PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G00120.1
Common NameBHLH40, EDA33, EN120, F6N15.18, GT140, IND, IND1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family bHLH
Protein Properties Length: 198aa    MW: 22949.3 Da    PI: 7.6909
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G00120.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH26.61.1e-08126167854
                  HHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS
          HLH   8 rErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 
                  + rrRR+ri +++  L++++P  a      K++ a++L +A++Y k L
  AT4G00120.1 126 VARRRRERISEKIRILKRIVPGgA------KMDTASMLDEAIRYTKFL 167
                  569******************966......**************8877 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088814.164118167IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.9E-12123175IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000832.69E-9124172No hitNo description
SuperFamilySSF474593.79E-13124177IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.1E-11124173IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000104.1E-6127167IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010197Biological Processpolar nucleus fusion
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 198 aa     Download sequence    Send to blast
MENGMYKKKG VCDSCVSSKS RSNHSPKRSM MEPQPHHLLM DWNKANDLLT QEHAAFLNDP  60
HHLMLDPPPE TLIHLDEDEE YDEDMDAMKE MQYMIAVMQP VDIDPATVPK PNRRNVRISD  120
DPQTVVARRR RERISEKIRI LKRIVPGGAK MDTASMLDEA IRYTKFLKRQ VRILQPHSQI  180
GAPMANPSYL CYYHNSQP
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.345980.0silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306785570.0
Expression AtlasAT4G00120-
AtGenExpressAT4G00120-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: After fertilization, it is expressed in stripes about four cells wide at the margins of developing wild-type fruit. Also expressed in the inner valve layer, which becomes lignified later in fruit development. Detected in roots. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:15035986}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription regulator required for seed dispersal. Involved in the differentiation of all three cell types required for fruit dehiscence. Acts as the key regulator in a network including SHP and ALC that controls specification of the valve margin. Works with ALC, SHP, and FUL to allow differentiation of the lignified valve layer, the spring-loaded mechanism of fruit that promotes opening. Regulates the expression of the YJ80 marker. {ECO:0000269|PubMed:15035986}.
Function -- GeneRIF ? help Back to Top
  1. results demonstrate a cellular mechanism for establishing the distinct cell types and a role for IND in regulating the unequal cell divisions in the seven-layer zone
    [PMID: 16845525]
  2. INDEHISCENT directly binds the promoter of PINOID kinase to regulate auxin transport via the PINFORMED auxin efflux transporters. In this way IND generates an auxin minima at the valve margins, which is required for valve margin development.
    [PMID: 19478783]
  3. Study show that IND may directly regulate SPT expression through variant E-box.
    [PMID: 20176890]
  4. SPT and IND at least partially mediate their joint functions in gynoecium and fruit development by controlling auxin distribution.
    [PMID: 21990939]
  5. INDEHISCENT is part of a regulatory network that specifies valve margin /dehiscence zone identity in Arabidopsis thaliana.
    [PMID: 23126654]
  6. ALCATRAZ is a negative regulator of INDEHISCENT, thereby shedding new light on how ALCATRAZ drives separation layer formation.
    [PMID: 24004048]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G00120.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By FUL, which restrict its expression to the margins.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT2G42830 (A), AT3G58780 (A), AT5G60910 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT3G57510(A), AT4G36930(A), ATMG00160(R)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G36930
IntActSearch O81313
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G00120
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankF6N150.0AF069299.1 Arabidopsis thaliana BAC F6N15.
GenBankCP0026870.0CP002687.1 Arabidopsis thaliana chromosome 4 sequence.
GenBankBT0294430.0BT029443.1 Arabidopsis thaliana At4g00120 mRNA, complete cds.
GenBankAL1614710.0AL161471.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 1.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_191923.11e-147transcription factor IND
SwissprotO813131e-149IND_ARATH; Transcription factor IND
TrEMBLD7M5S51e-128D7M5S5_ARALL; EDA33
STRINGAT4G00120.11e-147(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP7611568
MalvidsOGEM44492754
Publications ? help Back to Top
  1. Ferr
    Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development.
    Science, 2000. 289(5478): p. 436-8
    [PMID:10903201]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Han Z, et al.
    A Fas-associated death domain protein-dependent mechanism mediates the apoptotic action of non-steroidal anti-inflammatory drugs in the human leukemic Jurkat cell line.
    J. Biol. Chem., 2001. 276(42): p. 38748-54
    [PMID:11514566]
  4. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
    [PMID:12679534]
  5. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  6. Liljegren SJ, et al.
    Control of fruit patterning in Arabidopsis by INDEHISCENT.
    Cell, 2004. 116(6): p. 843-53
    [PMID:15035986]
  7. Pagnussat GC, et al.
    Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis.
    Development, 2005. 132(3): p. 603-14
    [PMID:15634699]
  8. Robles P,Pelaz S
    Flower and fruit development in Arabidopsis thaliana.
    Int. J. Dev. Biol., 2005. 49(5-6): p. 633-43
    [PMID:16096970]
  9. Wu H,Mori A,Jiang X,Wang Y,Yang M
    The INDEHISCENT protein regulates unequal cell divisions in Arabidopsis fruit.
    Planta, 2006. 224(4): p. 971-9
    [PMID:16845525]
  10. Mitsuda N,Ohme-Takagi M
    NAC transcription factors NST1 and NST3 regulate pod shattering in a partially redundant manner by promoting secondary wall formation after the establishment of tissue identity.
    Plant J., 2008. 56(5): p. 768-78
    [PMID:18657234]
  11. Mummenhoff K,Polster A,M
    Lepidium as a model system for studying the evolution of fruit development in Brassicaceae.
    J. Exp. Bot., 2009. 60(5): p. 1503-13
    [PMID:19052256]
  12. Ogawa M,Kay P,Wilson S,Swain SM
    ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE1 (ADPG1), ADPG2, and QUARTET2 are Polygalacturonases required for cell separation during reproductive development in Arabidopsis.
    Plant Cell, 2009. 21(1): p. 216-33
    [PMID:19168715]
  13. Mitsuda N,Ohme-Takagi M
    Functional analysis of transcription factors in Arabidopsis.
    Plant Cell Physiol., 2009. 50(7): p. 1232-48
    [PMID:19478073]
  14. Sorefan K, et al.
    A regulated auxin minimum is required for seed dispersal in Arabidopsis.
    Nature, 2009. 459(7246): p. 583-6
    [PMID:19478783]
  15. Rehrauer H, et al.
    AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
    Plant Physiol., 2010. 152(2): p. 487-99
    [PMID:20032078]
  16. Groszmann M,Bylstra Y,Lampugnani ER,Smyth DR
    Regulation of tissue-specific expression of SPATULA, a bHLH gene involved in carpel development, seedling germination, and lateral organ growth in Arabidopsis.
    J. Exp. Bot., 2010. 61(5): p. 1495-508
    [PMID:20176890]
  17. Irish VF
    The flowering of Arabidopsis flower development.
    Plant J., 2010. 61(6): p. 1014-28
    [PMID:20409275]
  18. Arnaud N, et al.
    Gibberellins control fruit patterning in Arabidopsis thaliana.
    Genes Dev., 2010. 24(19): p. 2127-32
    [PMID:20889713]
  19. Moran CN,Halliday KJ
    Fruit development: new directions for an old pathway.
    Curr. Biol., 2010. 20(24): p. R1081-3
    [PMID:21172630]
  20. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  21. Girin T, et al.
    INDEHISCENT and SPATULA interact to specify carpel and valve margin tissue and thus promote seed dispersal in Arabidopsis.
    Plant Cell, 2011. 23(10): p. 3641-53
    [PMID:21990939]
  22. Avino M,Kramer EM,Donohue K,Hammel AJ,Hall JC
    Understanding the basis of a novel fruit type in Brassicaceae: conservation and deviation in expression patterns of six genes.
    Evodevo, 2012. 3(1): p. 20
    [PMID:22943452]
  23. Kay P,Groszmann M,Ross JJ,Parish RW,Swain SM
    Modifications of a conserved regulatory network involving INDEHISCENT controls multiple aspects of reproductive tissue development in Arabidopsis.
    New Phytol., 2013. 197(1): p. 73-87
    [PMID:23126654]
  24. M
    Evidence that an evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) was caused by a change in the control of valve margin identity genes.
    Plant J., 2013. 73(5): p. 824-35
    [PMID:23173897]
  25. Gioia T,Logozzo G,Kami J,Spagnoletti Zeuli P,Gepts P
    Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common Bean.
    J. Hered., 2013. 104(2): p. 273-86
    [PMID:23235700]
  26. Lenser T,Thei
    Conservation of fruit dehiscence pathways between Lepidium campestre and Arabidopsis thaliana sheds light on the regulation of INDEHISCENT.
    Plant J., 2013. 76(4): p. 545-56
    [PMID:24004048]
  27. We
    Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
    Cell Host Microbe, 2014. 16(3): p. 364-75
    [PMID:25211078]
  28. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]