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

Csa15g085580.1

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: 529aa MW: 58733.2 Da PI: 7.6295

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa15g085580.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.4	8.4e-16	334	380	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn Er+RRdriN+++ L+el+P + K +Ka++L +A+eY+ksLq Csa15g085580.1 334 VHNLSERKRRDRINERMKALQELIPRC-----NKSDKASMLDEAIEYMKSLQ 380 6***********************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.09E-20	328	397	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	18.146	330	379	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.18E-16	333	384	No hit	No description
Pfam	PF00010	1.7E-13	334	380	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	2.6E-20	334	388	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.2E-17	336	385	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:0006783	Biological Process	heme biosynthetic process
GO:0009740	Biological Process	gibberellic acid mediated signaling pathway
GO:0009959	Biological Process	negative gravitropism
GO:0010100	Biological Process	negative regulation of photomorphogenesis
GO:0010161	Biological Process	red light signaling pathway
GO:0010187	Biological Process	negative regulation of seed germination
GO:0015995	Biological Process	chlorophyll biosynthetic process
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0010313	Molecular Function	phytochrome binding
GO:0042802	Molecular Function	identical protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 529 aa Download sequence Send to blast
MHHFVPDFDR DDDYVNSSSL NLPRKSITTM GGDDDNDLME LLWHNGQVVV HNQRLHHHNK 60 KPSSSPPKMF HPPPPPMQQQ QQPSDQNLFI HEDEMTSWLH YPLRDDNDDF CSDLLFSSVS 120 AAPTAPCVTA DRPMTSQAVT TARPPVAERQ MTSQAVTAER PPVAERQMTS QEVATAKPSL 180 PRPPVRNFMN FSRLRGDFTN GRGESGQPSV SKAVVRESTQ VNTFAAAAKP PAVVAGDSAL 240 LRRTDGTEKC SAVAGGGLDL KGKAVATMTT TPTIEILGTS TSIMSKREIG PEKTIVDERK 300 RKEREAIDEA ECRNENEETK QGRGSTKRTR AAEVHNLSER KRRDRINERM KALQELIPRC 360 NKSDKASMLD EAIEYMKSLQ LQIQMMSMGC GVMPMMYPGM QQYMAMGMGM GMNQPLPPPS 420 FMPFPNMLPA QRPLPTQTQP MGGASVFPAP QYPVHPSDPS RLYTQNQQCN PTLSQPPQYP 480 SYMDPYQQFR GVHPSQPPPF QNQATSYPSS SRASSSKESV DQENHTKG*

Sequence ? help Back to Top

Protein Sequence Length: 529 aa Download sequence Send to blast

MHHFVPDFDR DDDYVNSSSL NLPRKSITTM GGDDDNDLME LLWHNGQVVV HNQRLHHHNK  60
KPSSSPPKMF HPPPPPMQQQ QQPSDQNLFI HEDEMTSWLH YPLRDDNDDF CSDLLFSSVS  120
AAPTAPCVTA DRPMTSQAVT TARPPVAERQ MTSQAVTAER PPVAERQMTS QEVATAKPSL  180
PRPPVRNFMN FSRLRGDFTN GRGESGQPSV SKAVVRESTQ VNTFAAAAKP PAVVAGDSAL  240
LRRTDGTEKC SAVAGGGLDL KGKAVATMTT TPTIEILGTS TSIMSKREIG PEKTIVDERK  300
RKEREAIDEA ECRNENEETK QGRGSTKRTR AAEVHNLSER KRRDRINERM KALQELIPRC  360
NKSDKASMLD EAIEYMKSLQ LQIQMMSMGC GVMPMMYPGM QQYMAMGMGM GMNQPLPPPS  420
FMPFPNMLPA QRPLPTQTQP MGGASVFPAP QYPVHPSDPS RLYTQNQQCN PTLSQPPQYP  480
SYMDPYQQFR GVHPSQPPPF QNQATSYPSS SRASSSKESV DQENHTKG*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	338	343	ERKRRD

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA). {ECO:0000269\|PubMed:15448264, ECO:0000269\|PubMed:16359394, ECO:0000269\|PubMed:18487351, ECO:0000269\|PubMed:18539749, ECO:0000269\|PubMed:18591656}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00074	ChIP-chip	Transfer from AT2G20180	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa15g085580.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner. {ECO:0000269\|PubMed:15448264}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010467931.1	0.0	PREDICTED: transcription factor PIF1-like
Swissprot	Q8GZM7	0.0	PIF1_ARATH; Transcription factor PIF1
TrEMBL	A0A178VU82	0.0	A0A178VU82_ARATH; PIL5
STRING	XP_010467931.1	0.0	(Camelina sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7108	26	43

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G20180.3	1e-164	phytochrome interacting factor 3-like 5

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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Luo Q, et al. COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis. Plant Cell, 2014. 26(6): p. 2441-2456 [PMID:24951480] Krzymuski M, et al. Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Mol Plant, 2014. 7(9): p. 1415-1428 [PMID:25009301] Adams E,Diaz C,Hong JP,Shin R 14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs. Int J Mol Sci, 2014. 15(12): p. 22801-14 [PMID:25501334] Zhu L, et al. CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. Nat Commun, 2015. 6: p. 7245 [PMID:26037329] Bou-Torrent J, et al. Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors. Plant Physiol., 2015. 169(3): p. 1584-94 [PMID:26082398] 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] Zhu L, et al. A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis. Plant Cell, 2016. 28(4): p. 855-74 [PMID:27073231] 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] Kim J, et al. PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1. Plant Cell, 2016. 28(6): p. 1388-405 [PMID:27303023] 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] Zhu L,Xin R,Huq E A Protein-Based Genetic Screening Uncovers Mutants Involved in Phytochrome Signaling in Arabidopsis. Front Plant Sci, 2016. 7: p. 1086 [PMID:27499759] Gangl R,Tenhaken R Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark. Front Plant Sci, 2016. 7: p. 1115 [PMID:27507985] Kim K, et al. PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis. Mol Plant, 2016. 9(10): p. 1415-1427 [PMID:27591813] Kim J, et al. Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously. Plant Cell, 2016. 28(11): p. 2770-2785 [PMID:27758895] Zhang D,Li Y,Zhang X,Zha P,Lin R The SWI2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis. Mol Plant, 2017. 10(1): p. 155-167 [PMID:27865928] Xu X, et al. Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis. Development, 2017. 144(10): p. 1831-1840 [PMID:28420710] 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] Gu D, et al. Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark. Nucleic Acids Res., 2017. 45(12): p. 7137-7150 [PMID:28444370] Zhang X, et al. A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis. Plant Physiol., 2017. 174(4): p. 2487-2500 [PMID:28687557] 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] Li R, et al. Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1. Plant Physiol. Biochem., 2018. 123: p. 204-212 [PMID:29248678] Wu M, et al. PIL5 represses floral transition in Arabidopsis under long day conditions. Biochem. Biophys. Res. Commun., 2018. 499(3): p. 513-518 [PMID:29588173] Majee M, et al. KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1. Proc. Natl. Acad. Sci. U.S.A., 2018. 115(17): p. E4120-E4129 [PMID:29632208]