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

Carubv10005062m

Common Name

CARUB_v10005062mg

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: 376aa MW: 42186.1 Da PI: 6.7107

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10005062m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	30.3	7.3e-10	223	270	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +h+++Er RR++i +++ L++l+P + +k Ka +L + ++Y++sLq Carubv10005062m 223 SHSIAERVRREKISERMKFLQDLVPGC----DKITGKAGMLDEIINYVQSLQ 270 8***********************9....899***************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	1.44E-16	217	287	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.32E-11	217	274	No hit	No description
Gene3D	G3DSA:4.10.280.10	4.0E-16	219	280	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.593	219	269	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.9E-7	223	270	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.0E-8	225	275	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006351	Biological Process	transcription, DNA-templated
GO:0009637	Biological Process	response to blue light
GO:0009911	Biological Process	positive regulation of flower development
GO:0005634	Cellular Component	nucleus
GO:0016021	Cellular Component	integral component of membrane
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 376 aa Download sequence Send to blast
MGFSCYKYPF LLYPHLTLPL LCFFLTLFLT ATCFLNPKKK MKMNGGAIEA DLLLNCTDMS 60 VLERQRAHLK YLNPGFDSPL AGFFSGSSVI DGGVIDGFLG TDGLNLPMIY GENTVEGDPR 120 LSISPETMTG TRNFKKRKFD TETKDCDGKK KMMMNRHEEE VEEEEKSKIT EQNNGSTKSI 180 KKMKNKAKKE ENSCSNDSSK VTKELQKTDY IHVRARRGQA TDSHSIAERV RREKISERMK 240 FLQDLVPGCD KITGKAGMLD EIINYVQSLQ RQIEFLSMKL AVVNPRPDFD IDDIFAKEVA 300 STPMTVVPSP EMVNSGYSHE MVNSGYSNEM ASSGYLHFNP MQQVDTTTSD PLSCFNNGQA 360 PSMWDSHVQN LYGSL*

Sequence ? help Back to Top

Protein Sequence Length: 376 aa Download sequence Send to blast

MGFSCYKYPF LLYPHLTLPL LCFFLTLFLT ATCFLNPKKK MKMNGGAIEA DLLLNCTDMS  60
VLERQRAHLK YLNPGFDSPL AGFFSGSSVI DGGVIDGFLG TDGLNLPMIY GENTVEGDPR  120
LSISPETMTG TRNFKKRKFD TETKDCDGKK KMMMNRHEEE VEEEEKSKIT EQNNGSTKSI  180
KKMKNKAKKE ENSCSNDSSK VTKELQKTDY IHVRARRGQA TDSHSIAERV RREKISERMK  240
FLQDLVPGCD KITGKAGMLD EIINYVQSLQ RQIEFLSMKL AVVNPRPDFD IDDIFAKEVA  300
STPMTVVPSP EMVNSGYSHE MVNSGYSNEM ASSGYLHFNP MQQVDTTTSD PLSCFNNGQA  360
PSMWDSHVQN LYGSL*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that binds DNA to G box 5'-CACGTG-3' and, to a lower extent, to E-box 5'-CANNTG-3' in vitro. Binds to chromatin DNA of the FT gene and promotes its expression, and thus triggers flowering in response to blue light. {ECO:0000269\|PubMed:18988809, ECO:0000269\|PubMed:24130508}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10005062m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Accumulates strongly in response to blue light due to reduced preventing 26S proteasome-mediated degradation in an ADO1/ZTL and ADO2/LKP2 dependent manner, but levels decrease in the absence of blue light via 26S proteasome degradation (at protein level). {ECO:0000269\|PubMed:24101505}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK117846	0.0	AK117846.1 Arabidopsis thaliana At4g34530 mRNA for putative bHLH transcription factor (bHLH063), complete cds, clone: RAFL18-04-K08.
GenBank	AY120741	0.0	AY120741.1 Arabidopsis thaliana unknown protein (At4g34530:At4g34540) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006283943.2	0.0	transcription factor bHLH63
Swissprot	Q8GY61	0.0	BH063_ARATH; Transcription factor bHLH63
TrEMBL	R0F5T5	0.0	R0F5T5_9BRAS; Uncharacterized protein
STRING	XP_006283943.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5947	25	43

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G34530.1	0.0	cryptochrome-interacting basic-helix-loop-helix 1

Link Out ? help Back to Top
Phytozome	Carubv10005062m
Entrez Gene	17877802

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] Yang D,Zhao W,Meng Y,Li H,Liu B A CIB1-LIKE transcription factor GmCIL10 from soybean positively regulates plant flowering. Sci China Life Sci, 2015. 58(3): p. 261-9 [PMID:25651969] Katsura Y, et al. An optogenetic system for interrogating the temporal dynamics of Akt. Sci Rep, 2015. 5: p. 14589 [PMID:26423353] Taslimi A, et al. Optimized second-generation CRY2-CIB dimerizers and photoactivatable Cre recombinase. Nat. Chem. Biol., 2016. 12(6): p. 425-30 [PMID:27065233] Liu Q, et al. The Blue Light-Dependent Polyubiquitination and Degradation of Arabidopsis Cryptochrome2 Requires Multiple E3 Ubiquitin Ligases. Plant Cell Physiol., 2016. 57(10): p. 2175-2186 [PMID:27516416] Pathak GP, et al. Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2. Nucleic Acids Res., 2017. 45(20): p. e167 [PMID:28431041] Duan L, et al. Understanding CRY2 interactions for optical control of intracellular signaling. Nat Commun, 2017. 8(1): p. 547 [PMID:28916751] Quejada JR, et al. Optimized light-inducible transcription in mammalian cells using Flavin Kelch-repeat F-box1/GIGANTEA and CRY2/CIB1. Nucleic Acids Res., 2017. 45(20): p. e172 [PMID:29040770] Liu Y, et al. CIB1 and CO interact to mediate CRY2-dependent regulation of flowering. EMBO Rep., 2019. [PMID:30126927]