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

XP_009142577.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 400aa MW: 44841.4 Da PI: 8.7276

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009142577.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.5	1.8e-11	223	269	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 h Er+RR++i +++ L++llP++ K +K++ L +A++Y++ Lq XP_009142577.1 223 VHRLSERKRRHEISKKMRALQDLLPNC-----YKDDKVSLLDEAIKYMRTLQ 269 59999*******************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	1.1E-15	216	279	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.05E-12	217	273	No hit	No description
SuperFamily	SSF47459	3.53E-17	217	293	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.358	219	268	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.9E-9	223	269	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	5.1E-11	225	274	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: 400 aa Download sequence Send to blast
MGKNLCASSS QPNMISPSSS LKPTLNDQDY MELVCENGQI LAKSRKTNNN GYFQNQRRQS 60 ILDLYESEYD ESFKKNIKNH EETQVVPVSD EQTNNKKRTK PSKNELERDL LKGSKRFESP 120 TLNGYSLNGL KNVEVIKAPP DEQSEAVGRS TKLYFTPSSM LSRGTSRDLS SSSKKRKCGD 180 NEEEEEETTY LSNSSDDESD DAKTRVPART RKTMAKRKRS TEVHRLSERK RRHEISKKMR 240 ALQDLLPNCY KDDKVSLLDE AIKYMRTLQL QVQMMSMGNG FIQPSVMLPM GNYSPMGLGM 300 HMGAAATTPS LPQFMPMNVQ GTGFHGITNA SSQMLSAFLN HPTGLIPNSP IFSPLESCSQ 360 QLVTPSCFPE TQTTSFSQFP MSGSTTNFED AMQFRGSSGY

Sequence ? help Back to Top

Protein Sequence Length: 400 aa Download sequence Send to blast

MGKNLCASSS QPNMISPSSS LKPTLNDQDY MELVCENGQI LAKSRKTNNN GYFQNQRRQS  60
ILDLYESEYD ESFKKNIKNH EETQVVPVSD EQTNNKKRTK PSKNELERDL LKGSKRFESP  120
TLNGYSLNGL KNVEVIKAPP DEQSEAVGRS TKLYFTPSSM LSRGTSRDLS SSSKKRKCGD  180
NEEEEEETTY LSNSSDDESD DAKTRVPART RKTMAKRKRS TEVHRLSERK RRHEISKKMR  240
ALQDLLPNCY KDDKVSLLDE AIKYMRTLQL QVQMMSMGNG FIQPSVMLPM GNYSPMGLGM  300
HMGAAATTPS LPQFMPMNVQ GTGFHGITNA SSQMLSAFLN HPTGLIPNSP IFSPLESCSQ  360
QLVTPSCFPE TQTTSFSQFP MSGSTTNFED AMQFRGSSGY

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	216	231	RKRSTEVHRLSERKRR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.18784	0.0	bud

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Etiolated seedlings. {ECO:0000269\|PubMed:12826627}.

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	XP_009142577.1

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_009142577.1	0.0	PREDICTED: transcription factor PIL1
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
TrEMBL	M4CJV5	0.0	M4CJV5_BRARP; 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	1e-168	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]