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Structure of the rasS regulatory region

Listed are 13 possible structures of the regulatory region inferred using yakA- pufA- gene expression data.

Structure #1

Motif appears at position -920 to -41 relative to the ATG AND
motif appears in nonsense direction at position -920 to -41 relative to the ATG AND
motif appears at position -880 to -41 relative to the ATG.

Detailed description of sequence elements (putative binding sites)
Motif appears at these position(s): 
TATATGT|GTGAGATAAAAA|TAGAAAA (rasS) in nonsense dir., at pos. -798, p: 1.66e-06

This motif does not match any known binding sites.

Motif appears at these position(s): 
TTTCTAT|TTTTATCTCAC|ACATATA (rasS) in sense dir., at pos. -797, p: 1.1e-06
This motif matches the following known binding sites:
  • MOUSE$IGLL_04 - Ig-lambda (immunoglobulin lambda light chain)
  • MOUSE$TDT_01 - TdT (terminal deoxynucleotidyltransferase)
  • see details about this motif
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    • Structure #2

    Motif appears at position -400 to -241 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTCAAAT|CACCTCCAGA|AAAAAAA (rasS) in sense dir., at pos. -244, p: 8.61e-09
    This motif matches the following known binding sites:
  • AS$ZN_01 - artificial sequence., bound by: Zn-15
  • DROME$HSP26_08
  • see details about this motif
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    • Structure #3

    Motif appears at position -960 to -841 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTTATTT|GAAGAAGTGGAAAT|TAGAGCG (rasS) in nonsense dir., at pos. -936, p: 5.43e-07

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #4

    Motif appears at position -1000 to -961 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    ATTATTT|CCAACAACAACCAC|TTTTAAA (rasS) in sense dir., at pos. -967, p: 4.99e-10

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #5

    Motif appears at position -1000 to -721 relative to the ATG AND
    motif appears at position -1000 to -961 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTATTTC|CAACAACAACCAC|TTTTAAA (rasS) in sense dir., at pos. -966, p: 8.54e-08

    This motif does not match any known binding sites.

    Motif appears at these position(s): 
    TTTAAAA|GTGGTTGTTGTTG|GAAATAA (rasS) in nonsense dir., at pos. -966, p: 2.59e-08

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #6

    Motif appears at position -1000 to -721 relative to the ATG AND
    motif appears at position -1000 to -961 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTATTTC|CAACAACAACCAC|TTTTAAA (rasS) in sense dir., at pos. -966, p: 8.54e-08

    This motif does not match any known binding sites.

    Motif appears at these position(s): 
    ATTATTT|CCAACAACAACCAC|TTTTAAA (rasS) in sense dir., at pos. -967, p: 1.74e-09

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #7

    Motif appears in sense direction at position -560 to -441 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    AAGCAAT|CAAAACAAAACTCC|TCACCAC (rasS) in sense dir., at pos. -461, p: 9.14e-07

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #8

    Motif appears anywhere in the regulatory region AND
    motif appears at position -1000 to -881 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTTATTT|GAAGAAGTGGAAAT|TAGAGCG (rasS) in nonsense dir., at pos. -936, p: 5.43e-07

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #9

    Motif appears in nonsense direction at position -960 to -721 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTTATTT|GAAGAAGTGG|AAATTAG (rasS) in nonsense dir., at pos. -932, p: 2.64e-07
    This motif matches the following known binding sites:
  • MOUSE$CRISP1_03 - CRISP1 (cystein-rich secretory protein 1), bound by: AR
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    • Structure #10

    Motif appears in sense direction at position -960 to -721 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TCTAATT|TCCACTTCTTC|AAATAAA (rasS) in sense dir., at pos. -933, p: 5.87e-08

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #11

    Motif appears at position -960 to -121 relative to the ATG AND
    motif appears at position -960 to -121 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTCTGGA|GGTGATTTG|AATTCAA (rasS) in nonsense dir., at pos. -249, p: 7.03e-07
    This motif matches the following known binding sites:
  • HS$APOC3_01 - apoCIII (apolipoprotein CIII), bound by: COUP-TF1, COUP-TF2, HNF-4alpha1, HNF-4alpha1, HNF-4alpha2, NF-BA1
  • AS$TGIF_08 - artificial sequence., bound by: TGIF
  • see details about this motif
    • Motif appears at these position(s): 
    TTCTGGA|GGTGATTTGA|ATTCAAA (rasS) in nonsense dir., at pos. -250, p: 1e-06
    This motif matches the following known binding sites:
  • RAT$PEPCK_16 - PEPCK (phosphoenolpyruvate carboxykinase, cytosolic), bound by: AF-2, HNF-3alpha, HNF-3beta
  • SV$SV40_58 - SV40 (simian virus 40), bound by: HIP1
  • see details about this motif
  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #12

    Motif appears at position -1000 to -121 relative to the ATG AND
    motif appears anywhere in the regulatory region.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    TTCTGGA|GGTGATTTG|AATTCAA (rasS) in nonsense dir., at pos. -249, p: 7.03e-07
    This motif matches the following known binding sites:
  • HS$APOC3_01 - apoCIII (apolipoprotein CIII), bound by: COUP-TF1, COUP-TF2, HNF-4alpha1, HNF-4alpha1, HNF-4alpha2, NF-BA1
  • AS$TGIF_08 - artificial sequence., bound by: TGIF
  • see details about this motif
    • Motif appears at these position(s): 
    TTCTGGA|GGTGATTTGA|ATTCAAA (rasS) in nonsense dir., at pos. -250, p: 1e-06
    This motif matches the following known binding sites:
  • RAT$PEPCK_16 - PEPCK (phosphoenolpyruvate carboxykinase, cytosolic), bound by: AF-2, HNF-3alpha, HNF-3beta
  • SV$SV40_58 - SV40 (simian virus 40), bound by: HIP1
  • see details about this motif
  • Look at genes with similar expression patterns and regulatory domain structure.

    • Structure #13

    Motif appears at position -1000 to -321 relative to the ATG AND
    motif appears at position -1000 to -761 relative to the ATG.

    Detailed description of sequence elements (putative binding sites)
    Motif appears at these position(s): 
    GATTATT|TCCAACAACAACCA|CTTTTAA (rasS) in sense dir., at pos. -968, p: 1.37e-06

    This motif does not match any known binding sites.

  • Look at genes with similar expression patterns and regulatory domain structure.
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