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

Carubv10019965m

Common Name

CARUB_v10019965mg

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: 627aa MW: 70146.1 Da PI: 4.7228

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10019965m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	44.8	2.2e-14	434	480	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 +h E++RR+++N++f +Lr+++P+ + K +K++iL ++eY+++Lq Carubv10019965m 434 NHALCEKKRREKLNERFMTLRSIIPSiS------KIDKVSILDDTIEYLQELQ 480 79999*******************66......****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	1.3E-53	42	231	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	16.418	430	479	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.4E-17	434	497	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.54E-15	434	484	No hit	No description
SuperFamily	SSF47459	5.23E-18	434	498	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	7.7E-12	434	480	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.3E-16	436	485	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009957	Biological Process	epidermal cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 627 aa Download sequence Send to blast
FTQKTTKFCF FDIQILIFVF FMLHGDEETM TTEENRTVPE NLKKQLAVSV RNIQWSYGIF 60 WSVSPSQPGV LEWGDGYYNG DIKTRKTIQA AEVKVDQLGL ERSEQLRELY ESLSLAESSA 120 SGGSQVTRRA SAAALSPEDL TDTEWYYLVC MSFVFNIGEG IPGGALTNGE PIWLCNAETA 180 DSKVFTRSLL AKSASLQTVV CFPFLGGVLE IGTTEHITED LNVIQCVKTL FLEAPPYPTI 240 STRSDYQEVF DPLSDDKYIP VFGTEAFPTP STSGFEQEPE DHDSFINDGG ASQVQSWQFV 300 GEELSNCVHQ SLNSSDCVSQ TFVGPSGRVA CDPRKSTVQR LGQIQEQGNH VNMDDDVHYQ 360 GVISTIFKTT HQLILGPQFQ NFDKRSSFTR WKRSSSVKTL GETSQKMIKK ILFEVPLMNK 420 KEELLTDTPE ETGNHALCEK KRREKLNERF MTLRSIIPSI SKIDKVSILD DTIEYLQELQ 480 KRVQELESCR ESADTETRMT MMKRKKPEDE DERASANCMN SKRKGSDVNV VGEDEPVSTG 540 YAGLTDNLRI SSVGNEVVIE LRCAWREGIL LEIMDVISDL NLDSHSVQSS TGDGLLCLTV 600 NCKHKGTKIA TRGMIQEALQ KVAWIC*

Sequence ? help Back to Top

Protein Sequence Length: 627 aa Download sequence Send to blast

FTQKTTKFCF FDIQILIFVF FMLHGDEETM TTEENRTVPE NLKKQLAVSV RNIQWSYGIF  60
WSVSPSQPGV LEWGDGYYNG DIKTRKTIQA AEVKVDQLGL ERSEQLRELY ESLSLAESSA  120
SGGSQVTRRA SAAALSPEDL TDTEWYYLVC MSFVFNIGEG IPGGALTNGE PIWLCNAETA  180
DSKVFTRSLL AKSASLQTVV CFPFLGGVLE IGTTEHITED LNVIQCVKTL FLEAPPYPTI  240
STRSDYQEVF DPLSDDKYIP VFGTEAFPTP STSGFEQEPE DHDSFINDGG ASQVQSWQFV  300
GEELSNCVHQ SLNSSDCVSQ TFVGPSGRVA CDPRKSTVQR LGQIQEQGNH VNMDDDVHYQ  360
GVISTIFKTT HQLILGPQFQ NFDKRSSFTR WKRSSSVKTL GETSQKMIKK ILFEVPLMNK  420
KEELLTDTPE ETGNHALCEK KRREKLNERF MTLRSIIPSI SKIDKVSILD DTIEYLQELQ  480
KRVQELESCR ESADTETRMT MMKRKKPEDE DERASANCMN SKRKGSDVNV VGEDEPVSTG  540
YAGLTDNLRI SSVGNEVVIE LRCAWREGIL LEIMDVISDL NLDSHSVQSS TGDGLLCLTV  600
NCKHKGTKIA TRGMIQEALQ KVAWIC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rqw_A	2e-16	55	231	24	192	Transcription factor MYC3
4rqw_B	2e-16	55	231	24	192	Transcription factor MYC3
4rs9_A	2e-16	55	231	24	192	Transcription factor MYC3
4yz6_A	2e-16	55	231	24	192	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	439	444	KKRREK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2. {ECO:0000269\|PubMed:12917293, ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15590742}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10019965m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. Negatively regulated by MYB66/WER, GL3 and BHLH2 in the developing non-hair cells, and positively regulated by CPC and TRY in the developing hair cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15590742}.

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	AF027732	0.0	AF027732.1 Arabidopsis thaliana bHLH protein (Atmyc-2) mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006300873.2	0.0	transcription factor EGL1 isoform X1
Swissprot	Q9CAD0	0.0	EGL1_ARATH; Transcription factor EGL1
TrEMBL	R0GDR6	0.0	R0GDR6_9BRAS; Uncharacterized protein (Fragment)
STRING	XP_006300873.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2592	28	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G63650.3	0.0	bHLH family protein

Link Out ? help Back to Top
Phytozome	Carubv10019965m
Entrez Gene	17894080

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] Liu Z,Shi MZ,Xie DY Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. Planta, 2014. 239(4): p. 765-81 [PMID:24370633] Nayidu NK, et al. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS ONE, 2014. 9(4): p. e95877 [PMID:24755905] Cheng Y, et al. Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases. Elife, 2018. [PMID:24771765] Ranocha P,Francoz E,Burlat V,Dunand C Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Plant Signal Behav, 2014. 9(11): p. e977734 [PMID:25531128] Nemie-Feyissa D,Heidari B,Blaise M,Lillo C Analysis of interactions between heterologously produced bHLH and MYB proteins that regulate anthocyanin biosynthesis: quantitative interaction kinetics by Microscale Thermophoresis. Phytochemistry, 2015. 111: p. 21-6 [PMID:25659750] Kwak SH,Song SK,Lee MM,Schiefelbein J TORNADO1 regulates root epidermal patterning through the WEREWOLF pathway in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(12): p. e1103407 [PMID:26451798] Dai X, et al. A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3. Plant Cell Environ., 2016. 39(4): p. 897-907 [PMID:26667588] Friede A, et al. The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves. Front Plant Sci, 2017. 8: p. 1382 [PMID:28848584] Feng K, et al. An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica. Planta, 2018. 247(2): p. 301-315 [PMID:28965159] Wen J, et al. The C-terminal domains of Arabidopsis GL3/EGL3/TT8 interact with JAZ proteins and mediate dimeric interactions. Plant Signal Behav, 2018. 13(1): p. e1422460 [PMID:29293407]