AT4G25400

RNA polymerase II regulatory region DNA binding

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
4
OG0006649
Physical Location & Seq
Forward (+)
12981016 .. 12982584
1569 bp
Loading structure...
UTR
Exon/CDS
Intron
AT4G25400.1

Sequence Viewer

Length: 561 bp
ATGAATAATTTTCAGGAGAAGAAAAGAAGGCGTAGTAAAACGCCGAGAGTTTGTAATAACGAAGAAAACATGGAGAAGTTAGTACATAAAGAAATTGAGAAACGAAGGAGACAAGAAATGGCTTCTCTCTACGCGTCTCTCCGCTCTCTTCTCCCTTTAGAGTTCATCCAGGGAAAACGTTCAACGTCAGATCAGGTGAAAGGGGCAGTGAATTACATAGACTATTTGCAAAGGAATATCAAAGACATAAATTCCAAGAGAGATGACCTCGTGTTATTGTCTGGACGAAGCTTTAGGAGTAGTAATGAACAAGAATGGAATGAGATTTCGAATCATGTCGTGATTCGTCCGTGTTTGGTCGGCATAGAGATAGTGTTGAGCATTCTCCAAACGCCATTCTCAAGCGTTCTGCAAGTGCTTCGTGAACACGGTCTCTATGTTCTTGGCTACATCTGTTCCAGTGTAAATGATAGACTCATTCATACTCTACAGGCTGAGGTCAACGATCTGGCTTTGATCGACTTAGCAGACCTTAAGGATACACTTACCCTGATGAAGTAA
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
HLH

Protein Analysis

186

Amino Acids

21.56

Weight (kDa)

8.99

Isoelectric Point (pI)

69.78

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HLH PF00010 26 - 77 7e-13 Helix-loop-helix DNA-binding 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)
AccBSI CCGCTC 1 cut(s) 144
AccII CGCG 1 cut(s) 134
AciI CCGC 1 cut(s) 142
AclI AACGTT 1 cut(s) 178
AcsI RAATTY 1 cut(s) 250
AfaI GTAC 1 cut(s) 84
AflII CTTAAG 1 cut(s) 533
AflIII ACRYGT 1 cut(s) 132
AgsI TTSAA 1 cut(s) 183
AjnI CCWGG 1 cut(s) 168
AluBI AGCT 1 cut(s) 291
AluI AGCT 1 cut(s) 291
Alw26I GTCTC 3 cut(s) 103, 141, 437
ApoI RAATTY 1 cut(s) 250
Asp700I GAANNNNTTC 1 cut(s) 178
AsuHPI GGTGA 1 cut(s) 208
AsuII TTCGAA 1 cut(s) 329
BauI CACGAG 1 cut(s) 269
BbvCI CCTCAGC 1 cut(s) 495
BcgI CGANNNNNNTGC 2 cut(s) 401, 435
BciT130I CCWGG 1 cut(s) 170
BciVI GTATCC 1 cut(s) 532
BcoDI GTCTC 3 cut(s) 103, 141, 437
BfmI CTRYAG 1 cut(s) 488
BfrI CTTAAG 1 cut(s) 533
BfuI GTATCC 1 cut(s) 532
Bme1390I CCNGG 1 cut(s) 170
BmrFI CCNGG 1 cut(s) 170
BplI GAGNNNNNCTC 2 cut(s) 252, 284
Bpu10I CCTNAGC 1 cut(s) 495
Bpu14I TTCGAA 1 cut(s) 329
BpuEI CTTGAG 1 cut(s) 385
BsaI GGTCTC 1 cut(s) 437
BsaJI CCNNGG 1 cut(s) 169
Bse1I ACTGG 1 cut(s) 459
BseBI CCWGG 1 cut(s) 170
BseDI CCNNGG 1 cut(s) 169
BseGI GGATG 1 cut(s) 165
BseMII CTCAG 1 cut(s) 486
BseNI ACTGG 1 cut(s) 459
Bsh1236I CGCG 1 cut(s) 134
BsmAI GTCTC 3 cut(s) 103, 141, 437
BsmBI CGTCTC 1 cut(s) 141
BsmI GAATGC 1 cut(s) 381
Bso31I GGTCTC 1 cut(s) 437
Bsp119I TTCGAA 1 cut(s) 329
Bsp143I GATC 3 cut(s) 190, 505, 516
BspACI CCGC 1 cut(s) 142
BspCNI CTCAG 1 cut(s) 487
BspFNI CGCG 1 cut(s) 134
BspT104I TTCGAA 1 cut(s) 329
BspTI CTTAAG 1 cut(s) 533
BspTNI GGTCTC 1 cut(s) 437
BsrBI CCGCTC 1 cut(s) 144
BsrI ACTGG 1 cut(s) 459
BssECI CCNNGG 1 cut(s) 169
BssMI GATC 3 cut(s) 190, 505, 516
BssSI CACGAG 1 cut(s) 269
Bst2BI CACGAG 1 cut(s) 269
Bst2UI CCWGG 1 cut(s) 170
Bst4CI ACNGT 1 cut(s) 431
Bst6I CTCTTC 1 cut(s) 153
BstAFI CTTAAG 1 cut(s) 533
BstBI TTCGAA 1 cut(s) 329
BstDEI CTNAG 2 cut(s) 495, 523
BstF5I GGATG 1 cut(s) 165
BstFNI CGCG 1 cut(s) 134
BstKTI GATC 3 cut(s) 193, 508, 519
BstMAI GTCTC 3 cut(s) 103, 141, 437
BstMBI GATC 3 cut(s) 190, 505, 516
BstNI CCWGG 1 cut(s) 170
BstSCI CCNGG 1 cut(s) 168
BstSFI CTRYAG 1 cut(s) 488
BstUI CGCG 1 cut(s) 134
BsuI GTATCC 1 cut(s) 532
BtsCI GGATG 1 cut(s) 165
BtsI GCAGTG 1 cut(s) 213
BtsIMutI CAGTG 2 cut(s) 213, 466
CseI GACGC 1 cut(s) 123
Csp6I GTAC 1 cut(s) 83
CviAII CATG 2 cut(s) 70, 335
CviJI RGCY 5 cut(s) 122, 291, 447, 494, 512
CviKI_1 RGCY 5 cut(s) 122, 291, 447, 494, 512
CviQI GTAC 1 cut(s) 83
DdeI CTNAG 2 cut(s) 495, 523
DpnI GATC 3 cut(s) 192, 507, 518
DpnII GATC 3 cut(s) 190, 505, 516
Eam1104I CTCTTC 1 cut(s) 153
EarI CTCTTC 1 cut(s) 153
Eco31I GGTCTC 1 cut(s) 437
EcoRII CCWGG 1 cut(s) 168
Esp3I CGTCTC 1 cut(s) 141
FaeI CATG 2 cut(s) 73, 338
FaiI YATR 8 cut(s) 71, 87, 218, 248, 336, 365, 438, 483
FatI CATG 2 cut(s) 69, 334
FokI GGATG 1 cut(s) 152
HgaI GACGC 1 cut(s) 123
Hin1II CATG 2 cut(s) 73, 338
HincII GTYRAC 1 cut(s) 502
HindII GTYRAC 1 cut(s) 502
HindIII AAGCTT 1 cut(s) 289
HinfI GANTC 3 cut(s) 331, 343, 474
HphI GGTGA 1 cut(s) 208
Hpy166II GTNNAC 2 cut(s) 425, 502
Hpy188I TCNGA 1 cut(s) 190
Hpy188III TCNNGA 4 cut(s) 14, 282, 340, 422
Hpy8I GTNNAC 2 cut(s) 425, 502
HpyAV CCTTC 2 cut(s) 21, 99
HpyCH4III ACNGT 1 cut(s) 431
HpyCH4IV ACGT 2 cut(s) 178, 185
HpyCH4V TGCA 2 cut(s) 229, 412
HpyF3I CTNAG 2 cut(s) 495, 523
HpySE526I ACGT 2 cut(s) 178, 185
Hsp92II CATG 2 cut(s) 73, 338
Kzo9I GATC 3 cut(s) 190, 505, 516
LpnPI CCDG 7 cut(s) 155, 179, 182, 267, 472, 476, 494
MaeII ACGT 2 cut(s) 178, 185
MalI GATC 3 cut(s) 192, 507, 518
MbiI CCGCTC 1 cut(s) 144
MboI GATC 3 cut(s) 190, 505, 516
MboII GAAGA 3 cut(s) 31, 74, 140
MluCI AATT 4 cut(s) 7, 93, 211, 250
MluI ACGCGT 1 cut(s) 132
MlyI GAGTC 1 cut(s) 468
MnlI CCTC 2 cut(s) 278, 490
MroXI GAANNNNTTC 1 cut(s) 178
MseI TTAA 1 cut(s) 534
MspCI CTTAAG 1 cut(s) 533
MspR9I CCNGG 1 cut(s) 170
Mva1269I GAATGC 1 cut(s) 381
MvaI CCWGG 1 cut(s) 170
MvnI CGCG 1 cut(s) 134
NdeII GATC 3 cut(s) 190, 505, 516
NlaIII CATG 2 cut(s) 73, 338
NmeAIII GCCGAG 1 cut(s) 69
NspV TTCGAA 1 cut(s) 329
PctI GAATGC 1 cut(s) 381
PdmI GAANNNNTTC 1 cut(s) 178
PfeI GAWTC 2 cut(s) 331, 343
PleI GAGTC 1 cut(s) 468
PpsI GAGTC 1 cut(s) 468
Psp1406I AACGTT 1 cut(s) 178
Psp6I CCWGG 1 cut(s) 168
PspGI CCWGG 1 cut(s) 168
RsaI GTAC 1 cut(s) 84
RsaNI GTAC 1 cut(s) 83
SaqAI TTAA 1 cut(s) 534
Sau3AI GATC 3 cut(s) 190, 505, 516
SchI GAGTC 1 cut(s) 468
ScrFI CCNGG 1 cut(s) 170
SetI ASST 7 cut(s) 181, 188, 198, 270, 293, 501, 534
SfcI CTRYAG 1 cut(s) 488
SfuI TTCGAA 1 cut(s) 329
SmlI CTYRAG 2 cut(s) 400, 533
SmoI CTYRAG 2 cut(s) 400, 533
Sse9I AATT 4 cut(s) 7, 93, 211, 250
SsiI CCGC 1 cut(s) 142
StyD4I CCNGG 1 cut(s) 168
TaaI ACNGT 1 cut(s) 431
TaiI ACGT 2 cut(s) 181, 188
TaqI TCGA 2 cut(s) 329, 519
TasI AATT 4 cut(s) 7, 93, 211, 250
TatI WGTACW 1 cut(s) 82
TfiI GAWTC 2 cut(s) 331, 343
Tru1I TTAA 1 cut(s) 534
Tru9I TTAA 1 cut(s) 534
TscAI CASTG 2 cut(s) 213, 466
TspDTI ATGAA 4 cut(s) 17, 154, 321, 470
TspGWI ACGGA 1 cut(s) 339
TspRI CASTG 2 cut(s) 213, 466
Vha464I CTTAAG 1 cut(s) 533
XapI RAATTY 1 cut(s) 250
XmnI GAANNNNTTC 1 cut(s) 178
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.