AP2 Genomic sequences

Minimum number of tobacco AP2 genes: 35

Count of tobacco AP2 sequences: 60

Pfam accession: AP2

SHOULD possess AP2 domain and COULD   possess B3 SNF2_N domains

The APETELA2(AP2) family is part of the larger AP2/ERF superfamily that also contains the ERF and RAV families. The superfamily is defined by the presence of the approximately 60 amino acid AP2 domain that is involved in DNA binding and may be related to site-specific endonucleases that are found in bacteria and bacteriophages . In general, the ERF proteins have one AP2 domain, the AP2 proteins have two and the RAV proteins contain an AP2 domain together with another DNA binding domain, the B3 domain .

For our purposes, the tobacco AP2 genes contain two AP2 domains and lack the conserved WLG and the AEIRD parts of ERFs. Instead they have a conserved YLG.

Papers

Okamuro, JK; Caster, B; Villarroel, R; Van Montagu, M; Jofuku, KD. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 1997. 94(13):7076-81 PMID: 9192694

Nole-Wilson S, Krizek BA. DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. Nucleic Acids Res. 2000 Nov 1;28(21):4076-82. Erratum in: Nucleic Acids Res 2001 Mar 1;29(5):1261. PMID: 11058102

Shigyo, M; Hasebe, M; Ito, M. Molecular evolution of the AP2 subfamily. Gene 2006. 366(2):256-65 PMID: 16388920

Shigyo, M; Ito, M. Analysis of gymnosperm two-AP2-domain-containing genes. Dev. Genes Evol. 2004. 214(3):105-14 PMID: 14986134

Weigel, D. The APETALA2 domain is related to a novel type of DNA binding domain. Plant Cell 1995. 7(4):388-9 PMID: 7773013



R1 repeat contains WESHI or YEAH at the 5 ‘ end and LAALKY or YDRAA at the 3 ‘ end.

R2 repeat contains WEAR or WQAR at the 5 ‘ end and YDIAAI or NAVT at the 3 ‘ end.

Number of contigs: 53

Number of singlets: 12

R1 + R2 – 5

R1 – 8

R1 5 prime – 10

R1 3 prime – 5

R2 5 prime – 6

R2 3 prime – 10

R2 – 4

R1 + R2 5 prime – 12

Total minimum number – 35




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
AP2_1 [comment=R1] ET049546
AP2_2 [comment=R1] ET045341
ET046725
AP2_3 [comment=R1 first half] ET048563
ET050297
AP2_4 [comment=R1] ET047902
ET047520
AP2_5 [comment=R1 and first 10 amino acids of R2] ET047255
ET043379
AP2_6 [comment=R1 5 prime] ET046733
ET045128
AP2_7 [comment=R1 3 prime] ET050722
ET050552
AP2_8 [comment=R1 first half] ET050580
ET043213
AP2_9 [comment=R2 3 prime] ET048880
ET046156
AP2_10 [comment=R2 first half] ET048512
ET048340
AP2_11 [comment=R1 first half] ET050142
ET048261
AP2_12 [comment=R1 and first half of R2] ET045412
ET048381
AP2_13 [comment=R1 and start of R2] ET043265
ET050631
AP2_14 [comment=R2 3 prime] ET048095
ET048511
AP2_15 [comment=R1 5 prime] ET049970
ET045845
AP2_16 [comment=R1 5 prime] ET047235
ET047236
AP2_17 [comment=R2 second half] ET045599
ET044685
AP2_18 [comment=R2 3 prime] ET043125
ET042404
ET043757
AP2_19 [comment=R1 5 prime] ET045506
ET043697
ET047642
AP2_20 [comment=R1] ET049497
ET050072
ET044348
AP2_21 [comment=R2 3 prime] ET044524
ET044525
ET043535
AP2_22 [comment=R2] ET042915
ET042909
ET042910
AP2_23 [comment=R1 5 prime] ET049974
ET049571
ET041874
AP2_24 [comment=R2 3 prime] ET050661
ET049925
ET048445
AP2_25 [comment=R1 + R2 (minus 3 prime end)] ET049975
ET047799
ET047800
ET047528
AP2_26 [comment=R1 5 prime] ET043221
ET043222
ET044226
ET048180
AP2_27 [comment=R2 first half] ET042425
ET047249
ET043266
ET042426
AP2_28 [comment=R2 5 prime] ET044349
ET051490
ET049152
ET044914
AP2_29 [comment=R2 3 prime] ET043923
ET042276
ET042275
ET043959
ET044189
AP2_30 [comment=R2 3 prime] ET042791
ET048893
ET044091
ET046246
ET047207
AP2_31 [comment=R1 5 prime] ET043789
ET049151
ET045115
ET047474
ET045810
AP2_32 [comment=R2] ET044319
ET049226
ET042444
ET048032
ET046612
AP2_33 [comment=R2 3 prime] ET047315
ET042317
ET045511
ET042105
ET046388
AP2_34 [comment=R2] ET048911
ET042660
ET042661
ET044454
ET044453
AP2_35 [comment=R1 + R2 Very similar to ANT-like] ET042009
ET048221
ET048390
ET048220
ET051296
ET048389
AP2_36 [comment=R2 3 prime] ET046333
ET045814
ET047580
ET045343
ET051306
ET051601
AP2_39 [comment=R1] ET047319
ET051800
ET047678
ET050594
ET049475
ET047320
AP2_40 [comment=R1 + R2] ET042107
ET050392
ET050271
ET046452
ET046316
ET042108
ET048181
AP2_41 [comment=R1] ET048889
ET042508
ET051628
ET042554
ET042553
ET051631
ET051880
AP2_42 [comment=R1] ET048267
ET047238
ET048796
ET050381
ET045567
ET043110
ET043108
ET045568
AP2_43 [comment=R1 + R2] ET051237
ET042729
ET046904
ET043525
ET042730
ET042818
ET042817
ET048786
AP2_44 [comment=R1 and R2 5 prime] ET050496
ET045088
ET048753
ET045087
ET043022
ET050495
ET042346
ET048754
AP2_45 [comment=R1 + R2 5 prime] ET048197
ET044104
ET044105
ET050775
ET048810
ET050572
ET048198
ET044106
ET051417
AP2_46 [comment=R1 + R2] ET044772
ET048253
ET049197
ET043775
ET046099
ET048439
ET048085
ET043759
ET045173
AP2_47 [comment=R1 + R2 5 prime] ET051227
ET042050
ET042052
ET051226
ET042051
ET042053
ET050637
ET047712
ET049058
ET049126
AP2_48 [comment=R1 + R2 5 prime] ET045333
ET043268
ET048554
ET047434
ET046018
ET050151
ET049513
ET049512
ET043267
ET048553
ET045332
AP2_49 [comment=R1 + R2] ET051765
ET048127
ET050645
ET042022
ET048326
ET044168
ET044365
ET044469
ET047440
ET050827
ET044364
ET044167
ET048325
AP2_50 [comment=R1 + R2 5 prime] ET051863
ET046926
ET048869
ET045822
ET046137
ET043232
ET050870
ET045656
ET046601
ET047372
ET042353
ET043795
ET043794
AP2_51 [comment=R1 + R2 5 prime] ET046686
ET048740
ET042185
ET050998
ET044209
ET047152
ET042184
ET047829
ET043601
ET048440
ET050588
ET048056
ET047828
ET049120
AP2_52 [comment=R1 + R2 5 prime] ET047153
ET046964
ET044133
ET045978
ET045709
ET041795
ET050216
ET048861
ET047132
ET041796
ET042150
ET042151
ET046965
ET045708
ET049113
AP2_53 [comment=R1 + R2 5 prime] ET042492
ET043436
ET051664
ET051721
ET043619
ET043779
ET051665
ET047566
ET047497
ET050410
ET050050
ET048827
ET043435
ET051722
ET047567
ET042361
ET045683
AP2_54 [comment=R2 5 prime] ET046291
AP2_55 [comment=R2 5 prime] ET042582
AP2_56 [comment=R2] ET049384
AP2_58 [comment=R1 3 prime end] ET051832
AP2_59 [comment=R1] ET048910
AP2_60 [comment=R2 5 prime] ET045314
AP2_61 [comment=R1 3 prime] ET042785
AP2_62 [comment=R1 3 prime] ET050776
AP2_63 [comment=R1 3 prime] ET048105


Tobacco published genes related to transcription factor family AP2
Family Genbank ID Name
AP2 AY461432 NtANTL (AP2 family)
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu