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 | Consensus | Binding site | location | p-val | n |
|---|---|---|---|---|---|
V$ATF6.01 | SNGCCACNNNNNN | CCaCCACGCCCGG | B1_Mm (-3:-15) | 2.8E-02 | 1 |
V$ZBRK1_01 | SGGGSMRCAGNYMTTTKTKKSC | GGtGGCGCAcGCCTTTaaTcCC | B1_Mm (11:32) | 2.9E-02 | 2 |
V$BRN3.02 | NNYYWKTAATYWNWY | CGCCTTTAATCcCAg | B1_Mm (20:34) | 3.9E-02 | 2 |
V$GKLF_02 | NTYAMAGGRN | ATTAAAGGcG | B1_Mm (-20:-29) | 1.1E-02 | 2 |
V$CRX.01 | NNNGATTARNNT | TGGGATTAAAGg | B1_Mm (-22:-33) | 7.9E-03 | 2 |
V$OTX2.01 | NNGGATTAANNN | TGGGATTAAAGG | B1_Mm (-22:-33) | 3.0E-04 | 2 |
V$TTF1.01 | NNWSTCAAGYRYWN | CCTCcCAAGTGCTG | B1_Mus1 (-33:-46) | 4.6E-03 | 1 |
V$LEF1.02 | NNNWTCAAAGN | GTCTaCAAAGT | B1_Mm (83:93) | 1.4E-02 | 1 |
V$PAX6.02 | NNAGKKCCAGGNNMG | TGAGTTCCAGGACAG | B1_Mm (93:107) | 1.0E-05 | 2 |
V$ERR_01 | NNTCAAGGTCASNN | GTTCcAGGaCAGCC | B1_Mm (96:109) | 3.9E-02 | 2 |
V$GRE.01 | NNGGTWCNNNNTGTTCTNR | GTaGccCTGGCTGTcCTGG | B1_Mus1 (-100:-118) | 1.9E-02 | 1 |
V$CP2.02 | NWCYGSNNMWNNCTNGNY | CTCTGtATAgCCCTGGCT | B1_Mm (-106:-123) | 1.7E-02 | 1 |
V$MTATA.01 | NNNTWTAAANCNNNNNN | CTCTgTAtAGCCCTGGC | B1_Mm (-107:-123) | 4.6E-02 | 1 |
V$MEF2.04 | NNTGTTACTAAAAATAGAAMNN | AGgGTTtCTctgtATAGccCTG | B1_Mm (-109:-130) | 3.4E-02 | 1 |
V$RSRFC4.02 | ANKCTAWAAATAGMWNN | tTTCTcTgtATAGCcCT | B1_Mm (-110:-126) | 4.9E-02 | 1 |
V$MEF2.03 | NNKWKCTAWAAATAGMNN | GGTTTCTcTgtATAGCCC | B1_Mm (-111:-128) | 3.9E-02 | 1 |
V$RSRFC4.01 | NWKCTAWAAATAGMNN | TTTCTcTgtATAGCCC | B1_Mm (-111:-126) | 4.9E-02 | 1 |
V$AMEF2.01 | NNNNNTAAAAATANCNNN | CTGTCTcgAAAaAACAAA | B1_Mm (129:146) | 1.1E-02 | 2 |
V$FAST1.01 | NNTTGTKKATTGGS | TTTTGTTTtTTcGa | B1_Mm (-134:-147) | 3.9E-02 | 2 |
V$HFH8.01 | YRNATAAACANN | CGAAaAAACAAA | B1_Mm (135:146) | 1.1E-02 | 2 |
V$XFD2.01 | NNWATAAACANNN | CGAAaAAACAAAA | B1_Mm (135:147) | 4.5E-02 | 2 |
V$HFH1.01 | AWATAAACAWTN | gAAaAAACAAaA | B1_Mm (136:147) | 2.7E-02 | 2 |
V$HFH2.01 | RAANAAAYAWTN | GAAAAAACAAaA | B1_Mm (136:147) | 2.0E-03 | 2 |