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 XP_009106117.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family bHLH
Protein Properties Length: 90aa    MW: 10279.6 Da    PI: 9.3975
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009106117.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH30.85.2e-1017581454
                    HHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS
             HLH 14 driNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54
                    d+iN+ + +L++llP+ + + +s K+s + +L+++++YI++L
  XP_009106117.1 17 DQINDLIIKLQQLLPElRNSRRSDKVSASRVLQETCNYIRNL 58
                    79**************7779********************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088810.779358IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.4E-91772IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000835.01E-51762No hitNo description
PfamPF000102.7E-71758IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.62E-101777IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 90 aa     Download sequence    Send to blast
MSGRRSRSRQ SSGISEDQIN DLIIKLQQLL PELRNSRRSD KVSASRVLQE TCNYIRNLHR  60
EVDDLSERLS ELLANTDTAQ AALIRSLLTQ
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: At the globular stage, expressed in cells adjacent to the hypophysis and at later embryonic stages, restricted to the future root stem cells. {ECO:0000269|PubMed:20220754}.
UniprotTISSUE SPECIFICITY: Expressed in root and shoot meristems, and young siliques. Low levels detected in all aerial tissues. {ECO:0000269|PubMed:16527868, ECO:0000269|PubMed:20023194, ECO:0000269|PubMed:22339648}.
Functional Description ? help Back to Top
Source Description
UniProtAtypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. Promotes the correct definition of the hypophysis cell division plane. Transcriptionally controlled by MONOPTEROS. Moves from its site of synthesis in pro-embryos cells into the hypophysis. Regulates brassinosteroid (BR) signaling by sequestering negative BR signaling components. May function as positive regulator of gibberellin signaling. May play a role in the regulation of light signaling and possibly auxin signaling. {ECO:0000269|PubMed:16527868, ECO:0000269|PubMed:20023194, ECO:0000269|PubMed:20220754, ECO:0000269|PubMed:22339648}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009106117.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not induced by exogenous gibberellin. {ECO:0000269|PubMed:16527868}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2273951e-88AK227395.1 Arabidopsis thaliana mRNA for putative DNA-binding protein, complete cds, clone: RAFL14-05-N07.
GenBankAY0882861e-88AY088286.1 Arabidopsis thaliana clone 519 mRNA, complete sequence.
GenBankBT0030461e-88BT003046.1 Arabidopsis thaliana At1g74500 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009106117.19e-57PREDICTED: transcription factor PRE3-like
RefseqXP_013590973.19e-57PREDICTED: transcription factor PRE3-like
RefseqXP_013652409.19e-57transcription factor PRE3-like
RefseqXP_013701280.19e-57transcription factor PRE3-like
RefseqXP_018444670.19e-57PREDICTED: transcription factor PRE3-like
SwissprotQ9CA641e-45PRE3_ARATH; Transcription factor PRE3
TrEMBLA0A0D3D0N52e-55A0A0D3D0N5_BRAOL; Uncharacterized protein
TrEMBLA0A397YT542e-55A0A397YT54_BRACM; Uncharacterized protein
TrEMBLA0A3P6GW112e-55A0A3P6GW11_BRAOL; Uncharacterized protein
TrEMBLM4DHC92e-55M4DHC9_BRARP; Uncharacterized protein
STRINGBra015906.1-P4e-56(Brassica rapa)
STRINGBo6g118800.14e-56(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM25928225
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G74500.12e-46activation-tagged BRI1(brassinosteroid-insensitive 1)-suppressor 1
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. Ezer D, et al.
    The G-Box Transcriptional Regulatory Code in Arabidopsis.
    Plant Physiol., 2017. 175(2): p. 628-640
    [PMID:28864470]
  3. Lu KJ,De Rybel B,van Mourik H,Weijers D
    Regulation of intercellular TARGET OF MONOPTEROS 7 protein transport in the Arabidopsis root.
    Development, 2018.
    [PMID:29358212]
  4. Baesso B, et al.
    Transcription factors PRE3 and WOX11 are involved in the formation of new lateral roots from secondary growth taproot in A. thaliana.
    Plant Biol (Stuttg), 2018. 20(3): p. 426-432
    [PMID:29450949]