Bioinformatic analysis of putative transcription factor binding sites (oPOSSUM3 single site analysis method) in genes showing the highest downregulation in posterior or anterior tissues of Raldh2−/− embryos.

(a)59 genes analyzed from 63 genes downregulated with FC (b)137 genes analyzed from 146 genes downregulated with FC (c)The searched region encompassed 5 Kb upstream and 5 Kb downstream of the transcription start site. The top ten factors (highest Z-scores) appear in bold. Additional transcription factors (below) are the authors' seelection.(d)Genes with conserved RAR:RXR (DR5) binding sites are: Csn3, Dhrs3, Fap, Meox1, Metrn, Rarb, Stra6, 5730596B20Rik (NB: 5730596B20Rik is an antisense EST found between the Hoxa3 and Hoxa4 genes).(e)Genes with conserved Pax5 binding sites are: Apba2, Crabp2, Lgr5, Mettl1, NKx2-9, Pmm2, Ripply3, Rfx6.(f)Genes with conserved NR2F1 binding sites are: Apba2, Crabp2, Dhrs3, Dusp9, Fap, Gcsh, Hoxa1, Maob, NKx2-9, Pax6, Prdm13, Rarb, Sfrp5, Stra6, Timm8a1, Tmem56, 1700011H14Rik.(g)Genes with conserved STAT1 binding sites are: Apba2, Dbx1, Dhrs3, Fap, Hoxa1, Gcsh, Kynu, Lgr5, Meox1, Pax6, Prdm13, Ptprz1, Rarb, Ripply3, Slc25a10, Snora34, Stra6, Timm8a1, 5730596B20Rik.(h)Genes with conserved PBX1 binding sites are: Ccne1, Dbx1, Fap, Hoxa1, Kynu, Lgr5, Nepn, Nkx2-9, Nkx3-1, Pax6, Prdm13, Rarb, Rfx6, Ripply3, Tmem56.(i)Genes with conserved PPARG:RXRA binding sites are: Apba2, Cpn1, Crabp2, Dbx1, Dhrs3, Dusp9, Gcsh, Hoxa1, Lhx1, Meox1, Mtap7d2, Nkx3-1, Pax6, Prdm13, Ptprz1, Rarb, Sh3bgrl2, Snord118, Stra6, Trmt61a, 1700011H14Rik, 5730596B20Rik.(j)Genes with conserved T binding sites are: Lhx1, NKx2-9, Pmm2, Prdm13, Stra6, Timm8a1, Trmt61a, 5730596B20Rik.(k)Genes with conserved Pax6 binding sites are: Dbx1, Pax6, Rarb, Stra6, 5730596B20Rik.(l)Genes with conserved REST binding sites are: Acsl6, Ank1, Cntnap2, Lhx2, Mpped1.(m)Genes with conserved Pou5fI binding sites are: Abcb10, Acsl6, Ank1, Apba2, Arrdc4, Aven, Cdh20, Cntnap2, Dhrs11, Gas5, Htr3b, Ikzf1, Lhx2, Mrpl18, Muc1, Neto2, Nova1, Nr2e1, Pak3, Pcdh19, Prdm16, Rragb, Shox2, Slc25a21, Taf1d, Wnt7a.(n)Genes with conserved NR3C1 binding sites are: Cntnap2, Eef1d, Fez1, Hsd17b7, Htr3b, Itgb8, Klf1, Lrcc4, Lhx2, Mpped1, Mrpl20, Nova1, Nsdhl, Pcdh19, Pdss1, Phyhipl, Pou3f3, Rnf144b, Shox2, Syt11, AI504432.Transcription factor binding site (TFBS) analysis: genes downregulated in POSTERIOR tissues.(a)TFBS analysis: genes downregulated in ANTERIOR tissues.(b)