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

Rsa1.0_00064.1_g00024.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 384aa MW: 43189.7 Da PI: 9.2351

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00064.1_g00024.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	33.5	7.5e-11	208	252	5	54
HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS HLH 5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 h+ Er+RR++i +++ L++llP++ K++K++ L +A++Y++ L Rsa1.0_00064.1_g00024.1 208 HKLSERKRRHEISKKMRALQDLLPNC-----YKNDKVSLLDEAIKYMRTL 252 9999*******************8.....6*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	3.3E-15	200	263	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.33E-11	201	257	No hit	No description
SuperFamily	SSF47459	1.2E-16	201	273	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.491	203	252	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.0E-8	208	252	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.9E-11	209	258	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 384 aa Download sequence Send to blast
MISPSSSFKP TLNDQDYMEL VCENGQILAK SRKTNNNGYF QNKRTQSILD LYETEYDESF 60 KKNIKNLEET QVVPVSDEHT NNKKRTRSSK NELERDLLKG NKRFESPTLN DGSLKGLQNV 120 EAITTPDEQS TAVGRSTKLY FKPSSILSRG TSRDLSCSLK KRKHGDNEEE ETTYLSNSSD 180 DESDDAKTRV PARTRKTMAK RKRSTEIHKL SERKRRHEIS KKMRALQDLL PNCYKNDKVS 240 LLDEAIKYMR TLRLQVQMMS MGNGVIQPSM MLPMGNYFPM GLGMHMGAAT TTTSAPQFMP 300 MNVQGTAFHG INNASSHMLS AFLNHPTGLI PDSPIFSPLE SCSQHLVAPS CFPETQATSL 360 SQFPMSASTS NFEDAMQFRG SSGY

Sequence ? help Back to Top

Protein Sequence Length: 384 aa Download sequence Send to blast

MISPSSSFKP TLNDQDYMEL VCENGQILAK SRKTNNNGYF QNKRTQSILD LYETEYDESF  60
KKNIKNLEET QVVPVSDEHT NNKKRTRSSK NELERDLLKG NKRFESPTLN DGSLKGLQNV  120
EAITTPDEQS TAVGRSTKLY FKPSSILSRG TSRDLSCSLK KRKHGDNEEE ETTYLSNSSD  180
DESDDAKTRV PARTRKTMAK RKRSTEIHKL SERKRRHEIS KKMRALQDLL PNCYKNDKVS  240
LLDEAIKYMR TLRLQVQMMS MGNGVIQPSM MLPMGNYFPM GLGMHMGAAT TTTSAPQFMP  300
MNVQGTAFHG INNASSHMLS AFLNHPTGLI PDSPIFSPLE SCSQHLVAPS CFPETQATSL  360
SQFPMSASTS NFEDAMQFRG SSGY

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	200	215	RKRSTEIHKLSERKRR

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	Rsa1.0_00064.1_g00024.1

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_013690489.1	0.0	transcription factor PIL1-like
Refseq	XP_013690491.1	0.0	transcription factor PIL1-like
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]