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

GSBRNA2T00064456001

Common Name

GSBRNA2T00064456001, GSBRNA2T00110371001

Organism

Brassica napus

Taxonomic ID

3708

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: 275aa MW: 30814 Da PI: 9.8364

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00064456001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	54.6	2e-17	118	164	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn Er+RRdriN+++ L+el+P++ + +Ka+iL +A++Y+ksLq GSBRNA2T00064456001 118 VHNLSERKRRDRINERMKALQELIPHC-----NRTDKASILDEAIDYLKSLQ 164 6***********************8.....69***************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.36E-21	112	176	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	18.584	114	163	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.50E-16	117	168	No hit	No description
Pfam	PF00010	9.9E-15	118	164	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.4E-21	118	173	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.8E-18	120	169	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: 275 aa Download sequence Send to blast
MAPPKFRSSV VTVGTSHCGS NQSTNDHQVT HPQFPMSDRS KNVEQRLDTS SGGSSGCSKE 60 NESGRSVTIS RKRKHVMDTD QESVSQSDVR LMSTDDQIMG NKSSQRSGST RRSRAAEVHN 120 LSERKRRDRI NERMKALQEL IPHCNRTDKA SILDEAIDYL KSLQMQLQVM WMGRGMAAAA 180 ATPMMFPGVQ SSQYINQMAM QSQMQQPQFP VMNRLVAQSH PCLVCQNPVM QLQMQAQNHI 240 LSEQLSRYMG GFPPMPATTQ VQQQPMEETQ IIKK*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	122	127	ERKRRD

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Circadian-controlled expression. {ECO:0000269\|PubMed:15356333}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots, leaves, stems, and flowers. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting negatively in the phytochrome B signaling pathway to promote the shade-avoidance response. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. Promotes ethylene activity in the dark. May regulate the expression of a subset of genes by binding to the G-box motif. Might be involved in the integration of light-signals to control both circadian and photomorphogenic processes. Activated by CRY1 and CRY2 in response to low blue light (LBL) by direct binding at chromatin on E-box variant 5'-CA[CT]GTG-3' to stimulate specific gene expression to adapt global physiology (e.g. hypocotyl elongation in low blue light) (PubMed:26724867). {ECO:0000269\|PubMed:12826627, ECO:0000269\|PubMed:15356333, ECO:0000269\|PubMed:15486100, ECO:0000269\|PubMed:17589502, ECO:0000269\|PubMed:18047474, ECO:0000269\|PubMed:18065691, ECO:0000269\|PubMed:26724867}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00064456001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Follow a free-running robust circadian rhythm, with higher levels during the light phase. Rapidly induced by light in etiolated plants. Up-regulated by white light. Rapid degradation after red light exposure (at protein level). Accumulates to high levels in the dark, is selectively degraded in response to red light and remains at high levels under shade-mimicking conditions. {ECO:0000269\|PubMed:12826627, ECO:0000269\|PubMed:17589502, ECO:0000269\|PubMed:18047474}.

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	AK353428	0.0	AK353428.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-36-L20.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018478702.1	1e-172	PREDICTED: transcription factor PIF5-like isoform X1
Swissprot	Q84LH8	1e-133	PIF5_ARATH; Transcription factor PIF5
TrEMBL	A0A078JPB6	0.0	A0A078JPB6_BRANA; BnaCnng55460D protein
STRING	Bo4g108070.1	1e-142	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3468	25	61

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G59060.1	1e-117	phytochrome interacting factor 3-like 6

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] Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development. Plant Signal Behav, 2014. [PMID:23838958] Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation. Plant Cell, 2013. 25(8): p. 2892-906 [PMID:23933882] Mannen K, et al. Coordinated transcriptional regulation of isopentenyl diphosphate biosynthetic pathway enzymes in plastids by phytochrome-interacting factor 5. Biochem. Biophys. Res. Commun., 2014. 443(2): p. 768-74 [PMID:24342623] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Di C, et al. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J., 2014. 80(5): p. 848-61 [PMID:25256571] Dornbusch T,Michaud O,Xenarios I,Fankhauser C Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation. Plant Cell, 2014. 26(10): p. 3911-21 [PMID:25281688] Seaton DD, et al. Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature. Mol. Syst. Biol., 2015. 11(1): p. 776 [PMID:25600997] Filo J, et al. Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5. Plant Signal Behav, 2015. 10(3): p. e992707 [PMID:25738547] Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana. Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94 [PMID:26193333] Galvão VC,Collani S,Horrer D,Schmid M Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana. Plant J., 2015. 84(5): p. 949-62 [PMID:26466761] Miyazaki Y, et al. Enhancement of hypocotyl elongation by LOV KELCH PROTEIN2 production is mediated by auxin and phytochrome-interacting factors in Arabidopsis thaliana. Plant Cell Rep., 2016. 35(2): p. 455-67 [PMID:26601822] Yue J, et al. TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis. Plant Physiol., 2016. 170(3): p. 1381-97 [PMID:26704640] Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance. New Phytol., 2016. 211(3): p. 967-79 [PMID:27105120] Fernández V,Takahashi Y,Le Gourrierec J,Coupland G Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days. Plant J., 2016. 86(5): p. 426-40 [PMID:27117775] Martin G,Soy J,Monte E Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes. Front Plant Sci, 2016. 7: p. 962 [PMID:27458465] Gray JA,Shalit-Kaneh A,Chu DN,Hsu PY,Harmer SL The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size. Plant Physiol., 2017. 173(4): p. 2308-2322 [PMID:28254761] Kasulin L, et al. A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina. Mol. Ecol., 2017. 26(13): p. 3389-3404 [PMID:28316114] Wei Z, et al. Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5. Plant Physiol., 2017. 174(2): p. 1260-1273 [PMID:28438793] Shor E,Paik I,Kangisser S,Green R,Huq E PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis. New Phytol., 2017. 215(1): p. 217-228 [PMID:28440582] Paik I,Kathare PK,Kim JI,Huq E Expanding Roles of PIFs in Signal Integration from Multiple Processes. Mol Plant, 2017. 10(8): p. 1035-1046 [PMID:28711729] Swain S,Jiang HW,Hsieh HL FAR-RED INSENSITIVE 219/JAR1 Contributes to Shade Avoidance Responses of Arabidopsis Seedlings by Modulating Key Shade Signaling Components. Front Plant Sci, 2017. 8: p. 1901 [PMID:29163619]