PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10003520m
Common NameCARUB_v10003520mg
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; Capsella
Family bZIP
Protein Properties Length: 146aa    MW: 16234.8 Da    PI: 10.0483
Description bZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10003520mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1bZIP_149.77.8e-1686144159
                      XXXXCHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
           bZIP_1   1 ekelkrerrkqkNReAArrsRqRKkaeieeLeekvkeLeaeNkaLkkeleelkkevakl 59 
                      eke kr +r+ +NR++A+  R+RKka++ eLe++vk Le++N++L ++l++l++e + l
  Carubv10003520m  86 EKENKRLKRLLRNRVSAQQARERKKAYLSELENRVKDLENKNSELEERLSTLQNENQML 144
                      7999***************************************************9976 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PRINTSPR000415.4E-785101IPR001630cAMP response element binding (CREB) protein
PfamPF001703.3E-1486145IPR004827Basic-leucine zipper domain
SMARTSM003388.1E-1086146IPR004827Basic-leucine zipper domain
PROSITE profilePS5021712.86388146IPR004827Basic-leucine zipper domain
Gene3DG3DSA:1.20.5.1702.5E-1790142No hitNo description
SuperFamilySSF579592.81E-1390145No hitNo description
CDDcd147042.05E-1491142No hitNo description
PROSITE patternPS00036093108IPR004827Basic-leucine zipper domain
PRINTSPR000415.4E-7103123IPR001630cAMP response element binding (CREB) protein
PRINTSPR000415.4E-7123140IPR001630cAMP response element binding (CREB) protein
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009737Biological Processresponse to abscisic acid
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0010017Biological Processred or far-red light signaling pathway
GO:0010099Biological Processregulation of photomorphogenesis
GO:0010114Biological Processresponse to red light
GO:0010218Biological Processresponse to far red light
GO:0010224Biological Processresponse to UV-B
GO:0031539Biological Processpositive regulation of anthocyanin metabolic process
GO:0042753Biological Processpositive regulation of circadian rhythm
GO:0080167Biological Processresponse to karrikin
GO:0005634Cellular Componentnucleus
GO:0003690Molecular Functiondouble-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 146 aa     Download sequence    Send to blast
MQEQATSSLA ASSLPSSSER SSSSAPHLEI KEGIESDEEI RRVPEFGGGA AGKETSGRES  60
GSATGQERAQ ATAGESQRKR GRTPAEKENK RLKRLLRNRV SAQQARERKK AYLSELENRV  120
KDLENKNSEL EERLSTLQNE NQMLRH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2oqq_A1e-17111146338Transcription factor HY5
2oqq_B1e-17111146338Transcription factor HY5
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that promotes photomorphogenesis in light. Acts downstream of the light receptor network and directly affects transcription of light-induced genes. Specifically involved in the blue light specific pathway, suggesting that it participates in transmission of cryptochromes (CRY1 and CRY2) signals to downstream responses. In darkness, its degradation prevents the activation of light-induced genes (Probable). Acts coordinately with SPL7 to regulate the microRNA miR408 and its target genes in response to changes in light and copper conditions (PubMed:25516599). Regulates the abscisic acid (ABA) signaling pathway. Also involved in root gravitropism (PubMed:26474641). {ECO:0000269|PubMed:25516599, ECO:0000269|PubMed:26474641, ECO:0000305}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00117ampDAPTransfer from AT5G11260Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10003520m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0052951e-180AB005295.1 Arabidopsis thaliana mRNA for HY5, complete cds.
GenBankAB0054561e-180AB005456.1 Arabidopsis thaliana mRNA for HY5, complete cds.
GenBankAK2293621e-180AK229362.1 Arabidopsis thaliana mRNA for bZip transcription factor HY5 / AtbZip56, complete cds, clone: RAFL16-60-N08.
GenBankBT0255191e-180BT025519.1 Arabidopsis thaliana At5g11260 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006289904.21e-97transcription factor HY5
SwissprotO246467e-82HY5_ARATH; Transcription factor HY5
TrEMBLR0FK198e-97R0FK19_9BRAS; Uncharacterized protein (Fragment)
STRINGXP_006289904.11e-97(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM56912749
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G11260.15e-68bZIP family protein
Publications ? help Back to Top
  1. Jing Y,Lin R
    PICKLE is a repressor in seedling de-etiolation pathway.
    Plant Signal Behav, 2014.
    [PMID:23733056]
  2. Gangappa SN,Holm M,Botto JF
    Molecular interactions of BBX24 and BBX25 with HYH, HY5 HOMOLOG, to modulate Arabidopsis seedling development.
    Plant Signal Behav, 2014.
    [PMID:23733077]
  3. Ciolfi A, et al.
    Dynamics of the shade-avoidance response in Arabidopsis.
    Plant Physiol., 2013. 163(1): p. 331-53
    [PMID:23893169]
  4. Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ
    Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation.
    Plant Cell, 2013. 25(8): p. 2892-906
    [PMID:23933882]
  5. Huang X,Deng XW
    Organization of protein complexes under photomorphogenic UV-B in Arabidopsis.
    Plant Signal Behav, 2013. 8(11): p. e27206
    [PMID:24304604]
  6. Tossi V,Lamattina L,Jenkins GI,Cassia RO
    Ultraviolet-B-induced stomatal closure in Arabidopsis is regulated by the UV RESISTANCE LOCUS8 photoreceptor in a nitric oxide-dependent mechanism.
    Plant Physiol., 2014. 164(4): p. 2220-30
    [PMID:24586043]
  7. Ouyang X, et al.
    Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(31): p. 11539-44
    [PMID:25049395]
  8. Tsai HL, et al.
    HUA ENHANCER1 is involved in posttranscriptional regulation of positive and negative regulators in Arabidopsis photomorphogenesis.
    Plant Cell, 2014. 26(7): p. 2858-72
    [PMID:25052717]
  9. Yanagisawa S
    Transcription factors involved in controlling the expression of nitrate reductase genes in higher plants.
    Plant Sci., 2014. 229: p. 167-171
    [PMID:25443843]
  10. Zhang H, et al.
    MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper.
    Plant Cell, 2014. 26(12): p. 4933-53
    [PMID:25516599]
  11. Delker C, et al.
    The DET1-COP1-HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis.
    Cell Rep, 2014. 9(6): p. 1983-9
    [PMID:25533339]
  12. Kurihara Y, et al.
    Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.
    Genes (Basel), 2014. 5(4): p. 1115-31
    [PMID:25534860]
  13. Afitlhile M,Fry M,Workman S
    The TOC159 mutant of Arabidopsis thaliana accumulates altered levels of saturated and polyunsaturated fatty acids.
    Plant Physiol. Biochem., 2015. 87: p. 61-72
    [PMID:25557464]
  14. Karumuri S,Bandopadhyay R
    In silico analysis of the structure and interaction of COP1 protein of Arabidopsis thaliana.
    Indian J. Biochem. Biophys., 2014. 51(5): p. 343-9
    [PMID:25630103]
  15. Dong J,Terzaghi W,Deng XW,Chen H
    Multiple photomorphogenic repressors work in concert to regulate Arabidopsis seedling development.
    Plant Signal Behav, 2015. 10(3): p. e1011934
    [PMID:25853593]
  16. Su L, et al.
    Synergistic and Antagonistic Action of Phytochrome (Phy) A and PhyB during Seedling De-Etiolation in Arabidopsis thaliana.
    Int J Mol Sci, 2015. 16(6): p. 12199-212
    [PMID:26030677]
  17. Bou-Torrent J, et al.
    Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors.
    Plant Physiol., 2015. 169(3): p. 1584-94
    [PMID:26082398]
  18. Hayami N, et al.
    The Responses of Arabidopsis Early Light-Induced Protein2 to Ultraviolet B, High Light, and Cold Stress Are Regulated by a Transcriptional Regulatory Unit Composed of Two Elements.
    Plant Physiol., 2015. 169(1): p. 840-55
    [PMID:26175515]
  19. Fernando VC,Schroeder DF
    Genetic interactions between DET1 and intermediate genes in Arabidopsis ABA signalling.
    Plant Sci., 2015. 239: p. 166-79
    [PMID:26398801]
  20. Srivastava AK, et al.
    Short Hypocotyl in White Light1 Interacts with Elongated Hypocotyl5 (HY5) and Constitutive Photomorphogenic1 (COP1) and Promotes COP1-Mediated Degradation of HY5 during Arabidopsis Seedling Development.
    Plant Physiol., 2015. 169(4): p. 2922-34
    [PMID:26474641]
  21. Xie W, et al.
    Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach.
    Front Plant Sci, 2015. 6: p. 829
    [PMID:26528302]
  22. Xu D, et al.
    Arabidopsis COP1 SUPPRESSOR 2 Represses COP1 E3 Ubiquitin Ligase Activity through Their Coiled-Coil Domains Association.
    PLoS Genet., 2015. 11(12): p. e1005747
    [PMID:26714275]
  23. Yu Y, et al.
    Salt Stress and Ethylene Antagonistically Regulate Nucleocytoplasmic Partitioning of COP1 to Control Seed Germination.
    Plant Physiol., 2016. 170(4): p. 2340-50
    [PMID:26850275]
  24. Binkert M, et al.
    Revisiting chromatin binding of the Arabidopsis UV-B photoreceptor UVR8.
    BMC Plant Biol., 2016. 16: p. 42
    [PMID:26864020]
  25. Chen X, et al.
    Shoot-to-Root Mobile Transcription Factor HY5 Coordinates Plant Carbon and Nitrogen Acquisition.
    Curr. Biol., 2016. 26(5): p. 640-6
    [PMID:26877080]
  26. Yang M, et al.
    Arabidopsis atypical kinase ABC1K1 is involved in red light-mediated development.
    Plant Cell Rep., 2016. 35(6): p. 1213-20
    [PMID:27038938]
  27. Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
    [PMID:27105120]
  28. Lin XL, et al.
    An Arabidopsis SUMO E3 Ligase, SIZ1, Negatively Regulates Photomorphogenesis by Promoting COP1 Activity.
    PLoS Genet., 2016. 12(4): p. e1006016
    [PMID:27128446]
  29. Norén L, et al.
    Circadian and Plastid Signaling Pathways Are Integrated to Ensure Correct Expression of the CBF and COR Genes during Photoperiodic Growth.
    Plant Physiol., 2016. 171(2): p. 1392-406
    [PMID:27208227]
  30. Xu X, et al.
    Convergence of light and chloroplast signals for de-etiolation through ABI4-HY5 and COP1.
    Nat Plants, 2016. 2(6): p. 16066
    [PMID:27255835]
  31. Xu D, et al.
    BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(27): p. 7655-60
    [PMID:27325768]
  32. Carrió-Seguí À,Romero P,Sanz A,Peñarrubia L
    Interaction Between ABA Signaling and Copper Homeostasis in Arabidopsis thaliana.
    Plant Cell Physiol., 2016. 57(7): p. 1568-1582
    [PMID:27328696]
  33. Wang Y,Wang Y,Song Z,Zhang H
    Repression of MYBL2 by Both microRNA858a and HY5 Leads to the Activation of Anthocyanin Biosynthetic Pathway in Arabidopsis.
    Mol Plant, 2016. 9(10): p. 1395-1405
    [PMID:27450422]
  34. Wei CQ, et al.
    The Arabidopsis B-box protein BZS1/BBX20 interacts with HY5 and mediates strigolactone regulation of photomorphogenesis.
    J Genet Genomics, 2016. 43(9): p. 555-563
    [PMID:27523280]
  35. Velanis CN,Herzyk P,Jenkins GI
    Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification.
    Plant Mol. Biol., 2016. 92(4-5): p. 425-443
    [PMID:27534420]
  36. Loyola R, et al.
    The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment.
    J. Exp. Bot., 2016. 67(18): p. 5429-5445
    [PMID:27543604]
  37. Jaegle B, et al.
    A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s.
    BMC Plant Biol., 2016. 16(1): p. 190
    [PMID:27586417]
  38. Myers ZA, et al.
    NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana.
    PLoS Genet., 2016. 12(9): p. e1006333
    [PMID:27685091]
  39. Lee HJ, et al.
    Stem-piped light activates phytochrome B to trigger light responses in Arabidopsis thaliana roots.
    Sci Signal, 2016. 9(452): p. ra106
    [PMID:27803284]
  40. Feng XJ, et al.
    Light affects salt stress-induced transcriptional memory of P5CS1 in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(51): p. E8335-E8343
    [PMID:27930298]
  41. Gangappa SN,Kumar SV
    DET1 and HY5 Control PIF4-Mediated Thermosensory Elongation Growth through Distinct Mechanisms.
    Cell Rep, 2017. 18(2): p. 344-351
    [PMID:28076780]
  42. Nawkar GM, et al.
    HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(8): p. 2084-2089
    [PMID:28167764]
  43. Yu Y,Huang R
    Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 57
    [PMID:28174592]
  44. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
    [PMID:28316114]
  45. Li C, et al.
    Characterization and functional analysis of four HYH splicing variants in Arabidopsis hypocotyl elongation.
    Gene, 2017. 619: p. 44-49
    [PMID:28389360]
  46. Perea-Resa C,Rodríguez-Milla MA,Iniesto E,Rubio V,Salinas J
    Prefoldins Negatively Regulate Cold Acclimation in Arabidopsis thaliana by Promoting Nuclear Proteasome-Mediated HY5 Degradation.
    Mol Plant, 2017. 10(6): p. 791-804
    [PMID:28412546]
  47. Park YJ,Lee HJ,Ha JH,Kim JY,Park CM
    COP1 conveys warm temperature information to hypocotyl thermomorphogenesis.
    New Phytol., 2017. 215(1): p. 269-280
    [PMID:28418582]
  48. Zhang Y, et al.
    Dissection of HY5/HYH expression in Arabidopsis reveals a root-autonomous HY5-mediated photomorphogenic pathway.
    PLoS ONE, 2017. 12(7): p. e0180449
    [PMID:28683099]
  49. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
    [PMID:28687557]
  50. Kim SH,Kim H,Chung S,Lee JH
    DHU1 negatively regulates UV-B signaling via its direct interaction with COP1 and RUP1.
    Biochem. Biophys. Res. Commun., 2017. 491(2): p. 285-290
    [PMID:28735869]
  51. Burman N,Bhatnagar A,Khurana JP
    OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development.
    Plant Physiol., 2018. 176(2): p. 1262-1285
    [PMID:28775143]
  52. Wang X, et al.
    A CRY-BIC negative-feedback circuitry regulating blue light sensitivity of Arabidopsis.
    Plant J., 2017. 92(3): p. 426-436
    [PMID:28833729]
  53. Liu Y, et al.
    Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1.
    Plant Cell, 2017. 29(9): p. 2269-2284
    [PMID:28842534]
  54. Liu X,Li Y,Zhong S
    Interplay between Light and Plant Hormones in the Control of Arabidopsis Seedling Chlorophyll Biosynthesis.
    Front Plant Sci, 2017. 8: p. 1433
    [PMID:28861105]
  55. Kim S, et al.
    High Ambient Temperature Represses Anthocyanin Biosynthesis through Degradation of HY5.
    Front Plant Sci, 2017. 8: p. 1787
    [PMID:29104579]
  56. Gao L,Li Y,Shen Z,Han R
    Responses of He-Ne laser on agronomic traits and the crosstalk between UVR8 signaling and phytochrome B signaling pathway in Arabidopsis thaliana subjected to supplementary ultraviolet-B (UV-B) stress.
    Protoplasma, 2018. 255(3): p. 761-771
    [PMID:29138939]
  57. Xu D,Jiang Y,Li J,Holm M,Deng XW
    The B-Box Domain Protein BBX21 Promotes Photomorphogenesis.
    Plant Physiol., 2018. 176(3): p. 2365-2375
    [PMID:29259103]
  58. Sakuraba Y,Yanagisawa S
    Light signalling-induced regulation of nutrient acquisition and utilisation in plants.
    Semin. Cell Dev. Biol., 2018. 83: p. 123-132
    [PMID:29288799]
  59. van Gelderen K, et al.
    Far-Red Light Detection in the Shoot Regulates Lateral Root Development through the HY5 Transcription Factor.
    Plant Cell, 2018. 30(1): p. 101-116
    [PMID:29321188]
  60. Yang Y, et al.
    UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis.
    Nat Plants, 2018. 4(2): p. 98-107
    [PMID:29379156]
  61. Job N,Yadukrishnan P,Bursch K,Datta S,Johansson H
    Two B-Box Proteins Regulate Photomorphogenesis by Oppositely Modulating HY5 through their Diverse C-Terminal Domains.
    Plant Physiol., 2018. 176(4): p. 2963-2976
    [PMID:29439209]
  62. Moriconi V, et al.
    Perception of Sunflecks by the UV-B Photoreceptor UV RESISTANCE LOCUS8.
    Plant Physiol., 2018. 177(1): p. 75-81
    [PMID:29530938]
  63. Yang B, et al.
    RSM1, an Arabidopsis MYB protein, interacts with HY5/HYH to modulate seed germination and seedling development in response to abscisic acid and salinity.
    PLoS Genet., 2018. 14(12): p. e1007839
    [PMID:30566447]