AraC - UniProtKB: A0A0F6AWN9 regulon and binding site collection of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S


Sites are listed as curated.

GCGAATAATTACCGCCATC
CGTAGCCATTTAATCCATA
CATAGCATAATAATGAATA
ATTAGCATTTTTGTCCATA
TATGGCTGGAATGTCCACA

Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

GCGAATAATTACCGCCATC
CGTAGCCATTTAATCCATA
CATAGCATAATAATGAATA
ATTAGCATTTTTGTCCATA
TGTGGACATTCCAGCCATA

For the selected transcription factor and species, the list of curated binding sites in the database are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation.

    Genome TF TF conformation Site sequence Site location Experimental techniques Gene regulation Curations PMIDs
    NC_016856.1 A0A0F6AWN9 monomer GCGAATAATTACCGCCATC -[173950:173968] Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details RNA-Seq (ECO:0005664) STM14_0178 , STM14_0177 , STM14_0179
    ... ... STM14_0178 STM14_0177 STM14_0179
    629 24272778
    NC_016856.1 A0A0F6AWN9 monomer CGTAGCCATTTAATCCATA -[3197111:3197129] Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details RNA-Seq (ECO:0005664) araE (STM14_3641) , ygeA (STM14_3640)
    ... ... araE ygeA
    629 24272778
    NC_016856.1 A0A0F6AWN9 monomer CATAGCATAATAATGAATA -[446878:446896] Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details RNA-Seq (ECO:0005664) araJ (STM14_0466)
    ... ... araJ
    629 24272778
    NC_016856.1 A0A0F6AWN9 monomer ATTAGCATTTTTGTCCATA -[122093:122111] Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details RNA-Seq (ECO:0005664) araB (STM14_0122) , araA (STM14_0121) , araD (STM14_0120) , araC (STM14_0123) , yabI (STM14_0124)
    ... ... araB araA araD araC yabI
    629 24272778
    NC_016856.1 A0A0F6AWN9 monomer TATGGCTGGAATGTCCACA -[122146:122164] Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details RNA-Seq (ECO:0005664) araB (STM14_0122) , araA (STM14_0121) , araD (STM14_0120) , araC (STM14_0123) , yabI (STM14_0124)
    ... ... araB araA araD araC yabI
    629 24272778

    All binding sites in split view are combined and a sequence logo is generated. Note that it may contain binding site sequences from different transcription factors and different species. To see individiual sequence logos and curation details go to split view.


    Sites are listed as curated.

    GCGAATAATTACCGCCATC
    CGTAGCCATTTAATCCATA
    CATAGCATAATAATGAATA
    ATTAGCATTTTTGTCCATA
    TATGGCTGGAATGTCCACA

    Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

    GCGAATAATTACCGCCATC
    CGTAGCCATTTAATCCATA
    CATAGCATAATAATGAATA
    ATTAGCATTTTTGTCCATA
    TGTGGACATTCCAGCCATA
    Download data in FASTA format.
    Download data in TSV (tab-separated-value) format. For each binding site, all sources of evidence (i.e. experimental techniques and publication information) are combined into one record.
    Download raw data in TSV format. All reported sites are exported individually.
    Download data in Attribute-Relation File Format (ARFF).
    Download Position-Specific-Frequency-Matrix of the motif in TRANSFAC format.
    Download Position-Specific-Frequency-Matrix of the motif in JASPAR format.
    Download Position-Specific-Frequency-Matrix of the motif in raw FASTA format. The matrix consists of four columns in the order A C G T.