DATF - The Database of Arabidopsis Transcription Factor
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  • bHLH Family Introduction
  • bHLH Family Strucutre Information
  • Binding Site of This Family
  • Download Sequences of This Family
          Genomic sequence       cds sequence       protein sequence
  • Multi-alignment and Phylogenetic Tree for DNA binding domain   
         Multi-alignment     Phylogenetic Tree EMF vector Image format     Phylogenetic Tree JPG Image

    • List of bHLH family(Total: 127 Loci; 158 Gene Models):

    Page: 1 2 3 4 5 list all   (30 Loci a page)
    LocusGene ModelsDescription
    AT1G01260AT1G01260.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:109032-111609 FORWARD | Aliases: F6F3.7, F6F3_7
    AT1G02340AT1G02340.1 Symbol: HFR1 | long hypocotyl in far-red 1 (HFR1) / reduced phytochrome signaling (REP1) / basic helix-loop-helix FBI1 protein (FBI1) / reduced sensitivity to far-red light (RSF1) / bHLH protein 26 (BHLH026) (BHLH26), identical to SP:Q9FE22 Long hypocotyl in far-red 1 (bHLH-like protein HFR1) (Reduced phytochrome signaling) (Basic helix-loop-helix FBI1 protein) (Reduced sensitivity to far-red light) (Arabidopsis thaliana) | chr1:465718-467844 REVERSE | Aliases: FBI1, LONG HYPOCOTYL IN FAR RED, REDUCED PHYTOCHROME SIGNALING 1, REDUCED SENSITIVITY TO FAR RED LIGHT 1, REP1, RSF1, T6A9.4, T6A9_4
    AT1G03040AT1G03040.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, component of the pyruvate dehydrogenase complex E3, contains PF:00010 helix-loop-helix DNA-binding domain. ESTs gb:T45640 and gb:T22783 come from this gene | chr1:703906-706631 REVERSE | Aliases: F10O3.14, F10O3_14
    AT1G05805AT1G05805.1 Symbol: None | basic helix-loop-helix (bHLH) family protein | chr1:1744773-1747692 FORWARD | Aliases: None
    AT1G06170AT1G06170.1 AT1G06170.2 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile:PF00010 helix-loop-helix DNA-binding domain | chr1:1884980-1886723 REVERSE | Aliases: F9P14.3, F9P14_3
    AT1G09530AT1G09530.1 AT1G09530.2 Symbol: PIF3 | phytochrome interacting factor 3 (PIF3), identical to phytochrome interacting factor 3 (PIF3) GI:3929585 from (Arabidopsis thaliana) | chr1:3076604-3079541 FORWARD | Aliases: F14J9.19, F14J9_19, PAP3, PHOTOCURRENT 1, PHYTOCHROME INTERACTING FACTOR 3, PHYTOCHROME ASSOCIATED PROTEIN 3, POC1
    AT1G10120AT1G10120.1 Symbol: None | similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g68920.1); similar to TA1 protein-like [Oryza sativa (japonica cultivar-group)] (GB:BAD34345.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) | chr1:3304044-3306190 REVERSE | Aliases: T27I1.15, T27I1_15
    AT1G10585AT1G10585.1 Symbol: None | similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At4g20970.1); similar to unknown protein [Oryza sativa (japonica cultivar-group)] (GB:NP_908393.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) | chr1:3493958-3495136 REVERSE | Aliases: None
    AT1G10610AT1G10610.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:3506187-3508605 FORWARD | Aliases: F20B24.5
    AT1G12540AT1G12540.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:4273135-4274204 FORWARD | Aliases: F5O11.28, F5O11_28
    AT1G12860AT1G12860.1 Symbol: None | basic helix-loop-helix (bHLH) family protein / F-box family protein, contains Pfam profiles: PF00646 F-box domain, PF00010 helix-loop-helix DNA-binding domain | chr1:4382221-4386390 FORWARD | Aliases: F13K23.12, F13K23_12
    AT1G18400AT1G18400.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:6331391-6333736 FORWARD | Aliases: F15H18.11, F15H18_11
    AT1G22490AT1G22490.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:7938240-7940581 REVERSE | Aliases: F12K8.16, F12K8_16
    AT1G25330AT1G25330.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:8879863-8882085 REVERSE | Aliases: F4F7.28, F4F7_28
    AT1G26260AT1G26260.1 AT1G26260.2 AT1G26260.3 Symbol: None | similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g68920.2); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:NP_910691.1); similar to putative TA1 protein [Oryza sativa (japonica cultivar-group)] (GB:BAD68029.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) | chr1:9087201-9089365 FORWARD | Aliases: F28B23.8, F28B23_8
    AT1G27740AT1G27740.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:9654675-9656068 FORWARD | Aliases: T22C5.19, T22C5_19
    AT1G30670AT1G30670.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:10879155-10880170 REVERSE | Aliases: T5I8.12, T5I8_12
    AT1G32640AT1G32640.1 Symbol: ATMYC2 | basic helix-loop-helix (bHLH) protein (RAP-1), identical to bHLH protein GB:CAA67885 GI:1465368 from (Arabidopsis thaliana) | chr1:11798795-11800968 REVERSE | Aliases: F6N18.4, F6N18_4, JAI1, JASMONATE INSENSITIVE 1, JIN1, MYC2, RD22BP1, ZBF1
    AT1G35460AT1G35460.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, similar to GI:6166283 from (Pinus taeda) | chr1:13039894-13042080 FORWARD | Aliases: F12A4.2, F12A4_2
    AT1G49770AT1G49770.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains similarity to putative bHLH transcription factor GB:AAC63587 GI:3738090 from (Arabidopsis thaliana) | chr1:18428246-18430450 FORWARD | Aliases: F14J22.2, F14J22_2
    AT1G51070AT1G51070.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, similar to bHLH transcription factor GI:3757520 from (Arabidopsis thaliana) | chr1:18931559-18933430 FORWARD | Aliases: F23H24.8, F23H24_8
    AT1G51140AT1G51140.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:18947125-18949421 REVERSE | Aliases: F23H24.3, F23H24_3
    AT1G59640AT1G59640.1 AT1G59640.2 Symbol: ZCW32 | basic helix-loop-helix (bHLH) family protein | chr1:21913300-21914837 REVERSE | Aliases: T30E16.21, T30E16_21, ZCW32
    AT1G62975AT1G62975.1 Symbol: None | basic helix-loop-helix (bHLH) family protein (bHLH125), contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain; supporting cDNA gi:20805889:gb:AF506369.1: | chr1:23332515-23334187 FORWARD | Aliases: None
    AT1G63650AT1G63650.1 AT1G63650.2 Symbol: EGL3 | basic helix-loop-helix (bHLH) family protein, similar to bHLH transcription factor (JAF13) GB:AAC39455 (Petunia x hybrida); contains Pfam profile: PF00010 Helix-loop-helix DNA-binding domain | chr1:23603168-23606518 FORWARD | Aliases: ATMYC 2, EGL1, ENHANCER OF GLABRA3, F24D7.16, F24D7_16
    AT1G66470AT1G66470.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:24798877-24800651 FORWARD | Aliases: F28G11.9, F28G11_9
    AT1G68240AT1G68240.1 AT1G68240.2 Symbol: None | similar to phytochrome interacting factor 3 (PIF3) [Arabidopsis thaliana] (TAIR:At1g09530.1); similar to phytochrome interacting factor 3 (PIF3) [Arabidopsis thaliana] (TAIR:At1g09530.2); similar to putative BP-5 protein [Oryza sativa (japonica cultivar-group)] (GB:BAD81566.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) | chr1:25578527-25579791 REVERSE | Aliases: T22E19.13, T22E19_13
    AT1G68810AT1G68810.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:25864786-25866742 FORWARD | Aliases: T6L1.1, T6L1_1
    AT1G68920AT1G68920.1 AT1G68920.2 AT1G68920.3 Symbol: None | similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g26260.1); similar to basic helix-loop-helix (bHLH) family protein [Arabidopsis thaliana] (TAIR:At1g26260.2); similar to hypothetical protein [Oryza sativa (japonica cultivar-group)] (GB:NP_910691.1); similar to putative TA1 protein [Oryza sativa (japonica cultivar-group)] (GB:BAD68029.1); contains InterPro domain Basic helix-loop-helix dimerization domain bHLH (InterPro:IPR001092) | chr1:25918670-25921540 FORWARD | Aliases: T6L1.10, T6L1_10
    AT1G69010AT1G69010.1 Symbol: None | basic helix-loop-helix (bHLH) family protein, contains Pfam profile: PF00010 helix-loop-helix DNA-binding domain | chr1:25945374-25947495 FORWARD | Aliases: T6L1.19, T6L1_19
    Page: 1 2 3 4 5 list all

    bHLH Family Introduction

    The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that have been well characterized in nonplant eukaryotes, especially in mammalian systems, in which considerable structural, functional, and phylogenetic analyses have been performed. The data indicate that bHLH proteins are important regulatory components in transcriptional networks in these systems, controlling a diversity of processes from cell proliferation to cell lineage establishment.

    This family is defined by the bHLH signature domain, which consists of 60 amino acids with two functionally distinct regions. The basic region, located at the N-terminal end of the domain, is involved in DNA binding and consists of 15 amino acids with a high number of basic residues. The HLH region, at the C-terminal end, functions as a dimerization domain and is constituted mainly of hydrophobic residues that form two amphipathic -helices separated by a loop region of variable sequence and length. Outside of the conserved bHLH domain, these proteins exhibit considerable sequence divergence. Cocrystal structural analysis has shown that the interaction between the HLH regions of two separate polypeptides leads to the formation of homodimers and/or heterodimers and that the basic region of each partner binds to half of the DNA recognition sequence. Some bHLH proteins form homodimers or restrict their heterodimerization activity to closely related members of the family. On the other hand, some can form heterodimers with one or several different partners.

    The core DNA sequence motif recognized by the bHLH proteins is a consensus hexanucleotide sequence known as the E-box (5'-CANNTG-3'). There are different types of E-boxes, depending on the identity of the two central bases. One of the most common is the palindromic G-box (5'-CACGTG-3'). Certain conserved amino acids within the basic region of the protein provide recognition of the core consensus site, whereas other residues in the domain dictate specificity for a given type of E-box . In addition, flanking nucleotides outside of the hexanucleotide core have been shown to play a role in binding specificity, and there is evidence that a loop residue in the protein plays a role in DNA binding through elements that lie outside of the core recognition sequence.

    Toledo-Ortiz G, Huq E, Quail PH.
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell. 2003 Aug;15(8):1749-70
    PMID: 12897250

    bHLH Family Binding Site

    FamilySubfamily or DomainCis-element nameBinding siteReference
    bHLH  N-box variantCACGGC/CACGACFisher, EMBO J 11:4103-4109 (1992); Littlewood, HLH Transcription Factors, 3rd ed. (1998); Ledent, Genome Res. 11:754-770
    bHLH  G-boxCACGTGToledo-Ortiz G, Huq E, Quail PH. Plant Cell. 2003 Aug;15(8):1749-70
    bHLH  E-boxCANNTGToledo-Ortiz G, Huq E, Quail PH. Plant Cell. 2003 Aug;15(8):1749-70
    bHLH  T04492 
    bHLH  T05620 

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    last updated:2006-07-20