PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Tp4g28970

Organism

Thellungiella parvula

Taxonomic ID

98039

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassicaceae incertae sedis; Schrenkiella

Family

bHLH

Protein Properties

Length: 399aa MW: 44972.6 Da PI: 9.043

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp4g28970	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	34.3	4.4e-11	233	279	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 h+ Er+RR++i +++ L++llP++ K +K++ L +A++Y++ Lq Tp4g28970 233 VHKLSERNRRHEISKKMRALQDLLPNC-----YKEDKVSLLDEAIKYMRTLQ 279 6999********************8.....5****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	2.2E-15	226	289	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	7.59E-17	226	299	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.12E-11	227	283	No hit	No description
PROSITE profile	PS50888	15.307	229	278	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.1E-8	233	279	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.1E-11	235	284	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009641	Biological Process	shade avoidance
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 399 aa Download sequence Send to blast
MGKNQYASSS QPNKISPSSS FKPKLNDQDY MELVCENGQI FAKSRNNNGS FQIQRTQSIL 60 DLYETEYDEG FKKNIKNLGD SQVVPVSESQ QPQQHEEVDE LTDNNKKKKI KLSKIESERD 120 VLKSNKRIDS SKLIDDSLKG LKNVEVITAP PDEQSAAVGR STELYFASSS TFSRGTSRDL 180 SCSSLKRRKY DDIEEEESTY LNNNSDDESD DAKKRVTVRK RKTMSKRKRS TEVHKLSERN 240 RRHEISKKMR ALQDLLPNCY KEDKVSLLDE AIKYMRTLQL QVQMMRMGNG LIQPSMMLPM 300 GLGMHMGATT TSVPQVLPMN VQGSSFPDAS SQMLRAILNH STGLIPNSHI FSPLESCSQQ 360 FVVPSCAPQT HTTSFTEFTK SASVSNLGDT MQFRGSNGY

Sequence ? help Back to Top

Protein Sequence Length: 399 aa Download sequence Send to blast

MGKNQYASSS QPNKISPSSS FKPKLNDQDY MELVCENGQI FAKSRNNNGS FQIQRTQSIL  60
DLYETEYDEG FKKNIKNLGD SQVVPVSESQ QPQQHEEVDE LTDNNKKKKI KLSKIESERD  120
VLKSNKRIDS SKLIDDSLKG LKNVEVITAP PDEQSAAVGR STELYFASSS TFSRGTSRDL  180
SCSSLKRRKY DDIEEEESTY LNNNSDDESD DAKKRVTVRK RKTMSKRKRS TEVHKLSERN  240
RRHEISKKMR ALQDLLPNCY KEDKVSLLDE AIKYMRTLQL QVQMMRMGNG LIQPSMMLPM  300
GLGMHMGATT TSVPQVLPMN VQGSSFPDAS SQMLRAILNH STGLIPNSHI FSPLESCSQQ  360
FVVPSCAPQT HTTSFTEFTK SASVSNLGDT MQFRGSNGY

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	212	228	KKRVTVRKRKTMSKRKR

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp4g28970

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009133793.1	0.0	PREDICTED: transcription factor PIL1-like
Refseq	XP_013740663.1	0.0	transcription factor PIL1
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
TrEMBL	A0A397ZXK7	0.0	A0A397ZXK7_BRACM; Uncharacterized protein
TrEMBL	M4C8A8	0.0	M4C8A8_BRARP; Uncharacterized protein
STRING	Bra000436.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13937	17	25

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46970.1	1e-160	phytochrome interacting factor 3-like 1

Publications ? help Back to Top
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] Luo Q, et al. COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis. Plant Cell, 2014. 26(6): p. 2441-2456 [PMID:24951480] 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]