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

Carubv10008815m

Common Name

CARUB_v10008815mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 533aa MW: 57987.4 Da PI: 6.0385

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10008815m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	52.5	9.1e-17	348	394	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn ErrRRdriN+++ L+el+P++ K++Ka++L +A+eY+ksLq Carubv10008815m 348 VHNLSERRRRDRINEKMRALQELIPNC-----NKVDKASMLDEAIEYLKSLQ 394 6***********************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	1.15E-17	340	398	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.2E-20	341	402	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	7.2E-21	341	407	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	18.584	344	393	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.7E-14	348	394	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.9E-18	350	399	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009704	Biological Process	de-etiolation
GO:0009740	Biological Process	gibberellic acid mediated signaling pathway
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0031539	Biological Process	positive regulation of anthocyanin metabolic process
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0042802	Molecular Function	identical protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 533 aa Download sequence Send to blast
MPLFELFRLA NAKLESAQDN NPSPPVDEVV ELVWENGQIS TQSQSSRSRN IPPPQAVHQP 60 NSSRARDTGN GSKTTMVDEI PMSVPSLMTG MSQEDDFVPW LNHNQSLDGY CSDFLRDVSP 120 VTVNEQESDM AVNQTVFPLF QRRNNGNESA PAASSSQYNG FQSHSLYGSD RARDPPSQQT 180 NPDRVTQTQE TLIPSNKPSL VNFSHFLRPA TLVKIDNPHG TKEKSPPSPP NVFQTRVLGA 240 KDSEDKVLNE SIASATPMNN QKACLMSEDS CRKDQESEKA VVCSSVGSGN SLDGPYESPS 300 LSLKRKHSDI QDIDCHSEDA EEESGDGRKE AAPSRTGLGS KRSRSAEVHN LSERRRRDRI 360 NEKMRALQEL IPNCNKVDKA SMLDEAIEYL KSLQLQVQIM SMASGYYMPP VMFPPGMGHY 420 PAAAAAMAMG MGMPYAMGLP DLSRDTGGSS VNHGPQFQAS GVQQPVAMAN PRVSGGGFLA 480 GSSAMEMKKS SENGSTRELP GSKDQTRTNN NNSNLKPIKR KQASSEQFCG SS*

Sequence ? help Back to Top

Protein Sequence Length: 533 aa Download sequence Send to blast

MPLFELFRLA NAKLESAQDN NPSPPVDEVV ELVWENGQIS TQSQSSRSRN IPPPQAVHQP  60
NSSRARDTGN GSKTTMVDEI PMSVPSLMTG MSQEDDFVPW LNHNQSLDGY CSDFLRDVSP  120
VTVNEQESDM AVNQTVFPLF QRRNNGNESA PAASSSQYNG FQSHSLYGSD RARDPPSQQT  180
NPDRVTQTQE TLIPSNKPSL VNFSHFLRPA TLVKIDNPHG TKEKSPPSPP NVFQTRVLGA  240
KDSEDKVLNE SIASATPMNN QKACLMSEDS CRKDQESEKA VVCSSVGSGN SLDGPYESPS  300
LSLKRKHSDI QDIDCHSEDA EEESGDGRKE AAPSRTGLGS KRSRSAEVHN LSERRRRDRI  360
NEKMRALQEL IPNCNKVDKA SMLDEAIEYL KSLQLQVQIM SMASGYYMPP VMFPPGMGHY  420
PAAAAAMAMG MGMPYAMGLP DLSRDTGGSS VNHGPQFQAS GVQQPVAMAN PRVSGGGFLA  480
GSSAMEMKKS SENGSTRELP GSKDQTRTNN NNSNLKPIKR KQASSEQFCG SS*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	352	357	ERRRRD

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3'). {ECO:0000269\|PubMed:10466729, ECO:0000269\|PubMed:10797009}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00081	ChIP-seq	Transfer from AT1G09530	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10008815m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. {ECO:0000269\|PubMed:12679534}.

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	AF100166	0.0	AF100166.1 Arabidopsis thaliana phytochrome interacting factor 3 (PIF3) mRNA, complete cds.
GenBank	AK117255	0.0	AK117255.1 Arabidopsis thaliana At1g09530 mRNA for putative transcription factor BHLH8, complete cds, clone: RAFL16-81-C24.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006303172.1	0.0	transcription factor PIF3
Swissprot	O80536	0.0	PIF3_ARATH; Transcription factor PIF3
TrEMBL	R0ID12	0.0	R0ID12_9BRAS; Uncharacterized protein
STRING	XP_006303172.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7665	27	39

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G09530.2	0.0	phytochrome interacting factor 3

Link Out ? help Back to Top
Phytozome	Carubv10008815m
Entrez Gene	17897209

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] Zhong S, et al. Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(11): p. 3913-20 [PMID:24599595] Van Buskirk EK,Reddy AK,Nagatani A,Chen M Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark. Plant Physiol., 2014. 165(2): p. 595-607 [PMID:24769533] Zhao Y,Zhou J,Xing D Phytochrome B-mediated activation of lipoxygenase modulates an excess red light-induced defence response in Arabidopsis. J. Exp. Bot., 2014. 65(17): p. 4907-18 [PMID:24916071] Zhang D,Jing Y,Jiang Z,Lin R The Chromatin-Remodeling Factor PICKLE Integrates Brassinosteroid and Gibberellin Signaling during Skotomorphogenic Growth in Arabidopsis. Plant Cell, 2014. 26(6): p. 2472-2485 [PMID:24920333] Wang Y, et al. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(28): p. 10359-64 [PMID:24982146] Zhu L,Huq E Suicidal co-degradation of the phytochrome interacting factor 3 and phytochrome B in response to light. Mol Plant, 2014. 7(12): p. 1709-11 [PMID:25281666] 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] Horvath DP, et al. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. New Phytol., 2015. 207(1): p. 196-210 [PMID:25711503] Geilen K,Böhmer M Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep, 2015. 5: p. 13369 [PMID:26293691] 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] 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] Eprintsev AT,Fedorin DN,Sazonova OV,Igamberdiev AU Light inhibition of fumarase in Arabidopsis leaves is phytochrome A-dependent and mediated by calcium. Plant Physiol. Biochem., 2016. 102: p. 161-6 [PMID:26949024] Soy J, et al. Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(17): p. 4870-5 [PMID:27071129] 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] Yoo J,Cho MH,Lee SW,Bhoo SH Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction. J. Biochem., 2016. 160(4): p. 243-249 [PMID:27143545] Kumar I,Swaminathan K,Hudson K,Hudson ME Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling. J. Exp. Bot., 2016. 67(14): p. 4231-40 [PMID:27262126] Li K, et al. DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Nat Commun, 2016. 7: p. 11868 [PMID:27282989] Jeong AR, et al. New Constitutively Active Phytochromes Exhibit Light-Independent Signaling Activity. Plant Physiol., 2016. 171(4): p. 2826-40 [PMID:27325667] 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] Yu Y,Huang R Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis. Front Plant Sci, 2017. 8: p. 57 [PMID:28174592] Zentella R, et al. The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat. Chem. Biol., 2017. 13(5): p. 479-485 [PMID:28244988] Ling JJ,Li J,Zhu D,Deng XW Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(13): p. 3539-3544 [PMID:28292892] 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] 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] Ni W, et al. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun, 2017. 8: p. 15236 [PMID:28492231] 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] Dong J, et al. Light-Dependent Degradation of PIF3 by SCFEBF1/2 Promotes a Photomorphogenic Response in Arabidopsis. Curr. Biol., 2017. 27(16): p. 2420-2430.e6 [PMID:28736168] Jiang B, et al. PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(32): p. E6695-E6702 [PMID:28739888] Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B PhiReX: a programmable and red light-regulated protein expression switch for yeast. Nucleic Acids Res., 2017. 45(15): p. 9193-9205 [PMID:28911120] Liu X, et al. EIN3 and PIF3 Form an Interdependent Module That Represses Chloroplast Development in Buried Seedlings. Plant Cell, 2017. 29(12): p. 3051-3067 [PMID:29114016] Wang Y,Li J,Deng XW,Zhu D Arabidopsis noncoding RNA modulates seedling greening during deetiolation. Sci China Life Sci, 2018. 61(2): p. 199-203 [PMID:29143279] Ma Q,Wang X,Sun J,Mao T Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein. Plant Physiol., 2018. 176(1): p. 678-690 [PMID:29167353] Qiu Y, et al. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun, 2017. 8(1): p. 1905 [PMID:29199270] Xin X, et al. Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3. J. Exp. Bot., 2018. 69(3): p. 423-439 [PMID:29244171]