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_009103456.1

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: 214aa MW: 23411.7 Da PI: 9.8777

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009103456.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	51.2	2.2e-16	99	145	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn E+rRR++iN+++ L++l+P++ K +Ka++L +A+eY+k+Lq XP_009103456.1 99 FHNLSEKRRRSKINEKMKALQKLIPNS-----NKTDKASMLDEAIEYLKQLQ 145 6***********************7.....5****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	17.111	95	144	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	8.1E-14	99	145	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	4.32E-19	99	164	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.31E-15	100	147	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.7E-19	100	153	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.2E-16	101	150	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0010047	Biological Process	fruit dehiscence
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 214 aa Download sequence Send to blast
MGNSDEGDRL PAPSSSDELS SILRQVLSRA PTAQPSFSPK KIVSSAEMFN RTFPLVPGGA 60 VSYAACAAAE TGEGKCGFEN KRNGARQRNS LKRNIDAQFH NLSEKRRRSK INEKMKALQK 120 LIPNSNKTDK ASMLDEAIEY LKQLQLQFQT LAAMNGLGLN PLRLPPILPP TQTRITGTSE 180 QGLNLETLLG GSHSMANREP PETQEMCFPT TTLL

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. Confined to the valve margins of the silique. {ECO:0000269\|PubMed:11747817, ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
UniProt	Required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. Promotes the differentiation of a strip of labile nonlignified cells sandwiched between layers of lignified cells. {ECO:0000269\|PubMed:11747817}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009103456.1

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_009103456.1	1e-156	PREDICTED: transcription factor ALC
Swissprot	Q9FHA2	1e-104	ALC_ARATH; Transcription factor ALC
TrEMBL	A0A397YK68	1e-155	A0A397YK68_BRACM; Uncharacterized protein
TrEMBL	M4D6M4	1e-155	M4D6M4_BRARP; Uncharacterized protein
STRING	Bra012133.1-P	1e-156	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13982	17	24

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G67110.1	1e-87	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] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] Pfannebecker KC,Lange M,Rupp O,Becker A Seed Plant-Specific Gene Lineages Involved in Carpel Development. Mol. Biol. Evol., 2017. 34(4): p. 925-942 [PMID:28087776] Zumajo-Cardona C,Ambrose BA,Pabón-Mora N Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae). Evodevo, 2017. 8: p. 5 [PMID:28331573] He H, et al. CELLULASE6 and MANNANASE7 Affect Cell Differentiation and Silique Dehiscence. Plant Physiol., 2018. 176(3): p. 2186-2201 [PMID:29348141]