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

Thecc1EG000649t2

Common Name

TCM_000649

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

bHLH

Protein Properties

Length: 336aa MW: 36535.8 Da PI: 5.8637

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG000649t2	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.8	5.9e-16	153	199	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn E+rRR+riN+++ L+ l+P++ K +Ka++L +A+eY+k+Lq Thecc1EG000649t2 153 VHNLSEKRRRSRINEKMKALQNLIPNS-----NKTDKASMLDEAIEYLKQLQ 199 6***********************7.....5****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.22E-20	146	209	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	2.1E-20	146	209	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	17.86	149	198	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.77E-17	152	203	No hit	No description
Pfam	PF00010	2.0E-13	153	199	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	8.3E-18	155	204	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:0007623	Biological Process	circadian rhythm
GO:0009409	Biological Process	response to cold
GO:0010114	Biological Process	response to red light
GO:0010154	Biological Process	fruit development
GO:0010187	Biological Process	negative regulation of seed germination
GO:0048440	Biological Process	carpel development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
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: 336 aa Download sequence Send to blast
MGDNINVNMF HYNNNYTTTN DNNSNNGKCL SSASDDISNL LHQILVHSSS PSSGMAYLEG 60 PTENPRRLSR SPAPAGGEAK QGMILTVDSC GRGSGGSGLV GVAGEINDAE EYDCESEFES 120 CHKQEGLEAL VDEAPSKPAP PRSSSKRSRA AEVHNLSEKR RRSRINEKMK ALQNLIPNSN 180 KTDKASMLDE AIEYLKQLQL QVQMLTMRNG LSLHPMCLPG VLQPIQLPQT RIDFGEDNGS 240 LPMNASGTAP ANQEPSAQIV FDLPNQCSSS NHALVPNMSN IITSETSFSL ESIQAPFGPF 300 QLLTPTQGRH SATSSIEVQY IRIWFRGYKY SFTSL*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269\|PubMed:10225997, ECO:0000269\|Ref.8}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00035	PBM	Transfer from AT4G36930	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269\|PubMed:11245574}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY679615	3e-68	AY679615.1 Fragaria x ananassa basic helix-loop-helix protein mRNA, partial cds.
GenBank	KP689411	3e-68	KP689411.1 Prunus pseudocerasus isolate Unigene12366 bHLH transcription factor mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017982070.1	0.0	PREDICTED: transcription factor SPATULA isoform X1
Swissprot	Q9FUA4	3e-52	SPT_ARATH; Transcription factor SPATULA
TrEMBL	A0A061DH16	0.0	A0A061DH16_THECC; Homeodomain-like superfamily protein isoform 2
STRING	EOX91461	0.0	(Theobroma cacao)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G36930.1	2e-51	bHLH family protein

Link Out ? help Back to Top
Phytozome	Thecc1EG000649t2
Entrez Gene	18611155

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] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] Moubayidin L,Ostergaard L Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr. Biol., 2014. 24(22): p. 2743-8 [PMID:25455035] 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] Reyes-Olalde JI, et al. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet., 2017. 13(4): p. e1006726 [PMID:28388635] Wu M, et al. SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis. Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385 [PMID:29966653]