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

Carubv10011072m

Common Name

CARUB_v10011072mg

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: 259aa MW: 29071.7 Da PI: 6.6471

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10011072m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	34.3	4.4e-11	183	223	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r+RR++iN+++ +L+ l+P+ +K++ +++Le+Av+Y+k Lq Carubv10011072m 183 RKRREKINERLKTLQNLVPNG-----TKVDISTMLEEAVHYVKFLQ 223 9****************97.....8****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.123	173	222	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.09E-14	175	237	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	2.1E-13	178	232	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.0E-12	179	228	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.07E-11	182	227	No hit	No description
Pfam	PF00010	1.9E-8	183	223	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009733	Biological Process	response to auxin
GO:0016049	Biological Process	cell growth
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048766	Biological Process	root hair initiation
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 259 aa Download sequence Send to blast
MDVFVDGELE SLLGMFNFDQ CSSSKEDRPR DEMLGLASLY NGHIHQHHHQ NNVLSSDHHA 60 LLLPDMFPFG AMPGGNLPAM LDSWDQNHHL QETSSLKRKL LNVENLCKTN SDCDVTRQEL 120 AKSKKKQRVS SESNTVDESN TNCIDGQSLS NSSDDEKASV TSVKGKTRAT KGTATDPQSL 180 YARKRREKIN ERLKTLQNLV PNGTKVDIST MLEEAVHYVK FLQLQIKLLS SDDLWMYAPL 240 AYNGLDMGFH HNLLSRLM*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	120	126	AKSKKKQ
2	182	187	RKRREK

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10011072m

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	AY085436	0.0	AY085436.1 Arabidopsis thaliana clone 151587 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006304444.1	0.0	transcription factor bHLH54
Swissprot	Q8LEG1	1e-178	BH054_ARATH; Transcription factor bHLH54
TrEMBL	R0GN15	0.0	R0GN15_9BRAS; Uncharacterized protein
STRING	XP_006304444.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4132	22	57

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G27740.1	1e-169	root hair defective 6-like 4

Link Out ? help Back to Top
Phytozome	Carubv10011072m
Entrez Gene	17897304

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] Han Y, et al. Altered expression of TaRSL4 gene by genome interplay shapes root hair length in allopolyploid wheat. New Phytol., 2016. 209(2): p. 721-32 [PMID:26334764] Datta S,Prescott H,Dolan L Intensity of a pulse of RSL4 transcription factor synthesis determines Arabidopsis root hair cell size. Nat Plants, 2015. 1: p. 15138 [PMID:27251390] Song L, et al. The Molecular Mechanism of Ethylene-Mediated Root Hair Development Induced by Phosphate Starvation. PLoS Genet., 2016. 12(7): p. e1006194 [PMID:27427911] Vijayakumar P,Datta S,Dolan L ROOT HAIR DEFECTIVE SIX-LIKE4 (RSL4) promotes root hair elongation by transcriptionally regulating the expression of genes required for cell growth. New Phytol., 2016. 212(4): p. 944-953 [PMID:27452638] Hwang Y,Choi HS,Cho HM,Cho HT Tracheophytes Contain Conserved Orthologs of a Basic Helix-Loop-Helix Transcription Factor That Modulate ROOT HAIR SPECIFIC Genes. Plant Cell, 2017. 29(1): p. 39-53 [PMID:28087829] Marzol E,Borassi C,Denita Juárez SP,Mangano S,Estevez JM RSL4 Takes Control: Multiple Signals, One Transcription Factor. Trends Plant Sci., 2017. 22(7): p. 553-555 [PMID:28487046] Stanley CE, et al. Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels. New Phytol., 2018. 217(3): p. 1357-1369 [PMID:29125191] Feng Y, et al. Ethylene promotes root hair growth through coordinated EIN3/EIL1 and RHD6/RSL1 activity in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(52): p. 13834-13839 [PMID:29233944] Shibata M, et al. GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. Development, 2018. [PMID:29439132]