Data set 3 - 7 ACTB genes and 13 randomly picked genes

Data set 3 consists of the 7 ACTB upstream sequences complemented by 13 randomly picked upstream sequences from the EPD. The 20 sequences are given below in Fasta format with corresponding EPD or GenBank accession numbers. The three promoter motifs, V$MTATA, V$SRF, and V$CAAT, at present associated with beta-actin gene regulation, are highlighted in orange, red, and green respectively.

7 ACTB (beta-actin) upstream regions 

> GG_ACTB Gallus gallus ACTB (EP07061)
GCGGCGGCAGCCAATCAGAGCGGCGCGCTCCGAAAGTTTCCTTTTATGGCGAGGCGGCGG
CGGCGGCGGCCCTATAAAAAGCGAAGCGCGCGGCGGGCGGGAGTCGCTGCGTTGCCTTCG
CCCCGTGCCCCGCTCCGCGCCGCCTCGCGC
> HS_ACTB Homo sapiens ACTB (EP17045)
AGCGGCGCGGGGCCAATCGCGTGCGCCGTTCCGAAAGTTGCCTTTTATGGCTCGAGCGGC
CGCGGCGGCGCCCTATAAAACCCAGCGGCGCGACGCGCCACC
> RN_ACTB Rattus norvegicus (EP07062)
CGAGCCGGAGCCAATCAGCGCCCGCCGTTCCGAAATTGCCTTTTATGGCTCGAGTGGCCG
CTGTGGCGTCCTATAAAACCCGGCGGCGCAACGCGCGCCACTGTCGAGTCCGCGTCCACC
CGCGAGTACAACCTCCTTGCAGCTCCTCCG
> CG_ACTB Cricetulus griseus ACTB (U20114: 41-191)
GAGGGGAGAGGGGGTAAAAAAATGCTGCACTGTGCGGCTAGGCCGGTGAGTGAGCGGCGC
GGAGCCAATCAGCGCTCGCCGTTCCGAAAGTTGCCTTTTATGGCTCGAGTGGCCGCTGTG
GCGTCCTATAAAACCCGGCGGCGCAACGCGC
> MM_ACTB Misgurnus mizolepis ACTB (AF270649: 3177-3327)
GACTGGCCAATCACATCGCTCGATGCCGAAAGTTTACCTTATATGGAAGGAGTCGACCGC
CGCACCGGGTATAAAAATAGTGACCCGCCTCACGCTCGGTATTGTGAGTTTTCAGTGCAC
GCTGAGAAGAGCTTTCTTTCTTGTTCACAAT
> MA_ACTB Megalobrama amblycephala ACTB (AY170122: 1816-1966)
TGACGCTGGACCAATCAGAGCGCAGAGCTCCGAAAGTTTACCTTTTATGGCTAGAGCCGG
GCATATGCCGTCATATAAAAGAGCTCGCCCAGCCTTTCAACCTCACTTTGAGCTCCTCCA
CACGCAGCTAGTGCGGAATATCATCAGCTTG
> OL_ACTB Oryzias latipes ACTB (S74868: 744-994)
ACGCTGGACCAATCACATGCCGCGATTCCGAAAGTTTACCTTTTATGGAAAGAGCCGGGC
AACGGACGGACTATAAATACCACGTGCCCACGGCTAGCAAATTCACTCTGAGCGCCGTCA
CACACAGCTTGTGCGGATATCATTCGCCTGA

13 randomly picked upstream regions 

> HS_SR Homo sapiens SR (EP73476)
AAGGTGCCCGGGCCGCTCCGATTGGTCAGGGCGAGCCGTACCACGGCGGTGGCGGGGGAG
CGCTTCGTGGGCAGCCGGCGGGCTCCGAGGCCGTGAGCGCAAAGCCTCAGGCCCCGGCTC
CCTCCTGAGCTGCGCCGTGCCAGGCCGCCCG
> HS_APOD Homo sapiens APOD (EP73483)
CCCTCCTGACTGGATGGGGGCGGCGGGCGTGGCATGCATGAAAAGTAAACATCAGAGACC
TGAAGAAGCTTATAAAATAGCTTGGGAGAGGCCAGTCACCAAGACAGGCATCTCAAATCG
GCTGATTCTGCATCTGGAAACTGCCTTCATC
> HS_CFL1 Homo sapiens CFL1 (EP73520)
CGGACTCCATTTCCCGTCGGCTCGCGGTGGGAGCGCCGGAAGCCCGCCCCACCCCTCATT
GTGCGGCTCCTACTAAACGGAAGGGGCCGGGAGAGGCCGCGTTCAGTCGGGTCCCGGCAG
CGGCTGCAGCGCTCTCGTCTTCTGCGGCTCT
> HS_SDHA Homo sapiens SDHA (EP73493)
GCGATGTCCCCCACTGCAGCCCCGCTCGACTCCGGCGTGGTGCGCAGGCGCGGTATCCCC
CCTCCCCCGCCAGCTCGACCCCGGTGTGGTGCGCAGGCGCAGTCTGCGCAGGGACTGGCG
GGACTGCGCGGCGGCAACAGCAGACATGTCG
> HS_CNN1 Homo sapiens CNN1 (EP73481)
CCCCGCCCCTTGGCAGGCCCCTACAGCCAATGGAACGGCCCTGGAAGAGACCCGGGTCGC
CTCCGGAGCTTCAAAAACATGTGAGGAGGGAAGAGTGTGCAGACGGAACTTCAGCCGCTG
CCTCTGTTCTCAGCGTCAGTGCCGCCACTGC
> HS_VAMP3 Homo sapiens VAMP3 (EP73496)
CACCCACCCACGACGCCCCCGCCCACTTCCGGCGCGCCCCCTCTTCGCCCCGCCCACTCC
CCCGGCTCCGCCTAGTGACGTCTTTGCCCCGCGCCGCGCCGTCCCACCCATCTCCCTGGC
CTCCGGTCCCAACTTCGCTTCTCTGCTGACC
> HS_GBP2 Homo sapiens GBP2 (EP73490)
GTTCCTGGTTGAGAAATCATGACAAACCCTCTTACCAGCACAGCTGTCAACAATTCCTTT
TATGGTGAATGAGTCACTGCTTTAGTTGATACTTTGTTTCATATTAGTGCATTTCTTTGC
AGAGGTTACCTCTTTTTCTTGTCTCTCGTCA
> HS_TOM1 Homo sapiens TOM1 (EP73502)
GTGGTCGAGCTTCGCGGTGCCACCGCCCCGCCCACGCCTCCTCGCCGGCCTCCGAGTGCG
TCACGTGACGGGTCGGTGGCGCTGGCGGTTGCTGTCAGCTGATTCCCGGGGTTGGTGGCA
GCGGCGGTAGCAGCAATGGACTTTCTCCTGG
> HS_BNIP3 Homo sapiens BNIP3 (EP73504)
CGCAGGCCCCAAGTCGCGGCCAATGGGCGACGCGGCCGCAGATCCGCCCGGCCCCGCCCT
GCCCTGTGAGTTCCTCCGGCCGGGCTGCGGGGCTCCGCTCAGTCCGGGAGCGCAGCTGGG
CCGCGGCGCTCCGACCTCCGCTTTCCCACCG
> HS_LHFP Homo sapiens LHFP (EP73465)
GGGGCGCGAGGGGAGGGGACTGGAGAAAGAGGAGGGCCGGGCAGCGGAGGGGAGGAGGCG
GTGCGTGCCTCGCCTGCCAAAGGGAGATCCGCTCCTCTGCGTGCGATCCCCGGCGCCCGC
GCGCGCCCACAGCGCTCCGCCAGAGCTGCCG
> HS_PLS3 Homo sapiens PLS3 (EP73498)
CTAGCACCACCCGAGCCAATGGCGGCGGCCGAGGGGCGGAGGGGGCTGGCAGGAGGGGAG
GGAGCGCTGGCTTTAGAGCCACAGCTGCAAAGATTCCGAGGTGCAGAAGTTGTCTGAGTG
CGTTGGTCGGCGGCAGTCGGGCCAGACCCAG
> HS_SGK Homo sapiens SGK (EP73475)
AGGGGCGAGGCGAAGGGCGGGGCCACTTCTCACTGTCGCGCAGGCCCCGCCCCCGCGGCG
GTGCCTTTTTTATAAGGCCGAGCGCGCGGCCTGGCGCAGCATACGCCGAGCCGGTCTTTG
AGCGCTAACGTCTTTCTGTCTCCCCGCGGTG
> HS_CEPT1 Homo sapiens CEPT1 (EP73479)
CCGGCCGGCCCCGGGGCGCGCTCACGGCACCGAGGAGCGCGCCTGCGGCGCTGCTCGTTC
AAACCTTGTTCCCCTTTACGGCAATCGCGAAAGTGTCGTGAACGTGCTGCCGCCGATCAG
TCACCCAGTCGGCTGGAGTCGGAGGCGATAT

Table listing all TRANSFAC TF-matrices found in the set of 20 promoter sequences

The table below lists all promoter motifs found in the 20 upstream sequences of data set 3. The promoter motifs are sorted from left to right according to their total appearance in the dataset. Highlighted are the three promoter motifs (V$CAAT, V$MTATA, and V$SRF) at present associated with beta-actin gene regulation in addition to the three promoter motifs (V$NFY, V$TATA, V$TCF4) completing the promoter module consisting of 6 promoter motifs detected by the genetic algorithm.

V$CAAT V$NFY V$E2F1 V$TFIIA V$MAZ V$HNF4 V$TATA V$MTATA V$SRF V$TCF4 V$LEF1 V$SP3 V$CDX2 V$GATA4 V$USF V$VMYB V$KROX V$MINI20 V$PBX V$E2F V$AP1 V$HNF1 V$RFX1 V$CREB V$TCF1P V$PAX V$OCT1 V$CREL V$MEF2 V$DEAF1 V$MYCMAX V$MAZR V$CREBATF V$BACH2 V$TFIII V$DEC V$CETS1P54 V$ELK1 V$ARNT V$CDC5 V$CETS168 V$NMYC V$CEBPDELTA V$GFI1 V$PIT1 V$COMP1 V$PAX3 V$HNF3B V$CP2 V$NRF2 V$MMEF2 V$AHRARNT V$PAX9 V$FOX V$GABP V$HNF3ALPHA V$FOXO1 V$NFKB V$BRN2 V$VMAF V$LEF1TCF1 V$HP1SITEFACTOR V$WHN V$OSF2 V$ATF3 V$ATF4 V$FOXD3 V$NGFIC V$SMAD3 V$HAND1E47 V$SREBP1 V$SOX5 V$CDPCR1 V$CMYB V$ALPHACP1 V$STRA13 V$FREAC2 V$ELF1 V$MRF2 V$E2F1DP1 V$FOXP3 V$PTF1BETA V$ATF1 V$AMEF2 V$FOXO4 V$CEBPGAMMA V$SMAD4 V$EGR2 V$AHR V$ARP1 V$EFC V$XFD3 V$IRF7 V$ATF V$HLF V$TGIF V$HIF1 V$EGR3 V$SOX9 V$GCM V$MYC V$MAX V$ER V$LDSPOLYA
GG_ACTB 1 1 1 1 0 0 1 1 1 1 1 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
HS_ACTB 1 1 1 0 0 0 1 1 1 1 1 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RN_ACTB 1 1 1 1 0 0 1 1 1 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
CG_ACTB 1 1 0 1 1 0 1 1 1 1 1 0 1 0 0 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MM_ACTB 1 1 0 1 0 1 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MA_ACTB 1 1 0 0 0 1 1 1 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
OL_ACTB 1 1 0 1 0 1 1 1 1 1 0 0 0 0 1 1 0 0 1 0 0 0 1 0 0 0 1 1 0 0 1 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0
HS_SR 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
HS_APOD 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 1 0 0 1 1 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 1 1 1 1 1 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
HS_CFL1 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
HS_SDHA 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_CNN1 1 1 0 1 1 0 0 0 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_VAMP3 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0
HS_GBP2 0 0 0 1 0 0 1 0 1 1 1 0 0 1 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0
HS_TOM1 0 0 1 0 0 1 0 0 0 0 0 1 0 0 1 0 1 1 0 1 1 0 0 1 0 0 0 0 0 1 0 0 1 1 0 1 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
HS_BNIP3 1 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_LHFP 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_PLS3 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_SGK 0 0 1 1 1 1 0 1 0 1 0 1 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_CEPT1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Sum 12 11 9 9 9 8 8 8 8 8 7 6 6 6 6 6 6 5 5 5 4 4 4 4 4 4 4 4 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1