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

XP_009147892.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 300aa MW: 33406.8 Da PI: 7.0852

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009147892.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	35.2	2.2e-11	81	124	8	55
HHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 8 rErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 Er RR+++++ f++L llP++ +K +K++i+ +Av IksL+ XP_009147892.1 81 TERERRKKMRDMFSKLHALLPQL----PPKADKSTIVDEAVSSIKSLE 124 6*******************6....39***************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	13.338	73	123	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	3.4E-14	75	134	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.0E-14	77	135	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.22E-13	78	128	No hit	No description
Pfam	PF00010	1.1E-8	81	124	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.5E-8	81	129	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

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: 300 aa Download sequence Send to blast
MSIQFNMTNA QEGFMWGVSS SDDSGGGSRR IETQLPLLQP SLLLENPISM DKKDAKGKKR 60 TKRNGKNHVE DSPDHEIHIW TERERRKKMR DMFSKLHALL PQLPPKADKS TIVDEAVSSI 120 KSLEQTLQKL QMKKLEKLQY SSASNTTTSP TTLLTPISHH SQILPVGAAP ADCYSREAFL 180 ADQISSSITN LPYPCNDPTA AFDIWSSSNV VLNFCGNEAF FNICCPKDKS GVFTNVCYLF 240 EKYNIEVVFA NVSSNVYRST YVIQAQVSPS YENQLLGDGF GVGDIFKQAA NELALYFSSP

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during seed development (PubMed:18567831). Exclusively expressed in the endosperm of developing seeds (PubMed:18849529). {ECO:0000269\|PubMed:18567831, ECO:0000269\|PubMed:18849529}.
Uniprot	TISSUE SPECIFICITY: Siliques. Not detected in roots, rosette leaves or flowers. Expressed in endosperm cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:18567831}.

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	XP_009147892.1

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	AF488623	5e-85	AF488623.1 Arabidopsis thaliana clone bHLH095 putative bHLH transcription factor mRNA, partial sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009147892.1	0.0	PREDICTED: transcription factor bHLH95
Swissprot	Q9FXA3	1e-143	BH095_ARATH; Transcription factor bHLH95
TrEMBL	M4DQK3	0.0	M4DQK3_BRARP; Uncharacterized protein
STRING	Bra018796.1-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-103	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]