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

Csa05g089590.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 449aa MW: 49960.7 Da PI: 6.195

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa05g089590.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	56.9	3.6e-18	262	308	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn ErrRRdriN+++ L+el+P++ K +Ka+iL +A++Y+ksLq Csa05g089590.1 262 VHNLSERRRRDRINERMKALQELIPHC-----SKTDKASILDEAIDYLKSLQ 308 6***********************9.....7****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	3.4E-21	256	317	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	19.2	258	307	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.22E-11	261	312	No hit	No description
Pfam	PF00010	1.7E-15	262	308	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	6.9E-22	262	317	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.5E-18	264	313	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009585	Biological Process	red, far-red light phototransduction
GO:0009693	Biological Process	ethylene biosynthetic process
GO:0010244	Biological Process	response to low fluence blue light stimulus by blue low-fluence system
GO:0010600	Biological Process	regulation of auxin biosynthetic process
GO:0010928	Biological Process	regulation of auxin mediated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 449 aa Download sequence Send to blast
MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQDT 60 LRKPYNIFLD DQETVPKPNN NALLDDQETV SWIQYPPDDV VDPFESEFSS HLFSTVNHLD 120 SPEKPRSIEE TVKNEAQAMA PPKFRSSVIA VGPSHCGSNQ STNDHQVTTL PVSMTDRSKN 180 VEERLETSSG GSSGCSYGRN NKETVSGRSA TIDRKRKHVM DADQESVSQS DVPLTSTDDI 240 QVTGNKSSQR SGSTRRSRAA EVHNLSERRR RDRINERMKA LQELIPHCSK TDKASILDEA 300 IDYLKSLQMQ LQVMWMGSGM AAAAAAAATT PMMFPGVQSS PYINQMAMQS QMQLPQFPVM 360 NRSAQQNHPG LVCQNPVQLQ LQAQNQILSE QLARYMGGGF PQMPPAANQA VQQQQQPTDM 420 MRFGSPTGPQ SQLSAPASTD SLRMGKIG*

Sequence ? help Back to Top

Protein Sequence Length: 449 aa Download sequence Send to blast

MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQDT  60
LRKPYNIFLD DQETVPKPNN NALLDDQETV SWIQYPPDDV VDPFESEFSS HLFSTVNHLD  120
SPEKPRSIEE TVKNEAQAMA PPKFRSSVIA VGPSHCGSNQ STNDHQVTTL PVSMTDRSKN  180
VEERLETSSG GSSGCSYGRN NKETVSGRSA TIDRKRKHVM DADQESVSQS DVPLTSTDDI  240
QVTGNKSSQR SGSTRRSRAA EVHNLSERRR RDRINERMKA LQELIPHCSK TDKASILDEA  300
IDYLKSLQMQ LQVMWMGSGM AAAAAAAATT PMMFPGVQSS PYINQMAMQS QMQLPQFPVM  360
NRSAQQNHPG LVCQNPVQLQ LQAQNQILSE QLARYMGGGF PQMPPAANQA VQQQQQPTDM  420
MRFGSPTGPQ SQLSAPASTD SLRMGKIG*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	266	271	ERRRRD

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00082	ChIP-seq	Transfer from AT3G59060	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa05g089590.1

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK317374	0.0	AK317374.1 Arabidopsis thaliana AT3G59060 mRNA, complete cds, clone: RAFL25-22-H20.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010512135.1	0.0	PREDICTED: transcription factor PIF5-like
Refseq	XP_010512136.1	0.0	PREDICTED: transcription factor PIF5-like
Swissprot	Q84LH8	0.0	PIF5_ARATH; Transcription factor PIF5
TrEMBL	R0H467	0.0	R0H467_9BRAS; Uncharacterized protein
STRING	XP_010512135.1	0.0	(Camelina sativa)

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
AT3G59060.4	0.0	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] 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]