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Table 3 Annotated list of non-anthocyanin pathway genes in the maize genome with promoters containing all 5 of the anthocyanin/phlobaphene-related motifs predicted by Promzea (Motifs 1–5)

From: Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas

Maize ID Annotation (PFAM ID, Maize GDB)
Branched amino acid phenylpropanoid pathway  
GRMZM2G153536 Aminotransferase class IV -- Branched-chain-amino-acid aminotransferase
GRMZM2G055899 Aminotransferase class IV (branched-chain amino acid aminotransferase 5)
GRMZM2G074604 Phenylalanine ammonia lyase 1 (PAL1)
Putative light signaling  
GRMZM2G104920 COP1, putative; Zinc finger, C3HC4 type (RING finger)
GRMZM2G062541 HLH DNA-binding domain related to phytochrome interacting factor 3 (PIF3)
Putative gibberellin  
GRMZM2G013016 Gibberellin response modulator protein (GRAS family transcription factor)
GRMZM2G021051 2OG-Fe(II) oxygenase superfamily related to gibberellin 20 oxidase
GRMZM2G026095 Carboxylesterase family related to gibberellin receptor GID1L2
Sugar  
AC211474.3_FG006 GDP-fucose protein O-fucosyltransferase
GRMZM2G018022 UTP-glucose-1-phosphate uridylyltransferase
GRMZM2G021243 GDP-fucose protein O-fucosyltransferase
GRMZM2G035749 Glycosyl hydrolase family 14
GRMZM2G050273 Raffinose synthase or seed inhibition protein Sip1
GRMZM2G074462 Starch binding domain
GRMZM2G082037 UDP-glucoronosyl and UDP-glucosyl transferase related to Flavonol 3-O- glucosyltransferase
GRMZM2G176630 Galactosyltransferase
GRMZM2G178278 Galactosyltransferase
GRMZM2G368827 Sugar efflux transporter for intercellular exchange/MTN3 family protein
Transporter  
AC206030.4_FG001 Drug transmembrane transporter
GRMZM2G094490 ABC-2 type transporter domain containing protein
GRMZM2G361066 ABC-2 type transporter
Regulatory  
GRMZM2G074373 bZIP transcription factor
GRMZM2G366434 AP2-like ethylene-responsive transcription factor PLETHORA 2
GRMZM2G459540 C2H2-like zinc finger protein
GRMZM2G018631 Zinc finger, C3HC4 type (RING finger)
AC196161.3_FG002 Transcription factor
GRMZM2G356718 Myb-like DNA-binding domain and Protein Phosphatase 2C
GRMZM2G398758 Myb-like DNA-binding domain
GRMZM2G027253 B3 DNA binding domain
GRMZM2G109627 No apical meristem (NAM) protein
AC203972.3_FG001 NB-ARC domain
GRMZM2G088140 G-box binding protein MFMR
GRMZM2G063961 Protein kinase domain
GRMZM2G142390 Protein kinase domain
GRMZM2G166719 Protein kinase domain
GRMZM2G163297 RNA recognition motif.
GRMZM2G459746 RNA recognition motif
GRMZM2G005622 F-box family protein
AC209810.3_FG002 Cysteine protease
Ribosomal  
GRMZM2G018403 Ribosomal prokaryotic L21 protein
GRMZM2G135095 Ribosomal protein S18
GRMZM2G170420 Ribosomal family S4e
GRMZM5G861978 Chloroplast 50S ribosomal protein L22
Chaperone  
GRMZM2G005753 DnaJ domain (Chaperone)
GRMZM2G085934 Hsp20/alpha crystallin family chaperone
GRMZM2G434839 DnaJ central domain (Chaperone)
Cell trafficking  
AC155377.1_FG001 Myosin family protein
GRMZM2G044348 Signal peptide peptidase
GRMZM2G047214 Nuclear Pore Localization 4 (NPL4) family protein
GRMZM2G077696 Regulator of Vps4 ATPase activity in the MVB sorting pathway
GRMZM2G095441 Syntaxin
GRMZM2G113319 Myosin family protein
GRMZM2G115775 SNARE domain
Cytochrome P450 oxidoreductase  
GRMZM2G394783 Oxidoreductase
AC217947.4_FG002 NADPH cytochrome P450 reductase
GRMZM2G106650 Cytochrome P450
GRMZM2G147245 Cytochrome P450 related to cinnamate-4-hydroxylase
GRMZM2G415579 NAD(P)H-dependent oxidoreductase
Heme  
GRMZM2G025031 Uroporphyrinogen decarboxylase (URO-D), 5th step in heme biosynthesis
GRMZM2G071745 Cytochrome b5-like Heme/Steroid binding domain
GRMZM2G028986 Cytochrome b5-like Heme/Steroid binding domain
Cell wall or modification  
GRMZM2G110145 Cellulose synthase
GRMZM2G113057 Hydroxyproline-rich glycoprotein family protein
GRMZM2G336879 Pectinacetylesterase
GRMZM2G352381 Pectinacetylesterase
Other  
AC209810.3_FG002 Cysteine protease
GRMZM2G312061 Cystatin domain and phloem filament protein PP1, proteinase inhibitor
GRMZM2G325008 Cystatin domain and phloem filament protein PP1, proteinase inhibitor
GRMZM2G004188 Nuclear excision repair XPG N-terminal domain
GRMZM2G021277 Pyridoxal-dependent decarboxylase conserved domain
GRMZM2G027241 Abscisic acid responsive TB2/DP1, HVA22 family
GRMZM2G027851 Sodium/hydrogen exchanger family
GRMZM2G043749 Uncharacterised protein family (UPF0041)
GRMZM2G047412 Chromosome segregation protein Spc25
GRMZM2G070279 Short chain dehydrogenase
GRMZM2G125448 Transferase family
GRMZM2G129979 G10 protein
GRMZM2G143703 Hydrolase, alpha/beta fold family protein
GRMZM2G146207 Tetratricopeptide repeat containing protein
GRMZM2G152370 WD domain, G-beta repeat
GRMZM2G168675 Late embryogenesis abundant protein
GRMZM2G176129 NADH dehydrogenase transmembrane subunit
GRMZM2G325575 Ferritin-1, iron storage, chloroplastic precursor
GRMZM2G348039 Mitochondrial fission ELM1
GRMZM2G465046 GDSL-like Lipase/Acylhydrolase
GRMZM2G472236 Seed maturation protein/LEA
GRMZM5G838435 Hydrolase, alpha/beta fold family domain
GRMZM5G890241 Leucine rich repeat containing protein