static-content.springer.com10.1007... · Web viewDeihimi T, Niazi A, Ebrahimi M, et al (2012)...

Table S3 Literature evidences for randomly selected TF-gene pairs (290) from transcription factor binding site analysis (TFBS). Random selection was performed to cover the wide PCC range (0.8 to 1.0). TF-gene pairs without evidence are represented with ‘NA’.

Gene name of orthologs identified for R. serpentina transcripts

Transcript IDs of R. serpentina with corresponding A. thaliana ortholog’s ID

Transcript IDs of identified TFs in R. serpentina with TF family name

PCC References

Hydroxycinnamoyl-coa shikimate/quinate hydroxycinnamoyl transferase (HCT)

AT5G48930.1_rsa_locus_11410_iso_1_len_710_ver_2

AP2-EREBP_rsa_locus_35905_iso_1_len_331_ver_2 1

(Kumari, Taylor, and Deyholos, 2008)

AP2/B3-like transcriptional factor family protein


ABI3VP1_rsa_locus_10225_iso_3_len_880_ver_2 1

(Salma Balazadeh, Jaspert, Arif, Mueller-Roeber, and Maurino, 2012)

Short-chain dehydrogenase/reductase isoform D (SDRD) AT3G55290.1_rsa_locus_5

3731_iso_1_len_685_ver_2

AP2-EREBP_rsa_locus_35905_iso_1_len_331_ver_2 0.9997

(Baud and Lepiniec, 2010; Charlton et al., 2005; Reumann et al., 2007)

2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein



(Van Hoewyk et al 2008)

VQ motif-containing proteinAT3G58000.1_rsa_locus_16899_iso_1_len_845_ver_2


(C.-Y. Yang, Hsu, Li, Wang, and Shih, 2011)

Protein of unknown function (DUF674)


ABI3VP1_rsa_locus_15489_iso_4_len_2125_ver_2 0.9883

NA




(Guan, Wu, Yue, Zhang, and Zhu, 2013)

BEL1-like homeodomain 9 (BLH9)



(Balazadeh et al 2012; Hirano et al 2013)

Cytochrome P450 (CYP721A1) AT1G75130.1_rsa_locus_2

2522_iso_1_len_1226_ver_2


(Goda et al., 2008; Ogata, Sakurai, Provart, Steinhauser, and Krall, 2008)

Thiamine pyrophosphate dependent pyruvate decarboxylase family protein


ABI3VP1_rsa_locus_15489_iso_4_len_2125_ver_2

0.9702 (Cândido et al., 2011; Foster, Kim, Nakata, and Browse, 2012; González-Pérez et al., 2011; Saibo, Lourenço,

and Oliveira, 2009)

Polynucleotidyl transferase, ribonuclease H-like superfamily protein



(Gutiérrez-Nava, Gillmor, Jiménez, Guevara-García, and León, 2004; Rohde et al., 2000; Stoppel and Meurer, 2012)

KNOTTED1-like homeobox gene 6 (KNAT6)



(Dean, Casson, and Lindsey, 2004; Zeng, Zhao, and Kermode, 2013)

Pentatricopeptide repeat (PPR) superfamily protein



(S. Y. Kim, Ma, Perret, Li, and Thomas, 2002; Y. Liu et al., 2010; Prieto-Dapena, Almoguera, Rojas, and Jordano, 1999)

Coronatine insensitive 1 (COI1)



(Chen et al., 2012; Fernández-Arbaizar, Regalado, and Lorenzo, 2012; Mazzucotelli et al., 2006)

Hydroxycinnamoyl-coa shikimate/quinate hydroxycinnamoyl transferase (HCT)



(D. Y. Kim, Scalf, Smith, and Vierstra, 2013; Kumari et al., 2008; Mazzucotelli et al., 2006)

Embryo defective 1273 (Emb1273)



NA




(Saibo et al 2009; González-Pérez et al 2011; Guan et al 2013)

Homolog of bacterial RECA (RECA1)



(Jeon, Jin, Choi, Lee, and Kim, 2013; Mannuss, Trapp, and Puchta, 2012)

Unknown function AT4G26450.1_rsa_locus_9429_iso_4_len_4475_ver_2


0.9606 (Capron et al., 2008; Stasolla et al., 2004; Suzuki, Wang, and

McCarty, 2007)

Bcl-2-associated athanogene (BAG1)



(Mao and Chen, 2012; Sanghera, Wani, Hussain, and Singh, 2011)

Short-chain dehydrogenase/ reductase isoform D (SDRD)



(Cheng et al 2002; Reumann et al 2007; Mu et al 2008)




(Rock 2000; Haslekås et al 2003; Van Hoewyk et al 2008)




(Rohde et al 2002; Ruttink et al 2007; Hirano et al 2013)

Embryo defective 2083 (EMB2083)



(Casson, Spencer, Walker, and Lindsey, 2005; Kadirjan-Kalbach, Yoder, Ruckle, Larkin, and Osteryoung, 2012; Suzuki et al., 2007)

Cell wall / vacuolar inhibitor of fructosidase 1 (C/VIF1)



(Radomiljac, Whelan, and van der Merwe, 2013; S. Ye et al., 2011)

Arabidopsis homolog of Medicago truncatula (MTN3)



(Fabro et al 2008)

Peroxisomal NAD-malate dehydrogenase 2 (PMDH2)



(González-Pérez et al., 2011; Liang, 2010; Wong, Sweetman, Drew, and Ford, 2013)

Phosphoenolpyruvate carboxylase family protein



(Hudson, Lisch, and Quail, 2003; Pinheiro and Chaves, 2011; Saibo et al., 2009; Sharma, Lin, Villamor, and Verslues, 2013)

Rho GTPase activating protein with PAK-box/P21-Rho-binding domain



(Deihimi et al., 2012; Dreher and Callis, 2007; Haslekås et al., 2003; S. Ye et al., 2011)

Aldehyde oxidase 2 (AAO2) AT3G43600.1_rsa_locus_1 ABI3VP1_rsa_locus_1548 0.9545 (Seo et al 2000; Bray

4347_iso_1_len_2218_ver_2 9_iso_4_len_2125_ver_2

2002)

HD domain-containing metal-dependent phosphohydrolase family protein



NA

Stomatal density and distribution 1 (ATSDD1)



(Yoo et al 2010; Upadhyay et al 2013)

Tetraspanin 1 (TET1)AT5G46700.1_rsa_locus_158_iso_1_len_1390_ver_2


(Espinoza, Medina, Somerville, and Arce-Johnson, 2007; Woo et al., 2010)

UDP-glucosyl transferase 73B1 (UGT73B1)



(Haslekås et al 2003; Juenger et al 2010; Ye et al 2011b)



(Brady, Sarkar, Bonetta, and McCourt, 2003; Ogata et al., 2008; Y. Zheng, Ren, Wang, Stromberg, and Perry, 2009)

Silencing defective (SDE3)AT1G05460.1_rsa_locus_1429_iso_3_len_2757_ver_2


(Haslekås et al., 2003; Mochida, Uehara-Yamaguchi, Yoshida, Sakurai, and Shinozaki, 2011; Ogata et al., 2008; Shi et al., 2009; S. Ye et al., 2011)

Toprim domain-containing protein



(Mannuss et al 2012; Miller-Messmer et al 2012; Yu et al 2014)

Enhanced response to ABA 1 (ERA1)



(Brady et al 2003)

Ovule abortion 9 (OVA9)AT1G25350.1_rsa_locus_4941_iso_1_len_2772_ver_2


(Berg, Rogers, Muralla, and Meinke, 2005; Prieto-Dapena et al., 1999)

Zinc transporter 5 precursor (ZIP5)



(Z. Yang and Chu, 2011; Yura and Nakahigashi, 1999)

Stomatal density and distribution 1 (ATSDD1)



(Pinheiro and Chaves, 2011; Xiao et al., 2010)

Beta hlh protein 93 (BHLH093)


MYB_rsa_locus_36772_iso_1_len_857_ver_2 0.9487

(S Balazadeh, Riaño-Pachón, and Mueller-Roeber, 2008; Feller, Hernandez, and Grotewold, 2006; Ogata et al., 2008; Ohashi-Ito and Bergmann, 2006)

Transducin/WD40 repeat-like superfamily protein



(Dreher and Callis, 2007; Eckardt, 2001; Lau and Deng, 2012; Rohde et al., 2000)

Tetratricopeptide repeat (TPR)-like superfamily protein



(Rosado et al 2006)

Leucine-rich repeat protein kinase family protein



(Hong 1997; Osakabe et al 2005)

Thioredoxin putative plastidic (TRX P)



(Rohde et al 2000; Gutiérrez-Nava et al 2004; Arsova et al 2010)

Beta glucosidase 17 (BGLU17)



(Haslekås et al 2003; Gómez-Anduro et al 2011; Ye et al 2011b)

Calcium-binding EF-hand family protein



(Brady et al 2003; Ogata et al 2008; González-Pérez et al 2011; Li et al 2012; Yu et al 2014; Hwang et al 2014)

Hypersensitive to MMS, Irradiation AND MMC (MIM)



(Goda et al 2008; Mannuss et al 2012; Roth et al 2012; Sundaram et al 2013)

NAC secondary wall thickening promoting factor1 (NST1)



(Hirano et al., 2013; Mitsuda and Ohme-Takagi, 2008; Noda et al., 2013; Shobbar et al., 2008)

Trichome birefringence-like AT5G19160.1_rsa_locus_2 AP2- 0.9408 (Bischoff et al 2010;

11 (TBL11)0506_iso_3_len_1852_ver_2

EREBP_rsa_locus_35905_iso_1_len_331_ver_2

Cassan-Wang et al 2013)

BTB/POZ and MATH domain-containing protein 3 (BPM3)



(Lechner et al 2011; Yu et al 2014)




(Shobbar et al 2008; Brown et al 2011; Hirano et al 2013)

Plastid-specific ribosomal protein 3/2 (PSRP3/2)



(Gutiérrez-Nava et al 2004; Kleine 2012)

Neutral/alkaline non-lysosomal ceramidase



(Y. Guo, Cai, and Gan, 2004; Woo et al., 2010)

Shoot meristemless (STM)AT1G62360.1_rsa_locus_5172_iso_9_len_2061_ver_2


(Ikeda, Mitsuda, and Ohme-Takagi, 2009; Ogata et al., 2008; Rohrmann, McQuinn, Giovannoni, Fernie, and Tohge, 2012)

SNF2 domain-containing protein / helicase domain-containing protein / F-box family protein



(Mannuss et al., 2012; Mazzucotelli et al., 2006; Shaked, Avivi-Ragolsky, and Levy, 2006; Sundaram et al., 2013)

Arabidopsis phantastica-like 1 (ATPHAN)



(Cairney et al 2006; Balazadeh et al 2012; Delmas et al 2013)

Fructokinase-like 1 (FLN1)



(Morcuende et al., 2007; Pfalz and Pfannschmidt, 2013; Rohde et al., 2000)

Glutamine dumper 2 (GDU2)AT4G25760.1_rsa_locus_8761_iso_1_len_648_ver_2


NA

Suppressor of fatty acid desaturase deficiency 1 (SFD1)



(Baud, Dubreucq, Miquel, Rochat, and Lepiniec, 2008)

Cytochrome P450 90B1 (CYP90B1)



(H. Jia, Suzuki, and McCarty, 2014; Song et al., 2009)

Methionine sulfoxide reductase (MSS4-like) family protein



(Cominelli, Galbiati, and Tonelli, 2010; Gray, 2005; Y. M. Kim et al., 2012)

Basic helix-loop-helix (bHLH) DNA-binding superfamily protein



(Haslekås et al 2003; Balazadeh et al 2008; Woo et al 2010; Betti et al 2012)

Far-red impaired responsive (FAR1) family protein



(Rohde et al 2000; Hudson et al 2003; Tang et al 2013)

Pigment defective 149 (PDE149)



(Gutiérrez-Nava et al., 2004; Kwon and Cho, 2008; Rohde et al., 2000; Yu et al., 2014)

Pumilio homolog 4 (APUM-4)


MADS_rsa_locus_39727_iso_1_len_416_ver_2 0.9346

(Jammes et al., 2005; Tam et al., 2010; Qi Zhang, Jiang, Wang, Hong, and Wang, 2013)

Homolog of xeroderma pigmentosum complementation group B 1 (XPB1)



(Mannuss et al 2012)

Unknown protein



NA

Nucleotidyltransferases



NA

Plastid transcriptionally active 12 (PTAC12)



(Rohde et al 2000; Ogata et al 2008; Gao et al 2011)

Fasciated stem 4 (FAS4)



(Jen et al 2006)(Pogorelko, Fursova, and Klimov, 2008; S. Ye et al., 2011)

Calcium-binding EF-hand family protein


CCAAT_rsa_locus_39819_iso_1_len_965_ver_2 0.9332

(Ditt et al 2006; Cairney et al 2006)

Cation exchanger 11 (CAX11)



0.9324 (Bose, Pottosin, Shabala, Palmgren, and Shabala,

2011; Brady et al., 2003; Haslekås et al., 2003; Larkindale and Knight, 2002; L. Xu et al., 2013; S. Ye et al., 2011)

Galactose oxidase/kelch repeat superfamily protein



(Cserháti et al., 2011; Fowler and Thomashow, 2002; L. T. Yang et al., 2013)




(Kujur et al., 2013; Verdier and Thompson, 2008)




(Xiyan Yang and Zhang, 2010)

Lob domain-containing protein 25 (LBD25)



(Brady et al., 2003; Matsumura, Iwakawa, Machida, and Machida, 2009)

Glutamyl/glutaminyl-tRNA synthetase, class Ic



(Ge et al 2012)

Ariadne 2 (ARI2)AT2G16090.1_rsa_locus_2105_iso_2_len_2617_ver_2


(Leymarie, Bruneaux, Gibot-Leclerc, and Corbineau, 2007; Xiaodong Liu et al., 2013)

Lutein deficient 1 (LUT1)



(Lindgren 2003; Liu et al 2013)

N-Ethylmaleimide sensitive factor (NSF)



(Leyman 1999; Zhu et al 2002; Gray 2005; Cominelli et al 2010)

Zinc finger C-x8-C-x5-C-x3-H type family protein



(Park, Lee, Kim, Lim, and Choi, 2011)

Nitrilase-like protein 1 (NLP1)



(Haslekås et al., 2003; Marco, Alcázar, Tiburcio, and Carrasco, 2011; Urano et al., 2003; S. Ye et al., 2011; Yu et al., 2014)

Leunig (LUG)AT4G32551.1_rsa_locus_80568_iso_1_len_520_ver_2


(Z. Liu and Meyerowitz, 1995; Swaminathan, Peterson, and Jack, 2008; Tran et al., 2013)

Mitochondrial editing factor 18 (MEF18)



(Takenaka, Verbitskiy, Zehrmann, and Brennicke, 2010; Yuan and Liu, 2012)

Cyclophilin-like peptidyl-prolyl cis-trans isomerase family protein (AtCYP57)



(Nakano et al 2012)

Laccase 17 (LAC17)AT5G60020.1_rsa_locus_15353_iso_1_len_595_ver_2


(Shobbar et al 2008; Minic et al 2009; Hirano et al 2013; Zhang et al 2014)

Targeting protein for Xklp2 (TPX2) protein family



(Meier and Brkljacic, 2010)




(Prieto-Dapena et al., 1999; Tzafrir et al., 2004; Xiyan Yang and Zhang, 2010)

O-fucosyltransferase family protein



NA




(Prieto-Dapena et al 1999; Goda et al 2008; Kadirjan-Kalbach et al 2012; Yu et al 2014)

Pyrimidine deaminase (PYRD)



(Jakoby et al., 2008; Morohashi and Grotewold, 2009)

Alpha 1,4-glycosyltransferase family protein



NA

Paralog of TGD4AT2G44640.1_rsa_locus_580_iso_4_len_2584_ver_2


(Simm et al 2013; Kalidasan 2013)

Helicase domain-containing protein / IBR domain-containing protein / zinc finger protein-related



(J. Li et al., 2006; Ogata et al., 2008; R. Xu, Zhang, Huang, and Zheng, 2013)

C2H2-type zinc finger family AT2G28200.1_rsa_locus_1 MADS_rsa_locus_12900_ 0.92 (Kumari et al., 2008; B.

protein (ZAT5)9303_iso_1_len_1151_ver_2 iso_1_len_674_ver_2

Yang, Srivastava, Deyholos, and Kav, 2007)

B-box domain protein 28 (BBX28)



(Salma Balazadeh et al., 2012; Kumagai et al., 2008; Penfield and King, 2009)

Nuclear pore localisation protein NPL4



(Farmer et al., 2010; Lyzenga and Stone, 2012)




(Mu et al 2008)




(Braybrook et al 2006)

Suppressor of variegation 7 (SVR7)



(Gutiérrez-Nava et al., 2004; Xiayan Liu, Yu, and Rodermel, 2010; Majeran et al., 2012; Rohde et al., 2000)

Aminopeptidase M1 (APM1)AT4G33090.1_rsa_locus_464_iso_6_len_2932_ver_2


(Adie et al., 2007; Philippe, Ralph, Mansfield, and Bohlmann, 2010)



WRKY_rsa_locus_7993_iso_3_len_1494_ver_2 0.918

(Caillaud et al., 2013; Ogata et al., 2008; Pischke, Huttlin, Hegeman, and Sussman, 2006)

HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase



(Haslekås et al., 2003; C. Yan, Shen, Li, and He, 2006; S. Ye et al., 2011)

CHY-type/CTCHY-type/RING-type Zinc finger protein



(Dietz, Vogel, and Viehhauser, 2010; Haslekås et al., 2003; S. Ye et al., 2011)

Cytochrome P450, family 82, subfamily C, polypeptide 4 (CYP82C4)



0.9171 (Kobayashi and Nishizawa, 2012; Murgia, Tarantino, Soave, and Morandini,

2011)




(Rosado et al 2006)

Unknown proteinAT4G17540.1_rsa_locus_9632_iso_3_len_1730_ver_2


(Perez 2008; Saibo et al 2009; Kong et al 2012)



(Lamberti, Gügel, Meurer, Soll, and Schwenkert, 2011; Rohde et al., 2000)

Unknown protein



(Day, Reddy, Shad Ali, and Reddy, 2002; González-Pérez et al., 2011; Haslekås et al., 2003; Mochida et al., 2011; Ogata et al., 2008; Yu et al., 2014)



(Chinnusamy, Zhu, and Zhu, 2007; Zhou, Wang, Sutoh, Zhu, and Zhang, 2008)

Sequence-specific DNA binding transcription factors



(Prieto-Dapena et al 1999; de Vega-Bartol et al 2013)




(Gutiérrez-Nava et al., 2004; Pfalz and Pfannschmidt, 2013; Rohde et al., 2000)

Cell division cycle 45 (CDC45)



(Broderick and Nasheuer, 2009; Mannuss et al., 2012; Sundaram et al., 2013)

NAD(P)-binding Rossmann-fold superfamily protein



(Goda et al 2008; Jakoby et al 2008)

Patatin-like protein 6 (PLP6)



(Braybrook et al 2006)

Serine carboxypeptidase S28 family protein



(Yu et al 2014)

Minichromosome maintenance 9 (MCM9)



(Broderick and Nasheuer, 2009; Mannuss et al., 2012; Shultz, Tatineni, Hanley-Bowdoin, and Thompson, 2007; Sundaram et al., 2013)



NA

cAMP-regulated phosphoprotein 19-related protein



(Jakoby et al 2008; Yang et al 2013a)

Unknown protein



NA

Wings apart-like protein regulation of heterochromatin (WAPL) protein



NA

FKBP-like peptidyl-prolyl cis-trans isomerase family protein-FKP20.1



(Jakoby et al 2008; Teodor 2009)

Inaperturate pollen1 (INP1)



(Cipriano, Morais, and Aragao, 2013; Dobritsa and Coerper, 2012; Xiaodong Liu et al., 2009; Ogata et al., 2008)

Cactin (CTN)AT1G03910.1_rsa_locus_9222_iso_2_len_3066_ver_2


(Baldwin, Dinh, Hart, and Masson, 2013; Piyatrakul et al., 2012)



(Adie et al., 2007; Savitch, Subramaniam, Allard, and Singh, 2007)

RNA-binding (RRM/RBD/RNP motifs) family protein



(Gutiérrez-Nava et al., 2004; Rohde et al., 2000; Ruwe, Kupsch, Teubner, and Schmitz-Linneweber, 2011)

Protein of unknown function AT1G68220.1_rsa_locus_2 ABI3VP1_rsa_locus_1548 0.9108 (Ceserani, Trofka,

(DUF1218) 981_iso_3_len_826_ver_2 9_iso_4_len_2125_ver_2

Gandotra, and Nelson, 2009; Garcion et al., 2006; Xiaodong Liu et al., 2013; Nakashima et al., 2009)

UDP-glycosyltransferase superfamily protein



(Hirano et al., 2013; Shobbar et al., 2008; Xiaohui Yang, Li, Li, and Zhang, 2013)

Proton gradient regulation 7 (PGR7)



(Hudson et al 2003; Perez 2008; Saibo et al 2009; Jung et al 2010; Kong et al 2012)

UMP synthaseAT3G54470.1_rsa_locus_2013_iso_4_len_1909_ver_2


(Yu et al 2014)

Eukaryotic aspartyl protease family protein



(Hirano et al., 2013; Pavy et al., 2008; Pyo, Demura, and Fukuda, 2007; Shobbar et al., 2008)

MethyltransferasesAT4G01880.1_rsa_locus_3691_iso_5_len_1768_ver_2


(Adie et al 2007; Fabro et al 2008; Yu et al 2014)

Glycine-rich RNA-binding protein



(Haslekås et al 2003; Ye et al 2011b; Yu et al 2014)




(Tzafrir et al 2004; Ogata et al 2008; Mori et al 2012)



NA

Blade on petiole2 (BOP2)



(Brady et al., 2003; Engelhorn et al., 2012; Norberg, Holmlund, and Nilsson, 2005)

Alpha/beta-Hydrolases superfamily protein



0.9073 (Kobayashi and Nishizawa, 2012; Tarantino, Morandini, Ramirez, Soave, and Murgia, 2011; L. T.

Yang et al., 2013)



(Bae, Herman, Bailey, Bae, and Sicher, 2005; Wong et al., 2013)

Eukaryotic translation initiation factor 3K (EIF3K)



(Heydarian 2008; Piyatrakul et al 2012)



(Pyo et al 2007; Pavy et al 2008; Shobbar et al 2008; Hirano et al 2013)

Ran gtpase 3 (RAN3)



(González-Pérez et al., 2011; Ndimba, Chivasa, Simon, and Slabas, 2005; Yu et al., 2014)

Phytochrome-associated protein 2 (PAP2)



(Ogata et al 2008; Song et al 2009; Yu et al 2014)

Succinate dehydrogenase 5 (SDH5)



(Rocco et al 2006; Jia et al 2013; Yu et al 2014)

Eukaryotic translation initiation factor 3K (EIF3K)



(Yu et al 2014)

K+ uptake transporter 3 (KUP3)



(Ogata et al 2008; Heyl et al 2008)

Syntaxin/t-SNARE family protein



(Zhu et al 2002; Haslekås et al 2003; Ogata et al 2008)

Irregular xylem 10 (IRX10-L)AT5G61840.1_rsa_locus_3552_iso_1_len_1962_ver_2


(Hirano et al 2013)

ATP-binding cassette B15 (ABCB15)



(Shobbar et al 2008; Kaneda et al 2011; Hirano et al 2013)

Glabra 2 (GL2)



(Shobbar et al 2008; Ogata et al 2008; Marks et al 2008; Jakoby et al 2008; Tominaga-Wada et al 2009; Hirano et al 2013)

Unknown protein



NA

Irregular xylem 12 (IRX12)AT2G38080.1_rsa_locus_7545_iso_1_len_1900_ver_2


(Kubo et al 2005; Shobbar et al 2008; Yamaguchi et al 2011; Hirano et al 2013)

Pinoresinol reductase 1 (PRR1)



(Shobbar et al 2008; Ruprecht et al 2011; Zhao et al 2013; Hirano et al 2013)

Basic helix-loop-helix (bHLH) DNA-binding superfamily protein



(Ogata et al 2008; Hirano et al 2013)

Nitrate transporter 1.5 (NRT1.5)



(Yongfeng Guo and Gan, 2012; Ogata et al., 2008; Woo et al., 2010)

Slow growth 2 (SLO2)AT2G13600.1_rsa_locus_8739_iso_1_len_1916_ver_2


(Saibo et al 2009; Zhu et al 2014)



(Haslekås et al 2003; Ye et al 2011b; Rhodes 2012)

Plastid-lipid associated protein PAP / fibrillin family protein



(Suzuki et al 2007; Kourmpetli et al 2013)

Clavata3/esr-related 12 (CLE12)



(Fiume, Monfared, Jun, and Fletcher, 2014; Hirano et al., 2013; Suzuki et al., 2007; J. Zheng, Xi, Lü, Lu, and Shi, 2012)

Cactin (CTN)AT1G03910.1_rsa_locus_9222_iso_2_len_3066_ver_2


(Suzuki et al 2007; Baldwin et al 2013)

Encodes Lil3:1 (light-harvesting-like) protein ( LIL3:1)



(Balazadeh et al 2012)

Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein



(Hirano et al., 2013; C.-Y. Ye, Li, Tuskan, Tschaplinski, and Yang, 2011)




(Gao et al 2009)

Trichome birefringence-like 11 (TBL11)



(Shobbar et al 2008; Bischoff et al 2010; Hirano et al 2013)




(Fiume et al., 2014; Kao, Cocciolone, Vasil, and McCarty, 1996; Suzuki et al., 2007)

Fasciclin-like arabinogalactan-protein 12 (FLA12)



(Pyo et al 2007; Shobbar et al 2008; Ogata et al 2008; Hirano et al 2013)

Phosphate transporter 3;3 (PHT3;3)



(Gou, Yuan, Wei, and Russell, 2009; Morcuende et al., 2007)

Unknown protein (Located in: chloroplast )






(Fowler and Thomashow, 2002; Sanghera et al., 2011; Sasaki et al., 2008; Yu et al., 2014)

Synaptotagmin homolog E (SYTE)



(J. Lee, Lim, Han, Nou, and Hur, 2013; S. Ye et al., 2011)

Pentatricopeptide repeat (PPR-like) superfamily protein



(Prieto-Dapena et al 1999; Kim et al 2002; Liu et al 2010b)

Exocyst complex component sec3a (SEC3A)



(Day et al 2002; Haslekås et al 2003; Ogata et al 2008; Mochida et al 2011; González-Pérez et al 2011; Yu et al 2014; Hwang et al 2014)

Cytochrome P450, family 721, subfamily A, polypeptide 1 (CYP721A1)



(Adie et al 2007; Goda et al 2008; Cheng et al 2010)

Lupeol synthase 2 (LUP2)AT1G78960.1_rsa_locus_67365_iso_1_len_345_ver_2


(Ogata et al 2008)



(Yu et al 2014)

Protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferases



(Ogata et al 2008; Yu et al 2014)

Regulator of fatty-acid composition 3 (RFC3)




Auxin response factor 10 (ARF10)



(Liu et al 2013)

Germin-like protein 7 (GLP7)AT1G10460.1_rsa_locus_61839_iso_1_len_398_ver_2


(Pyo et al 2007; Shobbar et al 2008; Hirano et al 2013)

Beta-1,2-xylosyltransferase (XYLT)



(Shobbar et al 2008; Parsons et al 2012; Hirano et al 2013)

Peroxidase superfamily protein



(Herrero, Esteban-Carrasco, and Zapata, 2013; Hirano et al., 2013; Ogata et al., 2008; Shobbar et al., 2008)





Phospholipase D P1 (PLDP1)



(Laloum, De Mita, Gamas, Baudin, and Niebel, 2013; B. Lee, Henderson, and Zhu, 2005; Ogata et al., 2008; Tamminen, Mäkelä, Heino, and Palva, 2008)

Actin depolymerizing factor 6 (ADF6)



(Huang, Huang, Hong, Lur, and Chang, 2012; X.-B. Li et al., 2010)

DNA j protein A4 (DJA4) AT3G17830.1_rsa_locus_10477_iso_4_len_2723_ver_

ABI3VP1_rsa_locus_1022 0.8957 (Baniwal et al., 2004; Rajan and D’Silva, 2009;

2 5_iso_3_len_880_ver_2 S. Ye et al., 2011)

Vitamin E deficient 1 (VTE1)AT4G32770.1_rsa_locus_5734_iso_4_len_1740_ver_2


(Ogata et al 2008; Song et al 2009)

Ribosomal protein S18 gene (RPS18)



(Ogata et al., 2008; Peng and Weselake, 2011)

Domain of unknown function (DUF250)



(Shobbar et al 2008; Suren 2013; Hirano et al 2013)

HAPLESS 13 (HAP13)



(Ogata et al 2008; Qiao et al 2010; Woo et al 2010)







(Kaplan-Levy, Brewer, Quon, and Smyth, 2012; To et al., 2006)

Transducin family protein / WD-40 repeat family protein




Phosphoglycerate mutase family protein



(Davuluri et al 2003; Elhiti 2010)

Pentatricopeptide repeat (PPR) superfamily protein



(Jiang, González, and Ramachandran, 2013)

Leucine-rich repeat receptor-like protein kinase family protein



(Hong 1997; Osakabe et al 2005)

Mitochondrial editing factor 9 (MEF9)



(Ogata et al., 2008; Takenaka, 2010; Yuan and Liu, 2012)

K+ uptake transporter 3 (KUP3)



(Ogata et al 2008; Lieckfeldt et al 2008; Mochida et al 2011)

Sec14p-like phosphatidylinositol transfer family protein



(Goda et al 2008; Jakoby et al 2008)




(Rosado et al 2006)

RING/U-box superfamily protein or zinc finger (C3HC4-type RING finger) family protein



(Cassan-Wang et al 2013; Suren 2013)

Mitochondrial RNA editing factor 25 (MEF25)



(Yasala et al., 2012; Z.-L. Zheng and Zhao, 2013)

Inaperturate pollen1 (INP1)



(Brady et al., 2003; Dobritsa and Coerper, 2012; Firon, Nepi, and Pacini, 2012; Ji et al., 2011; Oliver, Dennis, and Dolferus, 2007; Phan, Iacuone, Li, and Parish, 2011)

Aluminum sensitive 1 (ALS1)



(Yu et al 2014)

NDR1/HIN1-LIKE 8 (NHL8)AT1G32340.1_rsa_locus_7304_iso_1_len_2437_ver_2


(Srivastava, Srivastava, Suprasanna, and D’Souza, 2013)

Glucuronoxylan methyltransferase 3 (GXM3)



(Shobbar et al 2008; Lee et al 2012; Hirano et al 2013)

Cofactor assembly, complex C (B6F) (CCB3)



(Hudson et al., 2003; Lau and Deng, 2010; Pinheiro and Chaves, 2011; Rohde et al., 2000; Yruela, 2013)

Zinc finger (Ran-binding) family protein



(Brady et al 2003; Berger 2007; Zhao 2010; Liu et al 2013)

Peroxisomal membrane 22 kDa (Mpv17/PMP22) family protein



(Daie and Wyse, 1983; Ferro et al., 2002; Shang et al., 2010; Wilhelm, Nasheuer, and Huang, 2003)

26S proteasome regulatory subunit S2 1A (RPN1A)



(Lyzenga and Stone, 2012; Tamminen et al., 2008; S. Wang, Kurepa, and Smalle, 2009)

Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein



(Ogata et al 2008)

Isoflavone reductase



(Huerta et al 2008)




(Gutiérrez-Nava et al., 2004; Pfalz, Liere, Kandlbinder, Dietz, and Oelmüller, 2006; Rohde et al., 2000; Saibo et al., 2009; X. Zhang, Garreton, and Chua, 2005)

Cysteine proteinases superfamily protein



(Luo, Mittal, Jia, and Rock, 2012; J. Xu et al., 2012)




(Hu et al 2011; González-Pérez et al 2011)




(Jakoby et al 2008; Yang et al 2013a)

SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein



(Kalidasan, 2013; Khan, Lindquist, and Aronsson, 2013; Yu et al., 2014)

Hydroxyproline-rich glycoprotein family protein



(de Torres-Zabala et al 2007; Brown et al 2011; Etchells et al 2012)




(Kumari et al 2008)

Chromatin remodeling 19 (CHR19)



(Knizewski, Ginalski, and Jerzmanowski, 2008; Rodrigues, 2009; Yu et al., 2014)




(Osakabe et al 2005)




(Breuers, Bräutigam, and Weber, 2011; González-Pérez et al., 2011; Kalidasan, 2013; F. Wang et al., 2012; L. Zhao, Luo, Yang, Han, and Li, 2008)

Polynucleotide adenylyltransferase family protein



(Odapalli 2008; Ogata et al 2008)



(Honys, Renák, and Twell, 2006)

Arabidopsis sulfate transporter 68 (AST68)



(Khraiwesh, Zhu, and Zhu, 2012; Phillips, Dalmay, and Bartels, 2007)

Beta-glucosidase 47 (BGLU47)



(Lee et al 2007; Ye et al 2011b)

Purine permease 3 (ATPUP3)AT1G28220.1_rsa_locus_4207_iso_1_len_1204_ver_2


(Brady et al., 2003; Qi and Xiong, 2013; Sanghera et al., 2011)

Ribonuclease III family protein



(Mönke et al., 2012; Sharwood, Hotto, Bollenbach, and Stern, 2011; Visioli, Marmiroli, and Marmiroli, 2010)

Phototropic-responsive NPH3 family protein



(Tiwari, Spielman, Day, and Scott, 2006; H. Yan, 2012)




(Tzafrir et al 2004; Casson et al 2005; Delmas et al 2013)

Phosphoglycerate mutase family protein



0.8848 (Brady et al., 2003; Goda et al., 2008; Xiaodong Liu et al., 2013; Maier, Stehling-Sun, Offenburger, and

Lohmann, 2011)

Pyridoxal phosphate (PLP)-dependent transferases superfamily protein



NA



(Nakano et al., 2012; Nambara, Keith, McCourt, and Naito, 1995)

Chromosome-associated polypeptide (CAP)-D2



(Grafi and Ohad, 2013; Meitzel et al., 2011; Mönke et al., 2012; Schubert, Lermontova, and Schubert, 2013)

Arabidopsis thaliana translocon outer complex protein 120 (ATTOC120)



(Changsong and Diqiu, 2010; Giraud et al., 2010)

Cytochrome P450, family 71, subfamily B, polypeptide 4 (CYP71B4)



(Carre and Kay, 1995; Massa, Buell, and Robin, 2013; Narusaka et al., 2004; Ogata et al., 2008; Pan, 2013)

Arabidopsis thaliana ent-copalyl diphosphate synthetase 1 (ATCPS1)



(Bassel, Mullen, and Bewley, 2006; Hilhorst, Finch-Savage, Buitink, William Bolingue, and Leubner-Metzger, 2010)



NA

Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family



(Adie et al., 2007; Marathe, Guan, Anandalakshmi, Zhao, and Dinesh-Kumar, 2004; Miranda et al., 2007)

Glutamate receptor 5 (GLR5)



(Brady et al., 2003; Jammes, Hu, Villiers, Bouten, and Kwak, 2011; Sanghera et al., 2011)

Protein kinase superfamily AT1G79570.1_rsa_locus_1 ARF_rsa_locus_83220_is 0.8836 (Fei, Tsang, and Cutler,

protein with octicosapeptide/Phox/Bem1p domain

13421_iso_1_len_286_ver_2 o_1_len_302_ver_2

2007; Ståldal, 2011)

Strictosidine synthase 2 (SS2)AT1G74020.1_rsa_locus_1050_iso_2_len_1136_ver_2


(Adie et al., 2007; Böhmer and Schroeder, 2011; Devoto et al., 2005; Hur, 2009)

Unknown protein



(Kagaya, Ohmiya, and Hattori, 1999; Merelo et al., 2013)

Acyl-CoA N-acyltransferases (NAT) superfamily protein



(Nogueira, De Rosa, Menossi, Ulian, and Arruda, 2003; Riechmann, 2002; Santamaría, Rodríguez, Cañal, and Toorop, 2011; Sutela et al., 2013)

Unknown protein (located in chloroplast)



(Ogata et al 2008; Shang et al 2010; Kalidasan 2013)

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase family protein






(Pratelli, Sutter, and Blatt, 2004; S. Ye et al., 2011)

MATE efflux family protein



(Ogawa, Nakanishi, Mori, and Nishizawa, 2009; Ogundiwin et al., 2008)

Unknown seed protein like 1 (USPL1)



(Van Son et al 2009)



(Rohde et al 2000; Lamberti et al 2011)




(Mane, 2007; Singh and McNellis, 2011; S. Ye et al., 2011)




0.8817 (Jurgens and Geldner, 2002; Rock, 2000;

Serrano, 2012)

Light sensitive hypocotyls 4 (LSH4)



(Goda et al 2008; Takeda et al 2011; Engelhorn et al 2012)

Related to ubiquitin 1 ; nedd8 (RUB1)



(Lyzenga and Stone, 2012; Yu et al., 2014)

S-adenosyl-L-methionine-dependent methyltransferases superfamily protein



(M.-C. Cheng, Liao, Kuo, and Lin, 2013; Y.-J. Li et al., 2013)

Ypt/Rab-GAP domain of gyp1p superfamily protein



(Goda et al 2008; Ma 2012)

Unknown protein



(Mahalingam et al 2006; Zhao et al 2008; González-Pérez et al 2011)

Unknown protein



NA

Pectin methylesterase 3 (PME3)



(Bassel et al., 2006; Cadman, Toorop, Hilhorst, and Finch-Savage, 2006; Penfield and Hall, 2009)

Wuschel related homeobox 4 (WOX4)



(Ikeda et al 2009; Balazadeh et al 2012)




(Xiyan Yang and Zhang, 2010)




(Suzuki et al 2007; Kourmpetli et al 2013)



(Adie et al 2007; Savitch et al 2007)

STOMATAL DENSITY AND DISTRIBUTION 1 (SDD1)



(Pinheiro and Chaves, 2011; Xiao et al., 2010)



NA

Hypersensitive to MMS, Irradiation AND MMC (MIM))



(Goda et al 2008; Mannuss et al 2012; Roth et al 2012; Sundaram et al 2013)




(Gao et al 2009)

Unknown protein



(Day et al 2002; Haslekås et al 2003; Mochida et al 2011; González-Pérez et al 2011; Yu et al 2014; Hwang et al 2014)

Leunig (LUG)AT4G32551.1_rsa_locus_80568_iso_1_len_520_ver_2


(Z. Liu and Meyerowitz, 1995; Sara, 2012; Swaminathan et al., 2008; Tran et al., 2013)

Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family



(Marathe et al 2004; Adie et al 2007; Miranda et al 2007)



(Pratelli et al 2004; Ye et al 2011b)

Lupeol synthase 2 (LUP2)AT1G78960.1_rsa_locus_67365_iso_1_len_345_ver_2


(Ogata et al 2008)




(Mazzucotelli et al 2006; Shaked et al 2006; Mannuss et al 2012; Sundaram et al 2013)

UDP-Glycosyltransferase superfamily protein



(Shobbar et al 2008; Yang et al 2013b; Hirano et al 2013)

BAG1 (Bcl-2-associated athanogene)



(Mao and Chen, 2012; Sanghera et al., 2011)




(Shobbar et al 2008; Ogata et al 2008; Kaneda et al 2011; Hirano et al 2013)

Thioredoxin putative plastidic AT3G06730.1_rsa_locus_3 ABI3VP1_rsa_locus_1841 0.8418 (Rohde et al 2000;

(TRX P) 201_iso_2_len_838_ver_2 5_iso_7_len_1695_ver_2Gutiérrez-Nava et al 2004; Arsova et al 2010)

Slow growth 2 (SLO2)AT2G13600.1_rsa_locus_5158_iso_1_len_2224_ver_2


(Saibo et al 2009; Zhu et al 2014)




(Mazzucotelli et al 2006; Shaked et al 2006; Mannuss et al 2012; Sundaram et al 2013)




(Prieto-Dapena et al 1999; Kadirjan-Kalbach et al 2012)

Zinc finger (Ran-binding) family protein



(Brady et al 2003; Berger 2007; Zhao 2010; Liu et al 2013)

Chromatin remodeling 19 (CHR19)



(Knizewski et al 2008; Rodrigues 2009; Yu et al 2014)

Glabra 2 (GL2)



(Shobbar et al 2008; Ogata et al 2008; Marks et al 2008; Tominaga-Wada et al 2009; Hirano et al 2013)




(Rosado et al 2006)

Beta glucosidase 17 (BGLU17)



(Gómez-Anduro et al 2011)




(Saibo et al 2009; González-Pérez et al 2011; Guan et al 2013)




(Shobbar et al 2008; Ogata et al 2008; Kaneda et al 2011; Hirano et al 2013)




(Kao et al 1996; Suzuki et al 2007; Fiume et al 2014)

Cytochrome P450 90B1 AT3G50660.1_rsa_locus_4 ABI3VP1_rsa_locus_1022 0.8039 (Song et al 2009; Jia et al

(CYP90B1)1470_iso_1_len_1266_ver_2 5_iso_3_len_880_ver_2

2014)




(Dean et al 2004; Zeng et al 2013)

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