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Table 5 List of 60 consensus sequences corresponding to selected motifs showing most conserved central regions. For each motif, consensus sequence, length and total number of occurrences in the 1000M dataset are reported, along with LocusLink symbols of corresponding genes. In the last column, for each consensus, the list of mammalian transcription factors recognising similar DNA sequences is reported.

From: A multistep bioinformatic approach detects putative regulatory elements in gene promoters

Consensus sequence Length Total occ. Genes in which promoter the motif was found Transcription factors
AAAAAAAAAAAAAA 14 151 EFEMP1, CCNI, CNGB3, KCNV2, IMPDH2, SLC24A1, DHRS3, G2AN, RTP801, MGC15WIF11, USH3A, CRX, 18, HMGA1, SLC24A2, RDS, TULP1, DC-TM4F2, OPN1SW, RP1, MGAT4B, GAPD, ELOVL4, RRAD, ARR3  
NGGCCCCGCCCCCN 14 114 EEF1G, HMGA1, EFEMP1, CYBA, KRT18, OPA1, DPYSL4, RAX, FLJ1415, MGC15WIF11, FLJ1415, ALMS1, EIF3S8, G2AN, ALMS1, DC-TM4F2, MSH6, RCV1, KRT19, DHRS3, PITPNC1, RRAD, HPCAL1, MGAT4B, SLC38A3, IMPDH2, CNGB1, RDH5, EFEMP1, CRABP1, C7orf20, CCNI, GNB1, CRX, GAPD, ARF4L, AIPL1, DKFZP564K0822 AP-1, GCF, Sp1, Sp3, TFIID
GCACCCCCAGCCCCN 15 101 RHO, G2AN, EFEMP1, SLCO4A1, CYBA, HPCAL1, KIFC3, RCV1, NK4, KRT18, CRX, ARR3, PPP1R3F, MGAT4B, NRL, RRAD, CCNI, SAG, ALMS1, MGC15WIF11, DKFZP564K0822, VMD2, DPYSL4, GNAT1, GAPD, OPN1SW, RAX, DHRS3, COPEB, SLC38A3, TMEM16B, SLC24A1 Sp1
NGAGGGCAGGGGCNN 15 94 GNB1, KRT19, ELOVL4, VMD2, MSH6, HMGA1, RHO, NK4, SLC38A3, LRRCGUCA1B, CYBA, RCV1, RRAD, GUCY2D, MGC15WIF11, AIPL1, MGAT4B, KIFC3, CRX, CRABP1, G2AN, ALMS1, RTP801, EEF1G, COPEB, OPA1, EFEMP1, KCNV2, PDE6A, AOC2, RLBP1, FLJ1415, RAX, DPYSL4, WIF1, DC-TM4F2 Sp1
CCTCCCTCCCTCCC 14 76 ARF4L, COPEB, RHO, SLC38A3, FLJ1415, WDR17, ELOVL4, DHRS3, KCNV2, OPA1, CCNI, GUCA1B, RDH5, RAX, ALMS1, DKFZP564K0822, NK4, RGS19IP1, RRAD, KIFC3, KRT19, SLCO4A1, HPCAL1, DPYSL4, TNFRSF6, CNGB1, DC-TM4F2 MAZ
NCTCCCCCTCCCCC 14 43 CNGB1, GAPD, RPE65, ALMS1, COPEB, MSH6, RRAD, CRABP1, TNFRSF6, CRX, WIF1, FLJ1415, DKFZP564K0822, PDE6A, RDH5, SLC38A3, CYBA, GNB1, MERTK, WDR17 Sp1, AP-2, MAZ
GNNTGGGGGAGGGGN 15 41 CYBA, RLBP1, KCNV2, CNGB1, COPEB, KIFC3, RDH5, CCNI, FLJ1415, MGC15WIF11, AIPL1, NK4, HPCAL1, CNGB1, GUCA1A, ALMS1 MAZ, Sp1
CNCCCCCACCCCCACC 16 40 RCV1, SLC38A3, HPCAL1, KIFC3, RLBP1, RPE65, DHRS3, RTP801, CYBA, DPYSL4, RDH5, RRAD, COPEB AP-2alphaB, Sp1, WT1
CTCCCCCTCCCCNNC 15 26 CNGB1, CRX, GAPD, RHO, CNGB1, COPEB, CYBA, AIPL1, RAX AP-2, MAZ, Sp1
CCCCAGCCCCNCA 13 23 CCNI, EFEMP1, SLCO4A1, MGC15WIF11, ARR3, CYBA, HPCAL1, KIFC3, RAX, RLBP1, MGAT4B, AIPL1, RGS19IP1, ALMS1 Sp1
NNGGCCCCTGCCCN 14 23 HMGA1, NK4, LRRCGUCA1B, FLJ1415, GNB1, KRT19, AIPL1, GUCA1A, DHRS3 Sp1
NCCCCCTCCACCN 13 22 ARR3, HMGA1, KRT19, VMD2, DHRS3, ARF4L, RAX, CCNI, SIRT3, GUCA1B, DC-TM4F2 Sp1
NCNGGGCTGGGGN 13 22 CYBA, HPCAL1, RRAD, GAPD, GUCA1A, RHO, G2AN, EFEMP1 Sp1
NNTCCCCCTCCCNN 14 22 TNFRSF6, CNGB1, CRX, EEF1G, GAPD, RPE65, ALMS1, DKFZP564K0822, COPEB, AIPL1 AP-2alphaB, MAZ, Sp1, WT1 -KTS
NNCCCAGCCCCCAN 14 20 RDH5, SLC38A3, EFEMP1, ARR3, CYBA, GAPD, HPCAL1, NK4, PPP1R3F Sp1
NTGGGGGAGGGGNA 14 20 COPEB, CYBA, RLBP1, PITPNC1, CNGB1, CRX, GAPD, MERTK, CCNI MAZ, Sp1, Sp3
CCNGCCCTGGCCT 13 18 GUCA1A, GUCY2D, RCV1, VMD2, EFEMP1, LRRCGUCA1B, C7orf20, 4, RRAD, UNC119, MERTK Sp1
GCNGCCCCTGCCN 13 18 CRX, CYBA, GNB1, HMGA1, RHO, SLC38A3, MGAT4B, FLJ1415, KRT18  
NCNGGGGGCGGGG 13 18 CYBA, RRAD, FLJ1415, HMGA1, RDH5, RGS19IP1, G2AN, RTP801, DC-TM4F2 AP-1, ER, Sp1
CTNCCCCTCCCC 12 17 RLBP1, AIPL1, PITPNC1, CNGB1, GAPD, RHO, CNGB1, EFEMP1, COPEB, CYBA, GNB1, PDE6A AP-2alphaB, MAZ, Sp1
GGGGTGGGGNTG 12 17 GUCY2D, FLJ1415, AIPL1, RDH5, CRABP1, HPCAL1, KIFC3, DHRS3, RTP801, CYBA, RLBP1 AP-2alphaB, Sp1, Sp3
CCCGCCCCTGNCC 13 16 GNB1, HPCAL1, KRT19, MGAT4B, G2AN, Sp1
NGGGGGTGGGGGN 13 16 HPCAL1, RRAD, DHRS3, FLJ1415, CYBA, GNB1, DPYSL4 Sp1
NNCCCCCGCCCCNN 14 16 GNB1, RGS19IP1, LRRCGUCA1B, ALMS1, DC-TM4F2, KRT18, SAG AP-1, AP-2alphaB, ER, Krox-20, Sp1, WT1, WT1 I, WT1 I -KTS
AGNGGGAGGGGCN 13 14 CYBA, EFEMP1, RAX, MGC15WIF11, ARF4L, CRX, SLCO4A1 MAZ, Sp1, Sp3
CCCTGTCCCTGGAN 14 14 ARR3, HPCAL1, FLJ1415, DC-TM4F2, KRT19, LRRCGUCA1B, TMEM16B GR
CGGGGCCGCCNCN 13 14 FLJ1415, DC-TM4F2, MGC15WIF11, COPEB, MGAT4B, SLCO4A1, RAX CUP, Sp1
CTCTCTCTCCNTN 13 14 GAPD, GUCA1A, NRL, RRAD, FLJ1415, GNAT2, KCNV2  
NANCTCTGCACCC 13 14 LRAT, TNFRSF6, CYBA, KIFC3, DPYSL4, G2AN, RTP801  
NCCGCCCCCGCCN 13 14 GNB1, IMPDH2, SLC38A3, COPEB, CYBA, KRT18, SLCO4A1 AP-1, ER, Kxox-20, Sp1, WT1 I -KTS, WT1-del2
NGGCCTCTGGNCN 13 14 CYBA, GAPD, KRT19, RDH5, DPYSL4, HPCAL1, MGAT4B  
NGGGAGGGGGAAG 13 14 GAPD, AIPL1, FLJ1415, EEF1G, RPE65, ALMS1, WDR17 AP-2alphaB, MAZ, Sp1, WT1 I -KTS
NGNCCCCAGCCCC 13 14 GAPD, GUCA1A, RHO, ARR3, CYBA, NK4, PPP1R3F AP-2, Sp1
NNCCCAGCCCAGNN 14 14 GAPD, RHO, ARR3, CRABP1, CYBA, RRAD, MGAT4B Sp1
TGGGGGTGGGGGN 13 14 HPCAL1, RLBP1, DHRS3, CYBA, HMGA1, RRAD, DPYSL4 Sp1
NGGCGGGGGCGGGG 14 13 EFEMP1, KRT18, RRAD, SLCO4A1, IMPDH2, EFEMP1, COPEB AP-1, Krox-20, Sp1, WT1 I -KTS, WT1-del2
GGNAGGGGCGGG 12 11 ELOVL4, REA, G2AN, GNB1, MSH6, GUCY2D, RGS19IP1, LRRC21, SLCO4A1, PITPNC1 MAZ, Sp1
CCCGCCCGCCCC 12 9 GNB1, RGS19IP1, WIF1, PITPNC1, DC-TM4F2, HMGA1, DPYSL4, KRT18, RAX Sp1
GGGCGGGGCNGG 12 9 CYBA, DPYSL4, MGAT4B, MSH6, RCV1, ALMS1, FLJ1415 ER, GCF, Sp1
GGGCTGGGGGTG 12 9 CYBA, HPCAL1, KIFC3, RCV1, RHO, G2AN, DKFZP564K0822 Sp1
GGGGAAGGGNGG 12 9 TULP1, CRX, MSH6, KRT19, CNGB1, SLC38A3, AIPL1, HMGA1, FLJ1415  
GGGGCGGGCNNG 12 9 EEF1G, KRT19, DC-TM4F2, GUCY2D, RGS19IP1, PITPNC1, C7orf20, RTP801 ER, Sp1
GGNGCGGGCGGG 12 9 HMGA1, KRT19, DPYSL4, DC-TM4F2, RGS19IP1, WIF1, PITPNC1, FLJ1415 AP-2, ETF, Krox-20, Sp1, WT1 I -KTS
GNNGGGGCTGGG 12 9 GAPD, HPCAL1, KIFC3, RCV1, RAX, COPEB, RDH5 WT1 -KTS
CAGGGGGCGGGG 12 8 CYBA, EFEMP1, HPCAL1, FLJ1415, GAPD, HMGA1, G2AN, DC-TM4F2 AP-1, ER, Sp1, Yi
CNCCCCCACCCC 12 8 CYBA, HMGA1, RCV1, SLC38A3, HPCAL1, RLBP1, DHRS3 AP-2alphaB, CACCC-binding, factor, Sp1, WT1
GAGTGGGGGAGG 12 8 DHRS3, KCNV2, COPEB, CYBA, HMGA1, WIF1, FLJ1415, MGC15WIF11  
GCCTGGGGGAGG 12 8 CYBA, SIRT3, KIFC3, CCNI, DKFZP564K0822, DC-TM4F2, MGC15WIF11 AP-2
GGGCAGGGGCNG 12 8 CYBA, GNB1, HPCAL1, HMGA1, RHO, SLC38A3, MGAT4B, G2AN Sp1
GGGCGGGGCTGG 12 8 CYBA, HPCAL1, RAX, MSH6, RCV1, ALMS1, DC-TM4F2 ER, GCF, Sp1
CCCTGTCCCTGG 12 7 CNGB1, GNB1, FLJ1415, KRT19, ELOVL4, TMEM16B, FLJ1415 GR
CCTTCCCCCNGC 12 7 GNB1, SLC38A3, AIPL1, SLCO4A1, RDH5, TULP1, NK4 MAZ
CNCCTCCTGCNC 12 7 CRABP1, GUCA1A, PDE6A, RGR, DPYSL4, WIF1, HPCAL1 PPUR, Sp1
CNGCCCCCAGNC 12 7 RHO, EFEMP1, DC-TM4F2, CNGB1, CYBA, NK4, MERTK Sp1
GCNCCCCTCCCC 12 7 COPEB, CRX, HPCAL1, RGR, CNGB1, MERTK, RAX MAZ, Sp1
GGGCAGGGGCGG 12 7 ELOVL4, HMGA1, HPCAL1, RHO, SLC38A3, MGAT4B, G2AN Sp1
GGGGCTGGGGNC 12 7 ARR3, CYBA, HPCAL1, NK4, RAX, PPP1R3F, RLBP1 AP-2alphaB, Sp1
GNAGGGGGCAGG 12 7 GAPD, NK4, GUCA1B, SLC38A3, WIF1, G2AN, EFEMP1 Sp1
TGGGGGAGGNNA 12 7 KCNV2, COPEB, HMGA1, KIFC3, RDH5, CCNI, FLJ1415 MAZ, Sp1
TTTTTTTTTNTA 12 7 IMPDH2, G2AN, SLC24A2, RTP801, KCNV2, USH3A-PROMB, CCNI TBP