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_02627.1_g00002.1

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: 414aa MW: 46699.4 Da PI: 9.2035

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_02627.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	34.7	3.2e-11	235	280	5	55
HHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 5 hnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 h+ Er+RR++i +++ L++llP+ K +K++ L +A++Y++ Lq Rsa1.0_02627.1_g00002.1 235 HKLSERKRRNEISKKMRALQDLLPNvY------KDDKVSLLDEAIKYMRTLQ 280 999********************55......****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	6.6E-16	227	299	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	5.36E-12	227	284	No hit	No description
SuperFamily	SSF47459	7.85E-16	228	301	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	14.805	230	279	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	8.0E-9	235	280	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.6E-10	236	285	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: 414 aa Download sequence Send to blast
MGKTPYASLS QPNVISPSSS FKPKLSDQDY MELVCENGQI FAKSRRPNNN GYFQSQRTQS 60 LLDLYETEYD EDFKKNIKNL GDSQVVPGSE PQHPQQDEET DEQTNDNNNK KKKKIKPSKT 120 ESERNIWKRN KRSESSKLMN DSLKGLKNIE VTTAPPDEQS VAVGRSRELY IASSSRGTSK 180 DLNCCSLKKR KYGDMEEEES TYLRNSDNGS DDARIRVTAT TRKTVAKRKR STEGHKLSER 240 KRRNEISKKM RALQDLLPNV YKDDKVSLLD EAIKYMRTLQ LQVQMMSMGN GMISSTSSML 300 PMGHYSPMGL GMHMGTATTT TSVQPFLPMN VQGTSCFPWI NDASSQMLRT FLNHPTGLIP 360 NSPIFSPLES CSQQFVVPSC FPDETHSTSF TQFSKFASTS NLEDAMQLRG SNGY

Sequence ? help Back to Top

Protein Sequence Length: 414 aa Download sequence Send to blast

MGKTPYASLS QPNVISPSSS FKPKLSDQDY MELVCENGQI FAKSRRPNNN GYFQSQRTQS  60
LLDLYETEYD EDFKKNIKNL GDSQVVPGSE PQHPQQDEET DEQTNDNNNK KKKKIKPSKT  120
ESERNIWKRN KRSESSKLMN DSLKGLKNIE VTTAPPDEQS VAVGRSRELY IASSSRGTSK  180
DLNCCSLKKR KYGDMEEEES TYLRNSDNGS DDARIRVTAT TRKTVAKRKR STEGHKLSER  240
KRRNEISKKM RALQDLLPNV YKDDKVSLLD EAIKYMRTLQ LQVQMMSMGN GMISSTSSML  300
PMGHYSPMGL GMHMGTATTT TSVQPFLPMN VQGTSCFPWI NDASSQMLRT FLNHPTGLIP  360
NSPIFSPLES CSQQFVVPSC FPDETHSTSF TQFSKFASTS NLEDAMQLRG SNGY

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	227	242	RKRSTEGHKLSERKRR

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_02627.1_g00002.1

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_009133793.1	0.0	PREDICTED: transcription factor PIL1-like
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
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-179	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]