BMC Genomics 2006, 7:133 http://www.biomedcentral.com/1471-2164/7/133 Table 7: BMs with target sites on B1_mM and B1_Mus ('Alu Like' sequence in mouse). The scores of the target sites were above T5 (those for which the corresponding ALU BS had scores greater than T5 are in bold). The IUPAC convention [33] consensus sites are in column 2, and the third column shows the target site with the highest score among all the major consensus sequence (nucleotides that agree with the consensus are denoted with capital letters). The location of the putative target sites is in column 4, given for the subfamily on which the target site of column 3 appears. Column 6 lists the number, n, of B1 subfamilies on which the BS shown in column 3 is located. BM name V$ATF6.01 V$ZBRK1_01 V$BRN3.02 V$GKLF_02 V$CRX.01 V$OTX2.01 V$TTF1.01 V$LEF1.02 V$PAX6.02 V$ERR_01 V$GRE.01 V$CP2.02 V$MTATA.01 V$MEF2.04 V$RSRFC4.02 V$MEF2.03 V$RSRFC4.01 V$AMEF2.01 V$FAST1.01 V$HFH8.01 V$XFD2.01 V$HFH1.01 V$HFH2.01 Consensus Binding site SNGCCACNNNNNN CCaCCACGCCCGG SGGGSMRCAGNYMTTTKTK GGtGGCGCAcGCCTTTaaTc KSC CC NNYYWKTAATYWNWY CGCCTTTAATCcCAg NTYAMAGGRN ATTAAAGGcG NNNGATTARNNT TGGGATTAAAGg NNGGATTAANNN TGGGATTAAAGG NNWSTCAAGYRYWN CCTCcCAAGTGCTG NNNWTCAAAGN GTCTaCAAAGT NNAGKKCCAGGNNMG TGAGTTCCAGGACAG NNTCAAGGTCASNN GTTCcAGGaCAGCC NNGGTWCNNNNTGTTCT GTaGccCTGGCTGTcCTGG NR NWCYGSNNMWNNCTNGN CTCTGtATAgCCCTGGCT Y NNNTWTAAANCNNNNNN CTCTgTAtAGCCCTGGC NNTGTTACTAAAAATAGAA AGgGTTtCTctgtATAGccCTG MNN ANKCTAWAAATAGMWNN tTTCTcTgtATAGCcCT NNKWKCTAWAAATAGMN GGTTTCTcTgtATAGCCC N NWKCTAWAAATAGMNN TTTCTcTgtATAGCCC NNNNNTAAAAATANCNN CTGTCTcgAAAaAACAAA N NNTTGTKKATTGGS TTTTGTTTtTTcGa YRNATAAACANN CGAAaAAACAAA NNWATAAACANNN CGAAaAAACAAAA AWATAAACAWTN gAAaAAACAAaA RAANAAAYAWTN GAAAAAACAAaA location B1_Mm (-3:-15) B1_Mm (11:32) B1_Mm (20:34) B1_Mm (-20:-29) B1_Mm (-22:-33) B1_Mm (-22:-33) B1_Mus1 (-33:-46) B1_Mm (83:93) B1_Mm (93:107) B1_Mm (96:109) B1_Mus1 (-100:-118) B1_Mm (-106:-123) B1_Mm (-107:-123) B1_Mm (-109:-130) B1_Mm (-110:-126) B1_Mm (-111:-128) B1_Mm (-111:-126) B1_Mm (129:146) B1_Mm (-134:-147) B1_Mm (135:146) B1_Mm (135:147) B1_Mm (136:147) B1_Mm (136:147) p-val 2.8E-02 2.9E-02 3.9E-02 1.1E-02 7.9E-03 3.0E-04 4.6E-03 1.4E-02 1.0E-05 3.9E-02 1.9E-02 1.7E-02 4.6E-02 3.4E-02 4.9E-02 3.9E-02 4.9E-02 1.1E-02 3.9E-02 1.1E-02 4.5E-02 2.7E-02 2.0E-03 n 1 2 2 2 2 2 1 1 2 2 1 1 1 1 1 1 1 2 2 2 2 2 2 esis is supported by the known suppressory role of GFI1, but the presently known activities on PITX2 and NKX2.5 do not fit this picture. Further experiments that address this issue by measuring the regulatory effects of other Alu- associated developmental TFs are needed. Clearly, many of the genes and their functions date earlier than the rodent/primate divergence, whereas the Alu insertions happened later. This poses an open and debated [20,51] question about the mechanism by which pre-existing reg- ulatory circuits must have been replaced, modified or sup- plemented by Alu insertions. Methods Downloads The Alu consensus sequences were downloaded from Rep- base [29]. Table 8: The nucleotides distribution in the consensus sequences of major Alu subfamilies. ALU name ALU length AluJo AluJb AluSc AluSg AluSp AluSq AluSx AluY 283 283 280 281 284 284 283 282 C 28.62% 28.98% 28.57% 28.83% 28.17% 28.17% 28.98% 28.37% G 33.92% 34.63% 33.57% 34.16% 33.10% 33.45% 33.92% 34.75% T 16.25% 15.55% 15.71% 15.30% 15.85% 15.85% 15.55% 14.89% G + C 62.54% 63.60% 62.14% 62.99% 61.27% 61.62% 62.90% 63.12% Page 12 of 15 (page number not for citation purposes)