Data set 2 - 7 ACTB genes and 13 randomly picked genes

Data set 2 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_CG1I Homo sapiens CG1I (EP73449)
CAAAGCTGTGGCGCACGCGCAGAAGTACAAGCTACCGGAAGTGATGGCGCCCCTACTAAA
GCCTTGGGGTTAGTACGCGTGCGCAGCAGTTTCTTCCGACAGTTGTGTTGTGCCAATGGT
GGAGAAGAAAACTTCGGGTATGTGAGCCCCC
> HS_ATF4 Homo sapiens ATF4 (EP73433)
CGGGAGGAGACGGTCACGTGGTCGCGGCGGAAGGATGCGTCTGTGCTGCGTCCCCATAGA
GACGAAGTCTATAAAGGGCCGGCGGGCGGCCACGGCAGCCATTTCTACTTTGCCCGCCCA
CAGATGTAGTTTTCTCTGCGCGTGTGCGTTT
> HS_SKB1 Homo sapiens SKB1 (EP73442)
GTGGCAGACGCTCTGGTTGTTAAGGCGACTCGTCCCGCCTTCTGGGGCACTAGTTTGACT
TTGTGATTGGCTACTAGTATCAAGGAATCCCGGCGTGGACAGCGCGAGGAGAAAGATGGC
GGCGATGGCGGTCGGGGGTGCTGGTGGGAGC
> HS_POR1 Homo sapiens POR1 (EP73377)
CCCTGGCTGCGACGTCAGCTCCGCCCTTATAATCTGCGACGTGGCCGGCTTCTTCTGCCC
GGAGAGGACGTCATTTCCGCCGAGTCCCTGACCTGCTGCTAGGATCGCGACGGGAACTGG
AGCCCGAGGTCCCCGCGCGGCCCGGGCCTGG
> HS_AQP1 Homo sapiens AQP1 (EP73458)
GTGTGGTGTGGGGCGGGCCAGGAGCGAAGAGAGGCCTTCCTCCCTTTGTGCTCCCCCCGC
CCCCCGGCCCTATAAATAGGCCCAGCCCAGGCTGTGGCTCAGCTCTCAGAGGGAATTGAG
CACCCGGCAGCGGTCTCAGGCCAAGCCCCCT
> HS_CST4 Homo sapiens CST4 (EP73409)
GGATGGGAAGAAAGAGGAGGAGGAGTCAGGGGTGGGGCATGGAGGTGGGTGGGGCTGGGC
TGCCAAAGCAGGATAAATGCACACCTGCCTGCTGGTCTGGGCTCCCTGCCTCGGGCTCTC
ACCCTCCTCTCCTGCAGCTCCAGCTTTGTGC
> HS_CALM1 Homo sapiens CALM1 (EP73392)
CCCGGCTGCCGCAGCGCCGCTCTGCGCGAGGCGGCTCCGCCGCGGCGGAGGGATACGGCG
CACCATATATATATCGCGGGGCGCAGACTCGCGCTCCGGCAGTGGTGCTGGGAGTGTCGT
GGACGCCGTGCCGTTACTCGTAGTCAGGCGG
> HS_PPIB Homo sapiens PPIB (EP73383)
CAGTCCCCCCCACCCGCGCGTGGCGGCGCCGGCTCCCTAGCCACCGCGGCCCCACCCTCT
TCCGGCCTCAGCTGTCCGGGCTGCTTTCGCCTCCGCCTGTGGATGCTGCGCCTCTCCGAA
CGCAACATGAAGGTGCTCCTTGCCGCCGCCC
> HS_JM5 Homo sapiens JM5 (EP73402)
CTCGCGATGCTCCGAAGACCCGGGAACTAGGCGAGGAAGGCGGTGGCCGCCTTTTTCCAG
CTGGGGTGAGTCATTTCCTGCGACAGGCTCCCTCCCCCGGAAGTAGGGCCTGATGTAAAC
ACCCGAGCCGGGCTCCAAGGCCCGGGAGGTC
> HS_NOL5A Homo sapiens NOL5A (EP73455)
CAAAGGCCGGAGATGGTGTCGTCCCCGGCCTCCGATTGGTCGGGGGGGCGGGGGCGTGGC
CTCTGGAGCCTGGTTCCGCGCGCCGGAGCGCGCTAGCCGCATTGCGAGCCGAACCCGGGA
GCTGGCGCCATGGTGAGGAGTGGTTGCGGGG
> HS_TXNIP Homo sapiens TXNIP (EP73422)
GGGAGGGATGTGCACGAGGGCAGCACGAGCCTCCGGGCCAGCGCTCGCGTGGCTCTTCTG
GCCCGGGCTACTATATAGAGACGTTTCCGCCTCCTGCTTGAAACTAACCCCTCTTTTTCT
CCAAAGGAGTGCTTGTGGAGATCGGATCTTT
> HS_CHSY Homo sapiens CHSY (EP11005)
CGTCACATACTGACCTTGCCTTTGCTAATAACCACGTATCTCAGCTACCATACTTGGTAC
CATCATTATAAATTCATTGATACATTTTTAACTTTGACTCACTGAAAAACACTTGTTCTA
CAACAATCATCTAGCACAACCACTTCCGTCA
> HS_OS Homo sapiens OS (EP73395)
GGTACGTGGGAGGGATAGAACGTACAGCCAATAAAATCATGTGGCGCCGATGGGCGTGTT
GAGGCCGCTGCCTGGCTTAGGGCGGAAACAGATTCTCTGCATAAGAAGGGGAACGAAAGA
TGGCGGCGGAAACGCTGCTGTCCAGTTTGTT

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 2. 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$NFY V$LEF1 V$CAAT V$E2F1 V$MTATA V$HNF4 V$ELK1 V$SRF V$MYCMAX V$CDX2 V$TFIIA V$TCF4 V$TATA V$USF V$TFIII V$RFX1 V$VMYB V$E2F V$MAZ V$SP3 V$PBX V$CETS1P54 V$PAX V$CP2 V$HNF1 V$GATA4 V$PAX3 V$AP1 V$NRF2 V$BACH2 V$TCF1P V$MEF2 V$OCT1 V$DEC V$VMAF V$COMP1 V$CETS168 V$MAZR V$CREBATF V$PIT1 V$NFMUE1 V$CREB V$GFI1 V$BARBIE V$DR4 V$MMEF2 V$AHR V$E2A V$NMYC V$KROX V$MYC V$MAX V$HEB V$GABP V$COREBINDINGFACTOR V$RSRFC4 V$SREBP1 V$CEBPDELTA V$TEL2 V$MRF2 V$WHN V$GATA3 V$ZTA V$SREBP V$SOX5 V$PAX5 V$SF1 V$BRN2 V$ETS2 V$NRF1 V$E47 V$ATF1 V$AHRARNT V$IRF7 V$POU1F1 V$CDPCR1 V$SMAD3 V$E12 V$CREL V$YY1 V$ALPHACP1 V$CMYB V$ELF1 V$CDC5 V$NKX25 V$ARNT V$CREBP1 V$HLF V$SOX9 V$AMEF2 V$MYOD V$PAX9 V$E2F1DP1 V$AP4 V$FOXO4 V$HNF3B V$BACH1 V$ZID V$ETS1
GG_ACTB 1 1 1 1 1 0 0 1 1 1 1 1 1 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 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 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_ACTB 1 1 1 1 1 0 0 1 0 1 0 1 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 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 1 0 0 0 0 0 0 0
RN_ACTB 1 1 1 1 1 0 0 1 0 1 1 1 1 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 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 1 0 0 0 0 0 0 0 0 0 0 0
CG_ACTB 1 1 1 0 1 0 0 1 0 1 1 1 1 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 0 1 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 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
MM_ACTB 1 0 1 0 0 1 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 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 1 0 0 0
MA_ACTB 1 1 1 0 1 1 0 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 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
OL_ACTB 1 0 1 0 1 1 0 1 1 0 1 1 1 1 0 1 1 0 0 0 1 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 1 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 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0
HS_CG1I 1 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 1 0 1 0 1 1 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 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_ATF4 0 1 0 0 1 1 1 0 1 0 1 0 0 1 0 0 0 0 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 1 0 1 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
HS_SKB1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_POR1 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 1 0 0 0 0 0 0 0 1 0 0 0 1 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 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 1 0
HS_AQP1 0 1 0 0 1 1 0 0 0 0 1 0 0 0 1 0 0 0 1 1 0 0 0 1 0 1 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 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
HS_CST4 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 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 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
HS_CALM1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 1 1 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 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
HS_PPIB 0 0 0 1 0 1 1 0 1 0 0 0 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 1 0 0 0 0 0 0 1 0 0 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0
HS_JM5 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 1 0 1 0 0 1 1 1 0 0 1 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 1 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 1 0 1 0 1
HS_NOL5A 1 0 1 1 0 0 1 0 0 0 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 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
HS_TXNIP 0 1 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 1 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 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_CHSY 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 1 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 1 0 1 0 1 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0
HS_OS 1 0 1 1 0 0 1 0 0 1 0 0 0 1 1 0 0 1 1 0 1 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 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
Sum 11 10 10 10 9 8 8 7 7 7 7 7 7 6 6 5 5 5 5 5 5 4 4 4 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 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