Data set 1 - 7 ACTB genes and 13 randomly picked genes

Data set 1 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_PU16 Homo sapiens PU16 (EP17030)
GTGTCAGGGCTAGGAAGGCTCGGGGGTGCGCGGGGCAAGTGACCATGTGTGTAAAGGGTG
AGGTATATGGAGCTGTGACAGGGCAGAAGTGTGTGAAGTCATACTTACCTGGCAGGGGAG
ATACCATGATCACGAAGGTGGTTTTCCCAGG
> HS_RPS14 Homo sapiens RPS14 (EP24040)
ATAATGCCGGCGTCTTCCGGAACCCGACCTCGCCCCGTGACCTCAGAGGTATACTTCCGG
GACACGGAAGTGACCCCCGTCGCTCCGCCCTCTCCCACTCTCTCTTTCCGGTGTGGAGTC
TGGAGACGACGTGCAGGTAGGAGCCCGGGCG
> HS_TUBA1 Homo sapiens TUBA1 (EP14030)
GGCTGTGTTATCCGAGAGATCTTTCGGGGGCCGCGGGCAGCCCGTCCTGCCGCGACCGAG
GGTCTGGGCGTCCCGGCTGGGCCCCGTGTCTGTGCGCACGGTTTCGCTGATGCTGAGGGG
CCACTTTCTGTCTCGCGTTGTTCTCTGGGGA
> HS_FN1 Homo sapiens FN1 (EP16038)
GGCGGGGCGGGGACAGCCCGGCGGGTCTCTCCTCCCCCGCGCCCCGGGCCTCCAGAGGGG
CGGGAGGGCCGTCCCATATAAGCCCGGCTCCCGCGCTCCGACGCCCGCGCCGGCTGTGCT
GCACAGGGGGAGGAGAGGGAACCCCAGGCGC
> HS_TK1 Homo sapiens TK1 (EP25035)
TCCCGCCAGGTCAGCGGCCGGGCGCTGATTGGCCCCATGGCGGCGGGGCCGGCTCGTGAT
TGGCCAGCACGCCGTGGTTTAAAGCGGTCGGCGCGGGACCAGGGGCTTACTGCGGGACGG
CCTTGGAGAGTACTCGGGTTCGTGAACTTCC
> HS_IL2 Homo sapiens IL2 (EP07114)
GTAAAGTCTTTGAAAATATGTGTAATATGTAAAACATTTTGACACCCCCATAATATTTTT
CCAGAATTAACAGTATAAATTGCATCTCTTGTTCAAGAGTTCCCTATCACTCTCTTTAAT
CACTACTCACAGTAACCTCAACTCCTGCCAC
> HS_TFRC Homo sapiens TFRC (EP15041)
TCGCGAGCGTACGTGCCTCAGGAAGTGACGCACAGCCCCCCTGGGGGCCGGGGGCGGGGC
CAGGCTATAAACCGCCGGTTAGGGGCCGCCATCCCCTCAGAGCGTCGGGATATC
> HS_ELK1 Homo sapiens ELK1 (EP59011)
TTCCCCTTACGCCAATCACGGCACAGCTCTGTAGGGAAGGGCCCGTCCCCCAACCCCTCG
AGGCCTTGCGGCCGATTAATAGCGCTTTGGCCAATCAGCGAGCGGCGGGACATTGGGCTC
CTCCTCCTCGGGCCCACGTGAGCTGTAGGGA
> HS_CARS Homo sapiens CARS (EP73102)
GCCGGCGACATCCGGAGCCCCTGGTAGTTGCCTAGCGACCGGGCGTGTCCCGGAAGACGG
GCCCGGCGTGGGGCGCGACTTCCGGGGCGGCGGTTGCATCAGATTCTAGGAAGTGTCTGT
AGCCGCAGCTGCGGGTCCGGGATTCCCAGCC
> HS_NONO Homo sapiens NONO (EP73112)
GCTAAACCTTGATTGGCAGTTTAGCTAACCAATCGAGAACGCCATTTTGTACCCCTTGGC
AGGCACCGAGCTCCGTCGTCTCGTTTCCGGCGGTCGCGCGCTCTTTTCTCGGGACGGGAG
AGGCCGTGTAGCGTCGCCGTTACTCCGAGGA
> HS_INDO Homo sapiens INDO (EP73148)
TCATATTACAAACAAAGAAACTAGAAAATGAAACCATTCCAAAAGTGGAAGTAATTTCTC
ACTGCCCCTGTGATAAACTGTGGTCACTGGCTGTGGCAGCAACTATTATAAGATGCTCTG
AAAACTCTTCAGACACTGAGGGGCACCAGAG
> HS_IK Homo sapiens IK (EP73202)
GGTTGGTCGGAGGGAAAAACAGGAAGCGGAAAGGCTGCGAACGCAAAGCAGTGTGGGTTG
ATTCTGAGGTGCACTGTGGGAAAGAGCTTGTCGCTGCGGTGTTGCTGTTGGAGACTCGAT
TGTTGGTGACAGCGAAAGAACGATAACAAAA
> HS_RAG1 Homo sapiens RAG1 (EP64001)
CATGATTGGCTGCCATCATTTGTGGTTAGCCCTCCATGGTGGGGAGGCTGGGAAGGACAG
TGGAAGCTGATAAACAGCTCAGCAGCATGTTCTGAGAAACA

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

The table below lists all promoter motifs found in the 20 upstream sequences of data set 1. 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$E2F1 V$CAAT V$NFY V$MTATA V$TFIIA V$SRF V$USF V$LEF1 V$TATA V$TCF4 V$HNF4 V$TCF1P V$CDX2 V$CETS1P54 V$VMYB V$ELK1 V$RFX1 V$GATA4 V$PAX V$PAX3 V$OCT1 V$CETS168 V$CREL V$DR4 V$CDC5 V$GFI1 V$ETS1 V$MYCMAX V$GATA1 V$CEBPDELTA V$ELF1 V$MAZ V$MINI20 V$E2F V$VMAF V$OSF2 V$PIT1 V$CREB V$NMYC V$BARBIE V$HAND1E47 V$COREBINDINGFACTOR V$TEL2 V$MAZR V$KROX V$FOXJ2 V$NFKB V$MYC V$CREBATF V$WHN V$COMP1 V$PEBP V$MMEF2 V$STAF V$EFC V$BACH2 V$IRF7 V$CDPCR1 V$TFIII V$HIF1 V$MEF2 V$ETS2 V$HNF1 V$AP1 V$FREAC7 V$ARNT V$AML V$MRF2 V$IK3 V$HNF3B V$PITX2 V$HNF3ALPHA V$CHOP V$CMYB V$T3R V$TITF1 V$NKX25 V$SOX5 V$YY1 V$TAXCREB V$FOXD3 V$ALPHACP1 V$FOX V$HLF V$MAX V$PAX9 V$AHR V$AMEF2 V$IK1 V$SOX9 V$LMO2COM V$LDSPOLYA V$CP2 V$CEBPGAMMA V$ATF3 V$STAT V$AHRARNT V$FOXO4 V$STAT5A V$NRF2 V$IRF
GG_ACTB 1 1 1 1 1 1 1 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 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 1 0 0 0 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
HS_ACTB 1 1 1 1 0 1 0 1 1 1 0 0 1 0 1 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 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0
RN_ACTB 1 1 1 1 1 1 0 1 1 1 0 1 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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
CG_ACTB 0 1 1 1 1 1 0 1 1 1 0 1 1 0 1 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 0 0 0 0 0 0 0 1 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 0 0 0 0
MM_ACTB 0 1 1 0 1 1 0 0 1 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 1 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 1 0 0 0 0 1 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
MA_ACTB 0 1 1 1 0 1 0 1 1 1 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 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
OL_ACTB 1 1 1 1 1 1 1 0 1 1 1 0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 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 1 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
HS_PU16 0 0 0 0 0 0 1 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 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 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
HS_RPS14 1 0 0 0 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 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 0 0 0 1 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
HS_TUBA1 1 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 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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_FN1 1 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 1 0 0 1 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
HS_TK1 1 1 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 1 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
HS_IL2 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 1 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 1 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 1 0 0 0 0 0 0 0 0 0 0
HS_TFRC 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 1 0 0 1 1 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 1 1 1 0 0 0 1 1 0 0 0 0 0 1 0 0 0 1 0 1 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
HS_ELK1 1 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 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 0 0 0 0 0 0 0
HS_CARS 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 1 0 0 1 1 1 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 1 1 0
HS_NONO 1 1 1 0 0 0 0 0 0 0 1 1 0 1 1 1 0 0 0 1 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 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 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
HS_INDO 0 1 0 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 1 0 0 0 0 0 1 0 0 0 0 0 1 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 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1
HS_IK 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 1 0 0 0 0 1 0 1 0 1 0 0 0 1 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 1 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 1 0 1 0 0 0 0 0 0 0 0 0
HS_RAG1 0 1 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 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 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 0 0 0 0 0 0 0 0 0 1 0 0 0
Sum 12 12 11 9 8 7 7 7 7 7 6 6 6 5 5 5 5 4 4 4 4 4 3 3 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 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