PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10027660m
Common NameCARUB_v10027660mg
Organism
Capsella rubella
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 bHLH
Protein Properties Length: 479aa    MW: 54719.6 Da    PI: 10.0935
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10027660mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH49.29.6e-16274319555
                      HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
              HLH   5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                      hne ErrRRdriN+++ +L++llP+a      K +K++iL  ++e++k+Lq
  Carubv10027660m 274 HNESERRRRDRINQRMRTLQKLLPTA-----SKADKVSILDDVIEHLKQLQ 319
                      *************************9.....7******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088817.06269318IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474595.5E-18272339IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.108.7E-17272328IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.60E-8274323No hitNo description
PfamPF000105.5E-13274319IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.9E-16275324IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009704Biological Processde-etiolation
GO:0016607Cellular Componentnuclear speck
GO:0003690Molecular Functiondouble-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 479 aa     Download sequence    Send to blast
MCFFVHIKTI LTFCRDHFRE REGERRQEER EPLYYNINMM DQRQIHCMSC RCVIVESLQT  60
KKKQDYNIFK AKKNERREKK IQPQKKRKKK KLIVSLFFAN VRSKSNYGVK ELTWENGQLT  120
VHGLGEEAEP TTSNNPIWTQ SLNGCETLES VVHQAALQQP SKLQLQSPNG PNHNYESKDG  180
SRSRKRGYTQ EMDRWFAVQE ESHRVGHSVT ASASGTNMSL ASFESGRSLK TARTGDRDYF  240
RSGSETQDTE GDEQETRGDA GRSNGRRGRA AAIHNESERR RRDRINQRMR TLQKLLPTAS  300
KADKVSILDD VIEHLKQLQA QVQFMSLRAN LPQQMMIPQL PPPQSVLSIQ QQQQQQQQQQ  360
QQQQQQQQQQ QQQQFQMSLL ATMARMGMGV SGNAYGGLVH PPPPPPPPLM VPPMANRDCT  420
NTSSAALTDP YSVFFAQTMN MDLYNKMAAA IYRQQSDQTS SKVNTGMPSS SLNHEKRD*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17591RREKKIQPQKKRKKKKL
28488KKRKK
38490KKRKKKK
4277282ERRRRD
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway under prolonged red light. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. May regulate the expression of a subset of genes by binding to the G-box motif. {ECO:0000269|PubMed:15486100, ECO:0000269|PubMed:18252845}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00571DAPTransfer from AT5G61270Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10027660m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By red light. Stable upon light exposure.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4938050.0AB493805.1 Arabidopsis thaliana At5g61270 mRNA for hypothetical protein, partial cds, clone: RAAt5g61270.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023644391.10.0transcription factor PIF7
SwissprotQ570R70.0PIF7_ARATH; Transcription factor PIF7
TrEMBLR0G8010.0R0G801_9BRAS; Uncharacterized protein
STRINGXP_006279746.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM141231822
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G61270.11e-151phytochrome-interacting factor7
Publications ? help Back to Top
  1. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. de Wit M,Ljung K,Fankhauser C
    Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels.
    New Phytol., 2015. 208(1): p. 198-209
    [PMID:25963518]
  4. 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]
  5. Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T
    Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94
    [PMID:26193333]
  6. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
    [PMID:28711729]
  7. Peng M, et al.
    Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance.
    Plant Physiol., 2018. 176(2): p. 1341-1351
    [PMID:29187567]
  8. Huang X, et al.
    Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis.
    Elife, 2019.
    [PMID:29926790]