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

Rsa1.0_00419.1_g00002.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 185aa MW: 20619.9 Da PI: 8.6324

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00419.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.4	2.3e-12	7	49	7	54
HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 ++ErrRR+++N+++ Lr+++Pk + K++ a+iL Av+Y+k+L Rsa1.0_00419.1_g00002.1 7 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAVDYLKEL 49 89*******************66......**************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.993	1	49	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.14E-16	5	69	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	5.0E-10	6	49	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.2E-14	6	55	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.88E-12	7	54	No hit	No description
Gene3D	G3DSA:4.10.280.10	4.5E-16	7	63	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	1.17E-8	114	174	No hit	No description

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: 185 aa Download sequence Send to blast
MPAKNLMAER RRRKKLNDRL YMLRSVVPKI SKMDRASILG DAVDYLKELL QRISDLHTEL 60 ESTPSSSSGL TLPSPQTLPY RVKEELCPSS SLPSPKGQQA RIEVNLREGK AVNIHMFCGR 120 RPGLLLSTMR ALDDLGLDVQ QAVISCFNGF ALDVFRAEQC QEGHEVLPEQ IKAVLLDTAG 180 YTGLL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5gnj_A	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_B	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_E	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_F	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_G	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_I	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_M	2e-14	2	59	6	63	Transcription factor MYC2
5gnj_N	2e-14	2	59	6	63	Transcription factor MYC2
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	8	15	ERRRRKKL

Functional Description ? help Back to Top
Source	Description
UniProt	Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA (PubMed:18641265). Functions as a dimer with SPCH during stomatal initiation (PubMed:18641265, PubMed:28507175). {ECO:0000269\|PubMed:18641265, ECO:0000269\|PubMed:28507175}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00419.1_g00002.1

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	AK118011	1e-179	AK118011.1 Arabidopsis thaliana At1g12860 mRNA for putative bHLH transcription factor (bHLH033), complete cds, clone: RAFL19-21-N13.
GenBank	BT005377	1e-179	BT005377.1 Arabidopsis thaliana At1g12860 mRNA, complete cds.
GenBank	EU369670	1e-179	EU369670.1 Arabidopsis thaliana bHLH protein (SCREAM2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018451374.1	1e-131	PREDICTED: transcription factor SCREAM2-like
Swissprot	Q9LPW3	1e-118	SCRM2_ARATH; Transcription factor SCREAM2
TrEMBL	A0A1J3DY25	1e-120	A0A1J3DY25_NOCCA; Transcription factor SCREAM2 (Fragment)
STRING	XP_006417184.1	1e-118	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1952	27	82

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G12860.1	1e-100	bHLH family protein

Publications ? help Back to Top
Tarasov VA,Khadeeva NV,Mel'nik VA,Ezhova TA,Shestakov SV The Atlg12860 gene of Arabidopsis thaliana determines cathelicidin-like antimicrobial activity. Dokl. Biol. Sci., 2009. [PMID:19760875] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Emmerstorfer A, et al. Over-expression of ICE2 stabilizes cytochrome P450 reductase in Saccharomyces cerevisiae and Pichia pastoris. Biotechnol J, 2015. 10(4): p. 623-35 [PMID:25641738] Lee HG,Seo PJ The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in Arabidopsis. Plant J., 2015. 82(6): p. 962-77 [PMID:25912720] Raissig MT,Abrash E,Bettadapur A,Vogel JP,Bergmann DC Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(29): p. 8326-31 [PMID:27382177] Fu ZW,Wang YL,Lu YT,Yuan TT Nitric oxide is involved in stomatal development by modulating the expression of stomatal regulator genes in Arabidopsis. Plant Sci., 2016. 252: p. 282-289 [PMID:27717464] de Marcos A, et al. A Mutation in the bHLH Domain of the SPCH Transcription Factor Uncovers a BR-Dependent Mechanism for Stomatal Development. Plant Physiol., 2017. 174(2): p. 823-842 [PMID:28507175]