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

XP_013593130.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 493aa MW: 54156 Da PI: 8.8978

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013593130.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.5	7.7e-16	299	345	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn Er+RRdriN+++ L+el+P + K +Ka++L +A+eY+ksLq XP_013593130.1 299 VHNLSERKRRDRINERMKALQELIPRC-----NKSDKASMLDEAIEYMKSLQ 345 6***********************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	18.146	295	344	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	8.24E-21	298	373	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.18E-16	298	349	No hit	No description
Pfam	PF00010	1.6E-13	299	345	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.5E-20	299	358	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.2E-17	301	350	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: 493 aa Download sequence Send to blast
MMIMSTLTQT LLLQIFLENP SCKGEEEDGD LMELLWHNGQ VVLQNQRPNT KKQPLSSSAA 60 VKLHNGAPPP PLDHNLFIQE DEMSSWLHYP LGSNDFCSDL FFPAARPPVP SSVRPPEPSS 120 MRPPAPSPVR PPAPSSVKPP VRNFMNFSRL RGDFTGRNGR GESGPSIAKS TVRESAKVNP 180 SATPASSAAR EPDLTRRTDG ADSRGAGDLG SKSAVDGGGA YTVGHNRKGK AVVTTERTSE 240 NLGASSSVAS KSEIEPLETI VDERKRKERE EVGSTECRNE EAKQGRGSSS TKRSRAAEVH 300 NLSERKRRDR INERMKALQE LIPRCNKSDK ASMLDEAIEY MKSLQLQIQM MSMGCGMMPM 360 MYTSMQQYMP HMAMGMGMGV EMGMNRPTPP PPPPFMPFPN MLASQRPLPP QTRMGGYPAV 420 QASDPSRVYG PNQQFDPNSS QAQFSGYMDP FQQFRSLHPS QPPQFQNQAA SYPSSSRVSS 480 SKESEDHGNQ TTS

Sequence ? help Back to Top

Protein Sequence Length: 493 aa Download sequence Send to blast

MMIMSTLTQT LLLQIFLENP SCKGEEEDGD LMELLWHNGQ VVLQNQRPNT KKQPLSSSAA  60
VKLHNGAPPP PLDHNLFIQE DEMSSWLHYP LGSNDFCSDL FFPAARPPVP SSVRPPEPSS  120
MRPPAPSPVR PPAPSSVKPP VRNFMNFSRL RGDFTGRNGR GESGPSIAKS TVRESAKVNP  180
SATPASSAAR EPDLTRRTDG ADSRGAGDLG SKSAVDGGGA YTVGHNRKGK AVVTTERTSE  240
NLGASSSVAS KSEIEPLETI VDERKRKERE EVGSTECRNE EAKQGRGSSS TKRSRAAEVH  300
NLSERKRRDR INERMKALQE LIPRCNKSDK ASMLDEAIEY MKSLQLQIQM MSMGCGMMPM  360
MYTSMQQYMP HMAMGMGMGV EMGMNRPTPP PPPPFMPFPN MLASQRPLPP QTRMGGYPAV  420
QASDPSRVYG PNQQFDPNSS QAQFSGYMDP FQQFRSLHPS QPPQFQNQAA SYPSSSRVSS  480
SKESEDHGNQ TTS

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	303	308	ERKRRD

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

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	XP_013593130.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF488560	3e-93	AF488560.2 Arabidopsis thaliana clone bHLH015 putative bHLH transcription factor mRNA, complete cds.
GenBank	AK228820	3e-93	AK228820.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL16-14-G11.
GenBank	BT029775	3e-93	BT029775.1 Arabidopsis thaliana At2g20180 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013593130.1	0.0	PREDICTED: transcription factor PIF1 isoform X2
Swissprot	Q8GZM7	1e-180	PIF1_ARATH; Transcription factor PIF1
TrEMBL	A0A0D3D2D2	0.0	A0A0D3D2D2_BRAOL; Uncharacterized protein
STRING	Bo7g003890.1	0.0	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G20180.3	1e-139	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]