As reported in Rodda, D. J., Chew, J-L., Lim, L-H., Loh, Y-H., Wang, B., Ng, H-H., Robson, P. (2005)."Transcriptional Regulation of Nanog by Oct4 and Sox2." The Journal of Biological Chemistry 280(26): 24731-24737 [Table I], six genes are identified as targets of Sox2-Oct4 transcription factors.

Gene Sox element Spacing Oct element Orientation Location (TSS)
Fgf4 CTTTGTT 3 ATGCTAAT Forward 3022
Utf1 CATTGTT 0 ATGCTAGT Reverse 1838
Sox2 CATTGTG 0 ATGCATAT Forward 4041
Fbxo15 CATTGTT 0 ATGATAAA Reverse -523
Nanog CATTGTA 0 ATGCAAAA Reverse -181
Pou5f1 CTTTGTT 0 ATGCATCT Reverse -1991
Using the Create a PWM from sequence aligment tool we create sox2 and oct4 matrixes using the following aligments:

For Sox2

>fgf4_binding_sequence
ctttgtt
>utf1_binding_sequence
cattgtt
>sox2_binding_sequence
cattgtg
>fbxo15_binding_sequence
cattgtt
>nanog_binding_sequence
cattgta
>pou5f1_binding_sequence
ctttgtt

For Oct4

>fgf4_binding_sequence
atgctaat
>utf1_binding_sequence
atgctagt
>sox2_binding_sequence
atgcatat
>fbxo15_binding_sequence
atgataaa
>nanog_binding_sequence
atgcaaaa
>pou5f1_binding_sequence
atgcatct
And search in the Fgf4, Utf1, Sox2, Fbxo15, Nanog and Pou5f1 genes, with the following search parameters:
params

Results

Fgf4

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Fgf4 CTTTGTT 3 ATGCTAAT Forward 3022

INSECT Fgf4

Utf1

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Utf1 CATTGTT 0 ATGCTAGT Reverse 1838

INSECT Utf1

Sox2

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Sox2 CATTGTG 0 ATGCATAT Forward 4041

INSECT Sox2

Fbxo15

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Fbxo15 CATTGTT 0 ATGATAAA Reverse -523

INSECT Fbxo15

Nanog

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Nanog CATTGTA 0 ATGCAAAA Reverse -181

INSECT Nanog

Pou5f1

Reported

GeneSox elementSpacingOct elementOrientationLocation (TSS)
Pou5f1 CTTTGTT 0 ATGCATCT Reverse -1991

INSECT Pou5f1