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Table 1 Predicted lengths and C-terminal motifs of spruce MYB proteins

From: Conifer R2R3-MYB transcription factors: sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca)

Sg1   Full length cDNA2 DNA Binding Domain3 C-terminal Domain3 Motifs Consensus sequences Angio-Gymno4 MEME E-value Start motif5 Ref.
4 Pg MYB5 -b- 115 142 F LlsrGiDP(at)tHrp(li)n 13/13-5/5 6.00e-14 1 a)
      G e(re)cpdLNLel(cr)ispp 13/13-4/5 3.31e-16 67 a), b)
  Pg MYB10 -a- 115 95 F LlsrGiDP(at)tHrp(li)n 13/13-5/5 6.52e-14 1 a)
      G e(re)cpdLNLel(cr)ispp 13/13-4/5 4.32e-15 67 a), b)
  Pg MYB13 -b- 116 80 F LlsrGiDP(at)tHrp(li)n 13/13-5/5 1.18e-14 1 a)
      G e(re)cpdLNLel(cr)ispp 13/13-4/5 5.43e-14 65 a), b)
22 Pg MYB6 -a- 115 235 H (cs)s(sv)DPpT(ls)LsLslPg 7/7-14/14 2.02e-14 99 d)
      I YlkaedaismmsaAv 0/7-13/14 1.87e-13 141 d)
      J vmremvakEVrsYmn 7/7-14/14 1.07e-17 188 a), b), c)
  Pg MYB7 -c- 116 257 K egdyEVesrgLKRln 0/7-13/14 1.34e-12 43 d)
      H (cs)s(sv)DPpT(ls)LsLslPg 7/7-14/14 4.28e-13 113 d)
      I YlkaedaismmsaAv 0/7-13/14 2.30e-10 161 d)
      J vmremvakEVrsYmn 7/7-14/14 6.15e-16 206 a), b), c)
  Pg MYB9 -a- 119 297 K egdyEVesrgLKRln 0/7-13/14 6.03e-16 60 d)
      P hRQSAFksYesqktp 0/7-11/14 1.19e-13 116 d)
      H (cs)s(sv)DPpT(ls)LsLslPg 7/7-14/14 2.91e-13 144 d)
      I YlkaedaismmsaAv 0/7-13/14 9.50e-16 205 d)
      J vmremvakEVrsYmn 7/7-14/14 1.09e-16 256 a), b), c)
8 Pg MYB1 -b- 115 217 A lr(kq)mGiDP(lv)THkpl 5/5-2/2 1.79e-18 1 a)
21 Pg MYB3 -c- 130 177 C (fg)Re(rq)S(rs)(is)(rg)(kr)R 4/5-2/2 4.69e-14 1 d)
      D e(en)s(l)(vs)(pt)ffDfl(g)vG(cn) 5/5-2/2 1.26e-13 35 a), b)
      E (cy)xi(sg)h(in)nh(v)q(sf)(jr)Kef 3/5-2/2 4.76e-14 123 d)
13 Pg MYB8 -c- 115 411 L LrrGIDP(n)THkpl 4/4-2/2 2.54e-17 1 a)
      M VC(dv)(yk)(np)SIm(al)nPsm(yn) 2/4-2/2 1.94e-18 199 d)
      N e(ye)(ae)vKWSEml 2/4-2/2 6.45e-14 317 d)
      O (pk)D(fl)(hq)R(im)Aa(vs)(lf)(dg)q 2/4-2/2 4.89e-15 399 a)
9 Pg MYB11 -a- 115 384 Q L(lv)kMGIDPvTHkp(k) 6/6-1/1 4.08e-16 1 a), b), c)
      R h(m)AQWEsARleAear 6/6-1/1 3.10e-13 35 a), b), c)
      S (yc)eDnknYw(nd)silnlV 4/6-1/1 6.79e-12 360 c)
2 Pg MYB12 -a- 115 254 T MdfW(fl)(dn)v(fl)(t) 5/5-1/1 2.39e-09 237 a)
nd Pg MYB2 -c- 115 333 B (c)SylPPL(y)d(v) 2/2-2/2 3.29e-13 249 d)
  Pg MYB4 -c- 120 214 none none 0/3-0/2 none none none
  1. Conserved amino acid regions were identified in angiosperm and gymnosperm C-terminal sequences by the use of MEME software (setting described in Methods). Motifs were detected among the sequences belonging to each phylogenetic clade comprised of at least one spruce MYB (Additional File 2). Sequences from Additional File 3 were used to identify more conifer members of the PgMYB6, 7, 9 clade. Within the consensus sequences, upper-case letters indicate amino acids found in all members of a subgroup, lower-case letters indicate amino acids conserved in more than 50% of the members, pairs of lower-case amino acid in brackets show the two most abundant amino acids present for 50% each and above, x indicates that no amino acid is conserved among the sequences.
  2. 1Sg, MYB subgroups identified by Kranz et al. [18].
  3. 2Source of full length cDNA sequence: -a-, full length cDNA clone identified from EST of Picea glauca database; b- partial cDNA clone identified from EST database of P. glauca, extended by RACE amplifications and finally amplified as a single clone by PCR with gene specific primers, and -c-, from non degenerates primers based on Pinus taeda MYB sequences and used on spruce cDNA followed by RACE amplifications.
  4. 3Lengths are expressed in amino acid (aa) residues.
  5. 4The number of MYB sequences, separately from angiosperm and gymnosperms, sharing the motif among all those used in each case.
  6. 5The position of the motif relative to the beginning of the C-terminal domain (5' end).
  7. Ref: references for previously reported motifs, a) Kranz et al. [18], b) Stracke et al. [31] and c) Jiang et al. [30] and d) new motifs.