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

29801.m003163

Common Name

RCOM_0812840

Organism

Ricinus communis

Taxonomic ID

3988

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus

Family

bHLH

Protein Properties

Length: 278aa MW: 30677.6 Da PI: 10.1898

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
29801.m003163	genome	JCVI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	41.5	2.4e-13	96	139	8	55
HHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 8 rErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 Er RR+++++ f++L llP++ +K +K++i+ +Av+YIk Lq 29801.m003163 96 TERERRKKMRNMFANLHALLPQL----PPKADKSTIVDEAVNYIKTLQ 139 6*******************6....39****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	13.827	88	138	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.62E-16	89	154	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.3E-15	92	149	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.59E-10	93	135	No hit	No description
Pfam	PF00010	1.3E-10	96	139	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.6E-9	96	144	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd04873	6.46E-4	229	272	No hit	No description

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: 278 aa Download sequence Send to blast
MKVSFGKTRH GFYPILTILQ LRGSEQKNKM AAGGSRSTNS QTEVGKEISL PNNNNKRRKN 60 GNKGSDSSDA KEEKAGGAGG GGGGGGESDH EIHIWTERER RKKMRNMFAN LHALLPQLPP 120 KADKSTIVDE AVNYIKTLQQ TLQKLQKQKL ERLQGGAATF CYEPSLVTPQ KIADSREAFM 180 ADQGSSNNNL SNVTTRSSNN VPSIPRYPVL FQTWTSSNVV LNICGDEAQI SICSSKKPGL 240 FTTICYVLEK HNIEMLSAHV SSDSNRNTYM IQAHFKKF

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	29801.m003163

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	AC237586	3e-33	AC237586.1 Populus trichocarpa clone POP031-J10, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015574371.1	0.0	LOW QUALITY PROTEIN: transcription factor bHLH95-like
Swissprot	Q9FXA3	2e-59	BH095_ARATH; Transcription factor bHLH95
TrEMBL	B9RYG0	0.0	B9RYG0_RICCO; Uncharacterized protein
STRING	XP_002518744.1	0.0	(Ricinus communis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4773	33	58

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G49770.1	3e-50	bHLH family protein

Link Out ? help Back to Top
Phytozome	29801.m003163

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]