cut(s) 113, 263, 320, 402
XspI CTAG 1 cut(s) 272
ZraI GACGTC 1 cut(s) 25
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.