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_00947.1_g00004.1

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: 313aa MW: 34768.3 Da PI: 7.1244

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00947.1_g00004.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.3	2.1e-11	84	127	8	55
HHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 8 rErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 Er RR+++++ f++L llP++ +K +K++i+ +Av IksL+ Rsa1.0_00947.1_g00004.1 84 TERERRKKMRDMFAKLHALLPQL----PPKADKSTIVDEAVSSIKSLE 127 6*******************6....39***************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	13.243	76	126	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.44E-13	78	137	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.4E-13	80	138	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	7.54E-12	81	131	No hit	No description
SMART	SM00353	3.6E-7	84	132	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	9.7E-9	84	127	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009793	Biological Process	embryo development ending in seed dormancy
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 313 aa Download sequence Send to blast
MSIQFNMTNA QELGQDSTMW GISNSDDSHG GCKRIDKQPP LLCPSHPSEI PTSDKKASKG 60 KKRTQRNEKN HVEESPDHEI HIWTERERRK KMRDMFAKLH ALLPQLPPKA DKSTIVDEAV 120 SSIKSLEKTL HSLQMKKLEK LQYSSASNTT TTTAFPYDPC SSPTTLLTPI SNQPQILPVG 180 AASADPYSRE ALLANQISSS SMNLPYPCND PTAEFDTWST RNAVLNICGN EAFFSLCCPK 240 DKSGVFTNVC YLLEKYNIDV MSANVSSNVF RSTYMIQAQV KPSYENQLLG DGFGAGEIFK 300 QAAQELALYF SSP

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that controls embryo growth (PubMed:18567831, PubMed:18849529, PubMed:23318634). Regulates endosperm breakdown and embryonic epidermal development. Regulates the expression of SBT2.4/ALE1 (PubMed:18849529, PubMed:23318634). Involved in embryonic cuticle formation upstream of SBT2.4/ALE1 (PubMed:23318634). Does not seem to be a general regulator of endosperm patterning. May control specific signaling pathways that coordinate embryo invasion and breakdown of surrounding endosperm tissues (PubMed:18849529). Required for the production the embryo sheath, an extracuticular endosperm-derived structure at the surface of the embryo. Acts upstream of KRS (PubMed:28696222). {ECO:0000269\|PubMed:18567831, ECO:0000269\|PubMed:18849529, ECO:0000269\|PubMed:23318634, ECO:0000269\|PubMed:28696222}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00947.1_g00004.1

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_018464501.1	0.0	PREDICTED: transcription factor bHLH95-like
Swissprot	Q9FXA3	1e-149	BH095_ARATH; Transcription factor bHLH95
TrEMBL	A0A397ZAF8	0.0	A0A397ZAF8_BRACM; Uncharacterized protein
TrEMBL	M4FHU2	0.0	M4FHU2_BRARP; Uncharacterized protein
STRING	Bra040671.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5074	25	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G49770.1	1e-151	bHLH family protein

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] Zhang Y, et al. Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through. Plant Mol. Biol., 2016. 91(4-5): p. 549-61 [PMID:27164978] Fourquin C, et al. Mechanical stress mediated by both endosperm softening and embryo growth underlies endosperm elimination in Arabidopsis seeds. Development, 2016. 143(18): p. 3300-5 [PMID:27287798] Du Q,Wang H Retarded Embryo Development 1 (RED1) regulates embryo development, seed maturation and plant growth in Arabidopsis. J Genet Genomics, 2016. 43(7): p. 439-49 [PMID:27477025] Moussu S, et al. ZHOUPI and KERBEROS Mediate Embryo/Endosperm Separation by Promoting the Formation of an Extracuticular Sheath at the Embryo Surface. Plant Cell, 2017. 29(7): p. 1642-1656 [PMID:28696222]