TapScan - v4


DUF296 domain containing	Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>"	PT
DUF547 domain containing	Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>"	PT
DUF632 domain containing	Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>"	PT
DUF833 domain containing/TANGO2	Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>"	PT
E2F/DP	de Jager et al (2001): E2F-DP transcription factors are key components of the cyclin D/retinoblastoma/E2F pathway, they regulate the expression of genes required for G1/S transition and S-phase progression.	de Jager, SM; Menges, M; Bauer, UM; Murra, JA. 2001. Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol. 47(4):555-68,"Zheng, N; Fraenkel, E; Pabo, CO; Pavletich, NP. 1999. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev. 13(6):666-74"	TF
EIL	Solano et al (1998): EIN-3-like transcription factors are involved in the ethylene signaling of higher plants.	Solano, R; Stepanova, A; Chao, Q; Ecker, JR. 1998. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 12(23):3703-14,"Yamasaki, K; Kigawa, T; Inoue, M; Yamasaki, T; Yabuki, T; Aoki, M; Seki, E; Matsuda, T; Tomo, Y; Terada, T; Shirouzu, M; Tanaka, A; Seki, M; Shinozaki, K; Yokoyama, S. 2005. Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3. J. Mol. Biol. 348(2):253-64"	TF
ET	Based on the study of (Raventós et al., 1998), the TF family HRT (Hordeum repressor of transcription) was previously integrated into TAPscan. The authors introduced this protein family as proteins containing a gibberellin phytohormone response element and are therefore involved in developmental and phytohormone-responsive regulations (Raventós et al., 1998). However, a more recent study by (Tedeschi et al., 2019) characterized this family as EFFECTORS OF TRANSCRIPTION (ET). ET proteins are plant-specific transcription factors specified by highly conserved ET repeats and a GIY-YIG domain, a DNA single-strand nuclease domain (Tedeschi et al., 2019). In line with (Raventós et al., 1998), also (Ivanov et al., 2012) were able to demonstrate an involvement in the regulation of gibberellin to ensure correct seed development. Moreover, it is suggested that ET proteins are involved in DNA repair (Tedeschi et al., 2019).	Raventós, D., Skriver, K., Schlein, M., Karnahl, K., Rogers, S. W., Rogers, J. C., & Mundy, J. (1998). HRT, a Novel Zinc Finger, Transcriptional Repressor from Barley. Journal of Biological Chemistry, 273(36), 23313–23320. https://doi.org/10.1074/jbc.273.36.23313,"Tedeschi, F., Rizzo, P., Huong, B. T. M., Czihal, A., Rutten, T., Altschmied, L., Scharfenberg, S., Grosse, I., Becker, C., Weigel, D., Bäumlein, H., & Kuhlmann, M. (2019). EFFECTOR OF TRANSCRIPTION factors are novel plant‐specific regulators associated with genomic DNA methylation in Arabidopsis. New Phytologist, 221(1), 261–278. https://doi.org/10.1111/nph.15439","Ivanov, R., Tiedemann, J., Czihal, A., & Baumlein, H. (2012). Transcriptional regulator AtET2 is required for the induction of dormancy during late seed development. Journal of Plant Physiology, 169(5), 501–508. https://doi.org/10.1016/j.jplph.2011.11.017"	TF
FHA	Hofmann & Bucher (1995): The typical FHA domain comprises approximately 55-75 amino acids and contains three highly conserved blocks separated by more divergent spacer regions.	Durocher, D; Jackson, SP. 2002. The FHA domain. FEBS Lett. 513(1):58-66,"Hofmann, K; Bucher, P. 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem. Sci. 20(9):347-9","Durocher, D; Jackson, SP. 2002. The FHA domain. FEBS Lett. 513(1):58-66","Hofmann, K; Bucher, P. 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem. Sci. 20(9):347-9"	TR
GARP_ARR-B	Tajima et al (2004): In Arabidopsis thaliana, a Histidine-to-Aspartate (His-->Asp) phosphorelay is involved in the signal transduction for propagation of certain stimuli, such as plant hormones. Through the phosphorelay, the type-B phospho-accepting response regulator (ARR) family members serve as DNA-binding transcriptional regulators, whose activities are most likely regulated by phosphorylation/dephosphorylation.	Aoyama, T; Oka, A. 2003. Cytokinin signal transduction in plant cells. J. Plant Res. 116(3):221-31,"D'Agostino, IB; Kieber, JJ. 1999. Phosphorelay signal transduction: the emerging family of plant response regulators. Trends Biochem. Sci. 24(11):452-6","Kakimoto, T. 2003. Perception and signal transduction of cytokinins. Annu Rev Plant Biol 54:605-27","Tajima, Y; Imamura, A; Kiba, T; Amano, Y; Yamashino, T; Mizuno, T. 2004. Comparative studies on the type-B response regulators revealing their distinctive properties in the His-to-Asp phosphorelay signal transduction of Arabidopsis thaliana. Plant Cell Physiol. 45(1):28-39"	TF
GARP_G2-like	Eshed et al (2001): G2-like transcription factors play a role in the establishment of polarity.	Bravo-Garcia, A; Yasumura, Y; Langdale, JA. 2009. Specialization of the Golden2-like regulatory pathway during land plant evolution. New Phytol.,"Eshed, Y; Baum, SF; Perea, JV; Bowman, JL. 2001. Establishment of polarity in lateral organs of plants. Curr. Biol. 11(16):1251-60","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Rossini, L; Cribb, L; Martin, DJ; Langdale, JA. 2001. The maize golden2 gene defines a novel class of transcriptional regulators in plants. Plant Cell 13(5):1231-44"	TF
GeBP	Curaba et al (2003): Trichomes of Arabidopsis are single-celled epidermal hair that are a useful model for studying plant cell fate determination. Trichome initiation requires the activity of the GLABROUS1 (GL1) gene whose expression in epidermal and trichome cells is dependent on the presence of a 3'-cis-regulatory element. Using a one-hybrid screen, we have isolated a cDNA, which encodes for a protein, GL1 enhancer binding protein (GeBP), that binds this regulatory element in yeast and in vitro. GeBP and its three homologues in Arabidopsis share two regions: a central region with no known motifs and a C-terminal region with a putative leucine-zipper motif. We show that both regions are necessary for trans-activation in yeast. A translational fusion with the Yellow Fluorescent Protein (YFP) indicates that GeBP is a nuclear protein whose localization is restricted to, on average, 3-5 subnuclear foci that might correspond to nucleoli. Transcriptional fusion with the GUS reporter indicates that GeBP is mainly expressed in vegetative meristematic tissues and in very young leaf primordia. We looked at GeBP expression in plants mutated in or misexpressing KNAT1, a KNOX gene, expressed in the shoot apical meristem and downregulated in leaf founder cells, and found that GeBP transcript level is regulated by KNAT1 suggesting that KNAT1 is a transcriptional activator of GeBP. This regulation suggests that GeBP is acting as a repressor of leaf cell fate.	Chevalier, F; Perazza, D; Laporte, F; Le Hénanff, G; Hornitschek, P; Bonneville, JM; Herzog, M; Vachon, G. 2008. GeBP and GeBP-like proteins are noncanonical leucine-zipper transcription factors that regulate cytokinin response in Arabidopsis. Plant Physiol. 146(3):1142-54,"Curaba, J; Herzog, M; Vachon, G. 2003. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA-binding activity and is regulated by KNAT1. Plant J. 33(2):305-17"	TF
GIF	Kim & Kende (2004): Previously, we described the AtGRF [Arabidopsis thaliana growth-regulating factor (GRF)] gene family, which encodes putative transcription factors that play a regulatory role in growth and development of leaves and cotyledons. We demonstrate here that the C-terminal region of GRF proteins has transactivation activity. In search of partner proteins for GRF1, we identified another gene family, GRF-interacting factor (GIF), which comprises three members. Sequence and molecular analysis showed that GIF1 is a functional homolog of the human SYT transcription coactivator. We found that the N-terminal region of GIF1 protein was involved in the interaction with GRF1.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <b><a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a></b>","Kim, JH; Kende, H. 2004. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis. Proc Natl Acad Sci U S A. 101(36):13374-9"	TR
GNAT	Vetting et al (2005): The Gcn5-related N-acetyltransferases are an enormous superfamily of enzymes that are universally distributed in nature and that use acyl-CoAs to acylate their cognate substrates. In this review, we will examine those members of this superfamily that have been both structurally and mechanistically characterized. These include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, protein N-myristoyltransferase, and the Fem family of amino acyl transferases.	Vetting, MW; S de Carvalho, LP; Yu, M; Hegde, SS; Magnet, S; Roderick, SL; Blanchard, JS. 2005. Structure and functions of the GNAT superfamily of acetyltransferases. Arch. Biochem. Biophys. 433(1):212-26	TR
GRAS	Li et al (2016): GRAS proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. The structure is a dimer, with a clear groove to accommodate double-stranded DNA.	Bolle, C. 2004. The role of GRAS proteins in plant signal transduction and development. Planta 218(5):683-92,"Richards, DE; Peng, J; Harberd, NP. 2000. Plant GRAS and metazoan STATs: one family? Bioessays 22(6):573-7","Tian, C; Wan, P; Sun, S; Li, J; Chen, M. 2004. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol. 54(4):519-32","Li, S; Zhao, Y; Zhao, Z; Wu, X; Sun, L; Liu, Q; Wu, Y. 2016. Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. Plant Cell. 28(5):1025-34"	TF
GRF	Kim et al (2003): Previously, we identified a novel rice gene, GROWTH-REGULATING FACTOR1 (OsGRF1), which encodes a putative transcription factor that appears to play a regulatory role in stem elongation. We now describe the GRF gene family of Arabidopsis thaliana (AtGRF), which comprises nine members. The deduced AtGRF proteins contain the same characteristic regions--the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains--as do OsGRF1 and related proteins in rice, as well as features indicating a function in transcriptional regulation. Most of the AtGRF genes are strongly expressed in actively growing and developing tissues, such as shoot tips, flower buds, and roots, but weakly in mature stem and leaf tissues. Overexpression of AtGRF1 and AtGRF2 resulted in larger leaves and cotyledons, as well as in delayed bolting of the inflorescence stem when compared to wild-type plants. In contrast, triple insertional null mutants of AtGRF1-AtGRF3 had smaller leaves and cotyledons, whereas single mutants displayed no changes in phenotype and double mutants displayed only minor ones. The alteration of leaf growth in overexpressors and triple mutants was based on an increase or decrease in cell size, respectively. These results indicate that AtGRF proteins play a role in the regulation of cell expansion in leaf and cotyledon tissues.	Kim, JH; Choi, D; Kende, H. 2003. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J. 36(1):94-104	TF
HD_DDT	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"	TF
HD_PHD	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"	TF
HD_PINTOX	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"	TF
HD_PLINC	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"	TF
HD_TALE	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"	TF
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DUF296 domain containing

Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>"

PT

DUF547 domain containing

Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>"

PT

DUF632 domain containing

Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>"

PT

DUF833 domain containing/TANGO2

Richardt et al (2007): This domain has been implicated in transcriptional regulation based on annotation of domain and/or family members.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>"

PT

E2F/DP

de Jager et al (2001): E2F-DP transcription factors are key components of the cyclin D/retinoblastoma/E2F pathway, they regulate the expression of genes required for G1/S transition and S-phase progression.

de Jager, SM; Menges, M; Bauer, UM; Murra, JA. 2001. Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol. 47(4):555-68,"Zheng, N; Fraenkel, E; Pabo, CO; Pavletich, NP. 1999. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev. 13(6):666-74"

TF

EIL

Solano et al (1998): EIN-3-like transcription factors are involved in the ethylene signaling of higher plants.

Solano, R; Stepanova, A; Chao, Q; Ecker, JR. 1998. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 12(23):3703-14,"Yamasaki, K; Kigawa, T; Inoue, M; Yamasaki, T; Yabuki, T; Aoki, M; Seki, E; Matsuda, T; Tomo, Y; Terada, T; Shirouzu, M; Tanaka, A; Seki, M; Shinozaki, K; Yokoyama, S. 2005. Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3. J. Mol. Biol. 348(2):253-64"

TF

ET

Based on the study of (Raventós et al., 1998), the TF family HRT (Hordeum repressor of transcription) was previously integrated into TAPscan. The authors introduced this protein family as proteins containing a gibberellin phytohormone response element and are therefore involved in developmental and phytohormone-responsive regulations (Raventós et al., 1998). However, a more recent study by (Tedeschi et al., 2019) characterized this family as EFFECTORS OF TRANSCRIPTION (ET). ET proteins are plant-specific transcription factors specified by highly conserved ET repeats and a GIY-YIG domain, a DNA single-strand nuclease domain (Tedeschi et al., 2019). In line with (Raventós et al., 1998), also (Ivanov et al., 2012) were able to demonstrate an involvement in the regulation of gibberellin to ensure correct seed development. Moreover, it is suggested that ET proteins are involved in DNA repair (Tedeschi et al., 2019).

Raventós, D., Skriver, K., Schlein, M., Karnahl, K., Rogers, S. W., Rogers, J. C., & Mundy, J. (1998). HRT, a Novel Zinc Finger, Transcriptional Repressor from Barley. Journal of Biological Chemistry, 273(36), 23313–23320. https://doi.org/10.1074/jbc.273.36.23313,"Tedeschi, F., Rizzo, P., Huong, B. T. M., Czihal, A., Rutten, T., Altschmied, L., Scharfenberg, S., Grosse, I., Becker, C., Weigel, D., Bäumlein, H., & Kuhlmann, M. (2019). EFFECTOR OF TRANSCRIPTION factors are novel plant‐specific regulators associated with genomic DNA methylation in Arabidopsis. New Phytologist, 221(1), 261–278. https://doi.org/10.1111/nph.15439","Ivanov, R., Tiedemann, J., Czihal, A., & Baumlein, H. (2012). Transcriptional regulator AtET2 is required for the induction of dormancy during late seed development. Journal of Plant Physiology, 169(5), 501–508. https://doi.org/10.1016/j.jplph.2011.11.017"

TF

FHA

Hofmann & Bucher (1995): The typical FHA domain comprises approximately 55-75 amino acids and contains three highly conserved blocks separated by more divergent spacer regions.

Durocher, D; Jackson, SP. 2002. The FHA domain. FEBS Lett. 513(1):58-66,"Hofmann, K; Bucher, P. 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem. Sci. 20(9):347-9","Durocher, D; Jackson, SP. 2002. The FHA domain. FEBS Lett. 513(1):58-66","Hofmann, K; Bucher, P. 1995. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem. Sci. 20(9):347-9"

TR

GARP_ARR-B

Tajima et al (2004): In Arabidopsis thaliana, a Histidine-to-Aspartate (His-->Asp) phosphorelay is involved in the signal transduction for propagation of certain stimuli, such as plant hormones. Through the phosphorelay, the type-B phospho-accepting response regulator (ARR) family members serve as DNA-binding transcriptional regulators, whose activities are most likely regulated by phosphorylation/dephosphorylation.

Aoyama, T; Oka, A. 2003. Cytokinin signal transduction in plant cells. J. Plant Res. 116(3):221-31,"D'Agostino, IB; Kieber, JJ. 1999. Phosphorelay signal transduction: the emerging family of plant response regulators. Trends Biochem. Sci. 24(11):452-6","Kakimoto, T. 2003. Perception and signal transduction of cytokinins. Annu Rev Plant Biol 54:605-27","Tajima, Y; Imamura, A; Kiba, T; Amano, Y; Yamashino, T; Mizuno, T. 2004. Comparative studies on the type-B response regulators revealing their distinctive properties in the His-to-Asp phosphorelay signal transduction of Arabidopsis thaliana. Plant Cell Physiol. 45(1):28-39"

TF

GARP_G2-like

Eshed et al (2001): G2-like transcription factors play a role in the establishment of polarity.

Bravo-Garcia, A; Yasumura, Y; Langdale, JA. 2009. Specialization of the Golden2-like regulatory pathway during land plant evolution. New Phytol.,"Eshed, Y; Baum, SF; Perea, JV; Bowman, JL. 2001. Establishment of polarity in lateral organs of plants. Curr. Biol. 11(16):1251-60","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Rossini, L; Cribb, L; Martin, DJ; Langdale, JA. 2001. The maize golden2 gene defines a novel class of transcriptional regulators in plants. Plant Cell 13(5):1231-44"

TF

GeBP

Curaba et al (2003): Trichomes of Arabidopsis are single-celled epidermal hair that are a useful model for studying plant cell fate determination. Trichome initiation requires the activity of the GLABROUS1 (GL1) gene whose expression in epidermal and trichome cells is dependent on the presence of a 3'-cis-regulatory element. Using a one-hybrid screen, we have isolated a cDNA, which encodes for a protein, GL1 enhancer binding protein (GeBP), that binds this regulatory element in yeast and in vitro. GeBP and its three homologues in Arabidopsis share two regions: a central region with no known motifs and a C-terminal region with a putative leucine-zipper motif. We show that both regions are necessary for trans-activation in yeast. A translational fusion with the Yellow Fluorescent Protein (YFP) indicates that GeBP is a nuclear protein whose localization is restricted to, on average, 3-5 subnuclear foci that might correspond to nucleoli. Transcriptional fusion with the GUS reporter indicates that GeBP is mainly expressed in vegetative meristematic tissues and in very young leaf primordia. We looked at GeBP expression in plants mutated in or misexpressing KNAT1, a KNOX gene, expressed in the shoot apical meristem and downregulated in leaf founder cells, and found that GeBP transcript level is regulated by KNAT1 suggesting that KNAT1 is a transcriptional activator of GeBP. This regulation suggests that GeBP is acting as a repressor of leaf cell fate.

Chevalier, F; Perazza, D; Laporte, F; Le Hénanff, G; Hornitschek, P; Bonneville, JM; Herzog, M; Vachon, G. 2008. GeBP and GeBP-like proteins are noncanonical leucine-zipper transcription factors that regulate cytokinin response in Arabidopsis. Plant Physiol. 146(3):1142-54,"Curaba, J; Herzog, M; Vachon, G. 2003. GeBP, the first member of a new gene family in Arabidopsis, encodes a nuclear protein with DNA-binding activity and is regulated by KNAT1. Plant J. 33(2):305-17"

TF

GIF

Kim & Kende (2004): Previously, we described the AtGRF [Arabidopsis thaliana growth-regulating factor (GRF)] gene family, which encodes putative transcription factors that play a regulatory role in growth and development of leaves and cotyledons. We demonstrate here that the C-terminal region of GRF proteins has transactivation activity. In search of partner proteins for GRF1, we identified another gene family, GRF-interacting factor (GIF), which comprises three members. Sequence and molecular analysis showed that GIF1 is a functional homolog of the human SYT transcription coactivator. We found that the N-terminal region of GIF1 protein was involved in the interaction with GRF1.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Richardt, S; Lang, D; Reski, R; Frank, W; Rensing, SA. 2007. PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins. Plant Physiol. 143(4): 1452–1466 <a target="_blank" class="awithout" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851845/">PubMed</a>","Kim, JH; Kende, H. 2004. A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis. Proc Natl Acad Sci U S A. 101(36):13374-9"

TR

GNAT

Vetting et al (2005): The Gcn5-related N-acetyltransferases are an enormous superfamily of enzymes that are universally distributed in nature and that use acyl-CoAs to acylate their cognate substrates. In this review, we will examine those members of this superfamily that have been both structurally and mechanistically characterized. These include aminoglycoside N-acetyltransferases, serotonin N-acetyltransferase, glucosamine-6-phosphate N-acetyltransferase, the histone acetyltransferases, mycothiol synthase, protein N-myristoyltransferase, and the Fem family of amino acyl transferases.

Vetting, MW; S de Carvalho, LP; Yu, M; Hegde, SS; Magnet, S; Roderick, SL; Blanchard, JS. 2005. Structure and functions of the GNAT superfamily of acetyltransferases. Arch. Biochem. Biophys. 433(1):212-26

TR

GRAS

Li et al (2016): GRAS proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. The structure is a dimer, with a clear groove to accommodate double-stranded DNA.

Bolle, C. 2004. The role of GRAS proteins in plant signal transduction and development. Planta 218(5):683-92,"Richards, DE; Peng, J; Harberd, NP. 2000. Plant GRAS and metazoan STATs: one family? Bioessays 22(6):573-7","Tian, C; Wan, P; Sun, S; Li, J; Chen, M. 2004. Genome-wide analysis of the GRAS gene family in rice and Arabidopsis. Plant Mol Biol. 54(4):519-32","Li, S; Zhao, Y; Zhao, Z; Wu, X; Sun, L; Liu, Q; Wu, Y. 2016. Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. Plant Cell. 28(5):1025-34"

TF

GRF

Kim et al (2003): Previously, we identified a novel rice gene, GROWTH-REGULATING FACTOR1 (OsGRF1), which encodes a putative transcription factor that appears to play a regulatory role in stem elongation. We now describe the GRF gene family of Arabidopsis thaliana (AtGRF), which comprises nine members. The deduced AtGRF proteins contain the same characteristic regions--the QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) domains--as do OsGRF1 and related proteins in rice, as well as features indicating a function in transcriptional regulation. Most of the AtGRF genes are strongly expressed in actively growing and developing tissues, such as shoot tips, flower buds, and roots, but weakly in mature stem and leaf tissues. Overexpression of AtGRF1 and AtGRF2 resulted in larger leaves and cotyledons, as well as in delayed bolting of the inflorescence stem when compared to wild-type plants. In contrast, triple insertional null mutants of AtGRF1-AtGRF3 had smaller leaves and cotyledons, whereas single mutants displayed no changes in phenotype and double mutants displayed only minor ones. The alteration of leaf growth in overexpressors and triple mutants was based on an increase or decrease in cell size, respectively. These results indicate that AtGRF proteins play a role in the regulation of cell expansion in leaf and cotyledon tissues.

Kim, JH; Choi, D; Kende, H. 2003. The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. Plant J. 36(1):94-104

TF

HD_DDT

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"

TF

HD_PHD

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"

TF

HD_PINTOX

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"

TF

HD_PLINC

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"

TF

HD_TALE

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"

TF

TAP information