AT2G42940

Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs)

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
2
OG0014578
Physical Location & Seq
Reverse (-)
17862254 .. 17863456
1203 bp
Loading structure...
UTR
Exon/CDS
Intron
AT2G42940.1

Sequence Viewer

Length: 774 bp
ATGGCTGGAGGTACAGCTCTAACTCCAACCTCTGTAGGATCCAAGTCTGTTCCAATGAGGAACCATGAAGCAACAGAGAGAGGCAACACCAACAACAACCTGAGAGCATTACCCAAAGCCGTCCAACCGGTTTCATCAATCGAAGGAGAGATGGCTAAGAGGCCACGTGGCAGACCCGCTGGCTCCAAGAACAAACCCAAACCACCAATCATTGTGACTCACGACAGTCCAAATTCCCTCAGAGCTAACGCCGTTGAGATCAGCTCAGGTTGTGACATCTGTGAGACTTTATCGGATTTTGCAAGAAGGAAACAGAGAGGTCTCTGCATTCTCAGTGCCAATGGTTGTGTCACCAATGTGACATTAAGGCAACCAGCTTCATCAGGAGCAATTGTCACATTACACGGACGTTACGAGATCCTCTCATTGCTTGGATCAATCTTGCCTCCACCAGCACCACTTGGAATAACTGGTCTGACCATTTACTTAGCCGGACCTCAAGGACAGGTTGTTGGTGGAGGAGTGGTTGGTGGGCTAATCGCATCTGGTCCTGTTGTTCTCATGGCTGCATCTTTCATGAATGCTGTTTTTGATCGTCTTCCTATGGATGATGATGAAGCTGCCTCTATGCAGAACCAGCAGTACTACCAGAATGGAAGATCCCGTCCTTTAGATGACATTCATGGACTGCCTCAAAATCTGCTCACTAATGGAAACTCGGCTTCTGATATCTACTCTTGGGGGCCTGCGCAGCGTGTCATGTCGAAACCTTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003677 GO:0003680 GO:0003682 GO:0003690 GO:0003700 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0007275 GO:0008150 GO:0009555 GO:0009653 GO:0009791 GO:0009889 GO:0009892 GO:0009893 GO:0009987 GO:0010208 GO:0010228 GO:0010468 GO:0010528 GO:0010529 GO:0010556 GO:0010604 GO:0010605 GO:0010638 GO:0010639 GO:0010927 GO:0016043 GO:0019219 GO:0019222 GO:0022414 GO:0022607 GO:0030198 GO:0031056 GO:0031057 GO:0031058 GO:0031060 GO:0031062 GO:0031323 GO:0031324 GO:0031325 GO:0031326 GO:0031399 GO:0031400 GO:0031401 GO:0031490 GO:0032268 GO:0032269 GO:0032270 GO:0032501 GO:0032502 GO:0032989 GO:0033043 GO:0033044 GO:0035065 GO:0035067 GO:0043062 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043565 GO:0044085 GO:0044424 GO:0044464 GO:0045229 GO:0048229 GO:0048518 GO:0048519 GO:0048522 GO:0048523 GO:0048608 GO:0048646 GO:0048731 GO:0048856 GO:0048869 GO:0050789 GO:0050794 GO:0051128 GO:0051129 GO:0051130 GO:0051171 GO:0051172 GO:0051173 GO:0051246 GO:0051247 GO:0051248 GO:0051252 GO:0051570 GO:0051574 GO:0060255 GO:0061458 GO:0065007 GO:0071840 GO:0080090 GO:0085029 GO:0097159 GO:0140110 GO:1900109 GO:1900111 GO:1901363 GO:1901983 GO:1901984 GO:1902275 GO:1903506 GO:1905268 GO:1905269 GO:1990837 GO:2000112 GO:2000756 GO:2000757 GO:2001141 GO:2001251 GO:2001252
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
DUF296

Protein Analysis

257

Amino Acids

27.0

Weight (kDa)

9.32

Isoelectric Point (pI)

40.66

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 84 - 193 3.8e-23 Plants and Prokaryotes Conserved (PCC) domain
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: OG0014578)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G42940
fragaria_vesca FvH4_6g38311
malus_domestica MD09G1151100.v1.1 MD17G1138700.v1.1
prunus_persica Prupe.3G173700_v2.0.a1
pyrus_communis pycom09g07090 pycom17g13180
rosa_chinensis RchiOBHm_Chr2g0151621
rosa_laevigata RLG00000020564
rosa_multiflora Rmu_sc0005287.1_g000005
rosa_roxburghii Rroxscaffold_2G00096310
rosa_rugosa Rorug02G0427300
rosa_samantha Rh2AG488200 Rh2BG500800 Rh2CG474700 Rh2DG511900
rosa_wichuraiana Rw2G040020

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 750
AciI CCGC 1 cut(s) 177
AclWI GGATC 5 cut(s) 33, 46, 412, 442, 654
AcsI RAATTY 1 cut(s) 232
AcvI CACGTG 1 cut(s) 167
AfaI GTAC 2 cut(s) 13, 644
AgeI ACCGGT 1 cut(s) 127
AleI CACNNNNGTG 1 cut(s) 356
AluBI AGCT 5 cut(s) 17, 245, 264, 377, 620
AluI AGCT 5 cut(s) 17, 245, 264, 377, 620
Alw26I GTCTC 2 cut(s) 278, 326
AlwI GGATC 5 cut(s) 33, 46, 412, 442, 654
AoxI GGCC 2 cut(s) 161, 743
ApeKI GCWGC 3 cut(s) 566, 620, 751
ApoI RAATTY 1 cut(s) 232
AsiGI ACCGGT 1 cut(s) 127
AspLEI GCGC 1 cut(s) 751
AspS9I GGNCC 3 cut(s) 494, 548, 743
AsuHPI GGTGA 1 cut(s) 343
AvaII GGWCC 2 cut(s) 494, 548
BamHI GGATCC 1 cut(s) 38
BbrPI CACGTG 1 cut(s) 167
BbsI GAAGAC 1 cut(s) 590
BbvI GCAGC 3 cut(s) 553, 607, 763
BccI CCATC 1 cut(s) 145
BceAI ACGGC 2 cut(s) 104, 236
BcoDI GTCTC 2 cut(s) 278, 326
BfmI CTRYAG 1 cut(s) 33
BisI GCNGC 3 cut(s) 567, 621, 752
BlsI GCNGC 3 cut(s) 568, 622, 753
BmcAI AGTACT 1 cut(s) 644
Bme18I GGWCC 2 cut(s) 494, 548
BmgT120I GGNCC 3 cut(s) 494, 548, 743
BmiI GGNNCC 4 cut(s) 40, 62, 184, 744
BmsI GCATC 2 cut(s) 551, 578
BpiI GAAGAC 1 cut(s) 590
BplI GAGNNNNNCTC 4 cut(s) 248, 280, 407, 439
BpmI CTGGAG 1 cut(s) 27
Bpu10I CCTNAGC 1 cut(s) 265
BpuEI CTTGAG 1 cut(s) 483
BsaAI YACGTR 1 cut(s) 167
BsaI GGTCTC 1 cut(s) 326
BsaWI WCCGGW 1 cut(s) 127
BsaXI ACNNNNNCTCC 4 cut(s) 378, 408, 510, 540
Bse118I RCCGGY 1 cut(s) 127
Bse1I ACTGG 1 cut(s) 475
Bse3DI GCAATG 1 cut(s) 425
BseGI GGATG 1 cut(s) 613
BseMI GCAATG 1 cut(s) 425
BseMII CTCAG 4 cut(s) 92, 253, 279, 346
BseNI ACTGG 1 cut(s) 475
BseRI GAGGAG 1 cut(s) 534
BseXI GCAGC 3 cut(s) 553, 607, 763
BshFI GGCC 2 cut(s) 163, 745
BshTI ACCGGT 1 cut(s) 127
BsiSI CCGG 2 cut(s) 128, 492
BsmAI GTCTC 2 cut(s) 278, 326
BsmI GAATGC 2 cut(s) 327, 586
BsnI GGCC 2 cut(s) 163, 745
Bso31I GGTCTC 1 cut(s) 326
Bsp143I GATC 6 cut(s) 38, 258, 417, 434, 592, 659
BspACI CCGC 1 cut(s) 177
BspANI GGCC 2 cut(s) 163, 745
BspCNI CTCAG 4 cut(s) 93, 252, 278, 345
BspHI TCATGA 1 cut(s) 576
BspLI GGNNCC 4 cut(s) 40, 62, 184, 744
BspPI GGATC 5 cut(s) 33, 46, 412, 442, 654
BspTNI GGTCTC 1 cut(s) 326
BsrDI GCAATG 1 cut(s) 425
BsrFI RCCGGY 1 cut(s) 127
BsrI ACTGG 1 cut(s) 475
BssAI RCCGGY 1 cut(s) 127
BssMI GATC 6 cut(s) 38, 258, 417, 434, 592, 659
Bst4CI ACNGT 1 cut(s) 227
BstBAI YACGTR 1 cut(s) 167
BstC8I GCNNGC 2 cut(s) 181, 747
BstDEI CTNAG 6 cut(s) 101, 156, 239, 265, 332, 487
BstF5I GGATG 1 cut(s) 613
BstHHI GCGC 1 cut(s) 751
BstKTI GATC 6 cut(s) 41, 261, 420, 437, 595, 662
BstMAI GTCTC 2 cut(s) 278, 326
BstMBI GATC 6 cut(s) 38, 258, 417, 434, 592, 659
BstMWI GCNNNNNNNGC 2 cut(s) 637, 751
BstSFI CTRYAG 1 cut(s) 33
BstV1I GCAGC 3 cut(s) 553, 607, 763
BstV2I GAAGAC 1 cut(s) 590
BstX2I RGATCY 3 cut(s) 38, 417, 659
BstYI RGATCY 3 cut(s) 38, 417, 659
BsuRI GGCC 2 cut(s) 163, 745
BtsCI GGATG 1 cut(s) 613
BtsIMutI CAGTG 1 cut(s) 340
Cac8I GCNNGC 2 cut(s) 181, 747
CciI TCATGA 1 cut(s) 576
CfoI GCGC 1 cut(s) 751
Cfr10I RCCGGY 1 cut(s) 127
Cfr13I GGNCC 3 cut(s) 494, 548, 743
Csp6I GTAC 2 cut(s) 12, 643
CspAI ACCGGT 1 cut(s) 127
CviAII CATG 5 cut(s) 65, 562, 577, 683, 760
CviQI GTAC 2 cut(s) 12, 643
DdeI CTNAG 6 cut(s) 101, 156, 239, 265, 332, 487
DpnI GATC 6 cut(s) 40, 260, 419, 436, 594, 661
DpnII GATC 6 cut(s) 38, 258, 417, 434, 592, 659
Eco31I GGTCTC 1 cut(s) 326
Eco32I GATATC 1 cut(s) 730
Eco47I GGWCC 2 cut(s) 494, 548
Eco72I CACGTG 1 cut(s) 167
EcoO109I RGGNCCY 1 cut(s) 743
EcoRV GATATC 1 cut(s) 730
FaeI CATG 5 cut(s) 68, 565, 580, 686, 763
FaiI YATR 7 cut(s) 66, 563, 578, 605, 629, 684, 761
FatI CATG 5 cut(s) 64, 561, 576, 682, 759
FauI CCCGC 1 cut(s) 184
Fnu4HI GCNGC 3 cut(s) 567, 621, 752
FokI GGATG 1 cut(s) 620
Fsp4HI GCNGC 3 cut(s) 567, 621, 752
FspI TGCGCA 1 cut(s) 750
GlaI GCGC 1 cut(s) 750
GluI GCNGC 3 cut(s) 567, 621, 752
GsuI CTGGAG 1 cut(s) 27
HaeIII GGCC 2 cut(s) 163, 745
HapII CCGG 2 cut(s) 128, 492
HhaI GCGC 1 cut(s) 751
Hin1II CATG 5 cut(s) 68, 565, 580, 686, 763
Hin6I GCGC 1 cut(s) 749
HinP1I GCGC 1 cut(s) 749
HinfI GANTC 1 cut(s) 217
HpaII CCGG 2 cut(s) 128, 492
HphI GGTGA 1 cut(s) 343
Hpy188I TCNGA 4 cut(s) 242, 295, 477, 727
Hpy188III TCNNGA 3 cut(s) 221, 384, 577
HpyAV CCTTC 2 cut(s) 137, 300
HpyCH4III ACNGT 1 cut(s) 227
HpyCH4IV ACGT 2 cut(s) 166, 409
HpyCH4V TGCA 4 cut(s) 302, 327, 569, 631
HpyF10VI GCNNNNNNNGC 2 cut(s) 637, 751
HpyF3I CTNAG 6 cut(s) 101, 156, 239, 265, 332, 487
HpySE526I ACGT 2 cut(s) 166, 409
Hsp92II CATG 5 cut(s) 68, 565, 580, 686, 763
HspAI GCGC 1 cut(s) 749
Kzo9I GATC 6 cut(s) 38, 258, 417, 434, 592, 659
LmnI GCTCC 2 cut(s) 188, 386
Lsp1109I GCAGC 3 cut(s) 553, 607, 763
LweI GCATC 2 cut(s) 551, 578
MaeII ACGT 2 cut(s) 166, 409
MaeIII GTNAC 6 cut(s) 214, 272, 349, 358, 394, 410
MalI GATC 6 cut(s) 40, 260, 419, 436, 594, 661
MboI GATC 6 cut(s) 38, 258, 417, 434, 592, 659
MboII GAAGA 2 cut(s) 590, 669
MfeI CAATTG 1 cut(s) 390
MflI RGATCY 3 cut(s) 38, 417, 659
MluCI AATT 2 cut(s) 232, 390
MlyI GAGTC 1 cut(s) 211
MmeI TCCRAC 2 cut(s) 50, 148
MseI TTAA 2 cut(s) 365, 772
MslI CAYNNNNRTG 1 cut(s) 356
MspA1I CMGCKG 1 cut(s) 179
MspI CCGG 2 cut(s) 128, 492
MunI CAATTG 1 cut(s) 390
Mva1269I GAATGC 2 cut(s) 327, 586
MwoI GCNNNNNNNGC 2 cut(s) 637, 751
NdeII GATC 6 cut(s) 38, 258, 417, 434, 592, 659
NlaIII CATG 5 cut(s) 68, 565, 580, 686, 763
NlaIV GGNNCC 4 cut(s) 40, 62, 184, 744
NmeAIII GCCGAG 1 cut(s) 698
NmuCI GTSAC 5 cut(s) 214, 272, 349, 358, 394
NsbI TGCGCA 1 cut(s) 750
OliI CACNNNNGTG 1 cut(s) 356
PagI TCATGA 1 cut(s) 576
PcsI WCGNNNNNNNCGW 1 cut(s) 411
PctI GAATGC 2 cut(s) 327, 586
PinAI ACCGGT 1 cut(s) 127
PkrI GCNGC 3 cut(s) 568, 622, 753
PleI GAGTC 1 cut(s) 211
PmaCI CACGTG 1 cut(s) 167
PmlI CACGTG 1 cut(s) 167
PpsI GAGTC 1 cut(s) 211
Ppu21I YACGTR 1 cut(s) 167
PspCI CACGTG 1 cut(s) 167
PspN4I GGNNCC 4 cut(s) 40, 62, 184, 744
PspPI GGNCC 3 cut(s) 494, 548, 743
PsrI GAACNNNNNNTAC 2 cut(s) 626, 658
PsuI RGATCY 3 cut(s) 38, 417, 659
RsaI GTAC 2 cut(s) 13, 644
RsaNI GTAC 2 cut(s) 12, 643
RseI CAYNNNNRTG 1 cut(s) 356
SaqAI TTAA 2 cut(s) 365, 772
SatI GCNGC 3 cut(s) 567, 621, 752
Sau3AI GATC 6 cut(s) 38, 258, 417, 434, 592, 659
Sau96I GGNCC 3 cut(s) 494, 548, 743
ScaI AGTACT 1 cut(s) 644
SchI GAGTC 1 cut(s) 211
SfaNI GCATC 2 cut(s) 551, 578
SfcI CTRYAG 1 cut(s) 33
SinI GGWCC 2 cut(s) 494, 548
SmiMI CAYNNNNRTG 1 cut(s) 356
SmlI CTYRAG 1 cut(s) 498
SmoI CTYRAG 1 cut(s) 498
Sse9I AATT 2 cut(s) 232, 390
SsiI CCGC 1 cut(s) 177
TaaI ACNGT 1 cut(s) 227
TaiI ACGT 2 cut(s) 169, 412
TaqI TCGA 2 cut(s) 141, 764
TasI AATT 2 cut(s) 232, 390
TatI WGTACW 1 cut(s) 642
Tru1I TTAA 2 cut(s) 365, 772
Tru9I TTAA 2 cut(s) 365, 772
TscAI CASTG 1 cut(s) 340
TseFI GTSAC 5 cut(s) 214, 272, 349, 358, 394
TseI GCWGC 3 cut(s) 566, 620, 751
Tsp45I GTSAC 5 cut(s) 214, 272, 349, 358, 394
TspDTI ATGAA 7 cut(s) 81, 123, 369, 565, 593, 630, 671
TspGWI ACGGA 1 cut(s) 420
TspRI CASTG 1 cut(s) 340
VpaK11BI GGWCC 2 cut(s) 494, 548
XapI RAATTY 1 cut(s) 232
ZrmI AGTACT 1 cut(s) 644
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.