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

RrC1366_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 366aa MW: 41013.4 Da PI: 8.1908

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1366_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	36.6	8.3e-12	190	236	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 h+ Er+RR++i +++ L++llP++ K +K++ L +A++Y++ Lq RrC1366_p2 190 VHKLSERKRRHEISKKMRALQDLLPNC-----YKDDKVSLLDEAIKYMRTLQ 236 6999********************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.12E-12	184	240	No hit	No description
SuperFamily	SSF47459	6.41E-17	184	259	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.37	186	235	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.7E-15	190	246	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.0E-9	190	236	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.3E-11	192	241	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: 366 aa Download sequence Send to blast
MELVCENGKI LAKSRKTNNI GYFQNQRTQS ILDLYETEYD ESFKKNIKNL DETQVVPVSD 60 EQTNNKNRTS SKNRIERDIL KGNKRFESPT LNDDSLNGLK YVEVSTAPPD EQSEAIGRST 120 KLYCTPSSML SRGTSRDLGC SLKKRKCGDN EEEETTYLSN NSDDESDDAK TRVPAKTRKT 180 MAKRKQSTEV HKLSERKRRH EISKKMRALQ DLLPNCYKDD KVSLLDEAIK YMRTLQLQVQ 240 MMSMGNVLIQ PSMILPMGNY SPMGLGMHMG AAATAPVPQF MPMNVQGTGF HGINNASSQM 300 LSAFLNHPTG LIPNSPIFSP LESCSQQLVV PSCFPETQAT SFSQFPMSGS TSNFEDAMQF 360 RGSCGY

Sequence ? help Back to Top

Protein Sequence Length: 366 aa Download sequence Send to blast

MELVCENGKI LAKSRKTNNI GYFQNQRTQS ILDLYETEYD ESFKKNIKNL DETQVVPVSD  60
EQTNNKNRTS SKNRIERDIL KGNKRFESPT LNDDSLNGLK YVEVSTAPPD EQSEAIGRST  120
KLYCTPSSML SRGTSRDLGC SLKKRKCGDN EEEETTYLSN NSDDESDDAK TRVPAKTRKT  180
MAKRKQSTEV HKLSERKRRH EISKKMRALQ DLLPNCYKDD KVSLLDEAIK YMRTLQLQVQ  240
MMSMGNVLIQ PSMILPMGNY SPMGLGMHMG AAATAPVPQF MPMNVQGTGF HGINNASSQM  300
LSAFLNHPTG LIPNSPIFSP LESCSQQLVV PSCFPETQAT SFSQFPMSGS TSNFEDAMQF  360
RGSCGY

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	182	198	KRKQSTEVHKLSERKRR

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}.

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_013751989.1	0.0	transcription factor PIL1
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
TrEMBL	A0A397ZC34	0.0	A0A397ZC34_BRACM; Uncharacterized protein
STRING	Bra004489.1-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	0.0	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]