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 |