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

Carubv10023299m

Common Name

CARUB_v10023299mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 417aa MW: 46490.1 Da PI: 9.0123

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10023299m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	39.7	8.9e-13	237	283	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 h+ Er+RRd+ N+++ L++llP++ K +Ka+ L +A++Y++ Lq Carubv10023299m 237 VHKLSERKRRDEFNKKMRALQDLLPSC-----VKDDKASLLDEAIKYMRTLQ 283 6999********************9.....8****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	7.4E-16	230	291	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.20E-12	231	287	No hit	No description
SuperFamily	SSF47459	3.14E-16	231	307	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.593	233	282	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.2E-10	237	283	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	9.5E-12	239	288	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: 417 aa Download sequence Send to blast
MEEKPLAPSS SSSQPNMVSP SSGFKPKLND QDYMELVWEN GQILAKSRRP KNNGSFQNRR 60 TQSLLDLYEA EYYDGRFKKN IKNLGDTQVV PVSESQPRQN KDNDEQMINK KKSSSKIESD 120 QRNVSKSNKR VASSTLIDDS AKGPKNVEVT TSPPDEQSVA VGRSTELYFA SSSMFSRGTS 180 IDQSFCSLKR NLGDTEEEES TYLISNNSDD ESDDDEKTQV HVRTRKPAAK RKRSTEVHKL 240 SERKRRDEFN KKMRALQDLL PSCVKDDKAS LLDEAIKYMR TLQLQVQMMS VGNGLIRPPT 300 MLPVGHYSHP MGLGMHMGAA TTPVVPQFLP MNVHGNGFPG INNVSSQMLS FLSHPTGLIP 360 NSPIFSPLEN CSQQFVVPSC VPQTQATSFT HQFPKSASSS NLEDAMQFRG SNGYYR*

Sequence ? help Back to Top

Protein Sequence Length: 417 aa Download sequence Send to blast

MEEKPLAPSS SSSQPNMVSP SSGFKPKLND QDYMELVWEN GQILAKSRRP KNNGSFQNRR  60
TQSLLDLYEA EYYDGRFKKN IKNLGDTQVV PVSESQPRQN KDNDEQMINK KKSSSKIESD  120
QRNVSKSNKR VASSTLIDDS AKGPKNVEVT TSPPDEQSVA VGRSTELYFA SSSMFSRGTS  180
IDQSFCSLKR NLGDTEEEES TYLISNNSDD ESDDDEKTQV HVRTRKPAAK RKRSTEVHKL  240
SERKRRDEFN KKMRALQDLL PSCVKDDKAS LLDEAIKYMR TLQLQVQMMS VGNGLIRPPT  300
MLPVGHYSHP MGLGMHMGAA TTPVVPQFLP MNVHGNGFPG INNVSSQMLS FLSHPTGLIP  360
NSPIFSPLEN CSQQFVVPSC VPQTQATSFT HQFPKSASSS NLEDAMQFRG SNGYYR*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	230	245	RKRSTEVHKLSERKRR
2	241	246	ERKRRD

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	Carubv10023299m

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_006294290.1	0.0	transcription factor PIL1
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
TrEMBL	R0HT07	0.0	R0HT07_9BRAS; Uncharacterized protein
STRING	XP_006294290.1	0.0	(Capsella rubella)

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

Link Out ? help Back to Top
Phytozome	Carubv10023299m
Entrez Gene	17889957

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]