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

Cotton_A_12302_BGI-A2_v1.0

Organism

Gossypium arboreum

Taxonomic ID

29729

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

FAR1

Protein Properties

Length: 843aa MW: 97002.7 Da PI: 7.0463

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_12302_BGI-A2_v1.0	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	89.1	6.3e-28	80	167	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtklel 83 +fY+eYAk++GF++++++s++sk+++e+++++f Cs++g + e++ ++r++++++t+Cka+++vk++ dgkw ++++++ Cotton_A_12302_BGI-A2_v1.0 80 SFYQEYAKSMGFTTSIKNSRRSKKSKEFIDAKFACSRYGVTPESDVG---SSRRSSVKKTDCKASMHVKRRPDGKWIIHEFVK 159 5**************************************999877...889999*********************** PP FAR1 84 eHnHelap 91 eHnHel p Cotton_A_12302_BGI-A2_v1.0 160 EHNHELLP 167 ***975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	2.3E-25	80	167	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	1.0E-28	287	380	IPR018289	MULE transposase domain
PROSITE profile	PS50966	10.373	567	603	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	9.4E-7	576	602	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	8.4E-8	578	605	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010018	Biological Process	far-red light signaling pathway
GO:0042753	Biological Process	positive regulation of circadian rhythm
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 843 aa Download sequence Send to blast
MMIKIGENQN AISNMVDCRD AMPCNDGVNE NMVDIVDETA RSRDSGIVDT SKRAVVGFEG 60 DAEFEPHNGI EFESHEAAYS FYQEYAKSMG FTTSIKNSRR SKKSKEFIDA KFACSRYGVT 120 PESDVGSSRR SSVKKTDCKA SMHVKRRPDG KWIIHEFVKE HNHELLPALA YHFRIYRNVK 180 LAEKNNIDIL NAVSERTRKM YVEMSRQSGG YQNVNMLQSD IKNQFDKSRH LVVDEGDAQI 240 MLEYFKRIKK ENPDFFYAID LNEEQRLRNL FWVDAKSRND YPSFNDVVSF DTTYVKFNEK 300 LPFAPFVGVN HHFQSMLLGC ALLADETKPT FVWLMKTWLR AMGGQAPKVI ITDQDKELKA 360 AVEEVFPNTR HCFALWHILE KIPKSLAHVI GPHENFLPKF NKCIFKSWTD EEFDMRWWKM 420 ITLFELQDDE WVQSLYEDRK RWVPAFMDNV FLAGMSTSQR SESMNSFFDK YIHKKITLKE 480 FVKQYGAILQ NRYEEEAVAD FDTWQKQPAL RSPSPWEKQM SIVYTHAIFK RFQVEVLGVV 540 GCHPKRENEN QGTIPFRVQD CEKDENFMVI WNEEKSEVSC SCRLFEYRGF LCRHAMIVLQ 600 MCGRTSIPPR YILKRWTKDA KSGQSTTEGT DRVQTRVQRY NDLCKHAIEL SEEGSLSEES 660 YNIAFCVLVE ALKNCVNVNN SCISAVESTG HAQGLREAEE KNQGSLASKS SKKKSTSRKR 720 KGQSEPALMF VDTQDSLQPM ENLSSDGITL NGYYGAQQNV QGLVQLNLME PPHDGYYVNQ 780 QSMQGLGQLN SMAPGHDSFF GTQQSMHGLG QLDYRPSASF TYALQDESQL RSTQLHGGVS 840 RHP

Sequence ? help Back to Top

Protein Sequence Length: 843 aa Download sequence Send to blast

MMIKIGENQN AISNMVDCRD AMPCNDGVNE NMVDIVDETA RSRDSGIVDT SKRAVVGFEG  60
DAEFEPHNGI EFESHEAAYS FYQEYAKSMG FTTSIKNSRR SKKSKEFIDA KFACSRYGVT  120
PESDVGSSRR SSVKKTDCKA SMHVKRRPDG KWIIHEFVKE HNHELLPALA YHFRIYRNVK  180
LAEKNNIDIL NAVSERTRKM YVEMSRQSGG YQNVNMLQSD IKNQFDKSRH LVVDEGDAQI  240
MLEYFKRIKK ENPDFFYAID LNEEQRLRNL FWVDAKSRND YPSFNDVVSF DTTYVKFNEK  300
LPFAPFVGVN HHFQSMLLGC ALLADETKPT FVWLMKTWLR AMGGQAPKVI ITDQDKELKA  360
AVEEVFPNTR HCFALWHILE KIPKSLAHVI GPHENFLPKF NKCIFKSWTD EEFDMRWWKM  420
ITLFELQDDE WVQSLYEDRK RWVPAFMDNV FLAGMSTSQR SESMNSFFDK YIHKKITLKE  480
FVKQYGAILQ NRYEEEAVAD FDTWQKQPAL RSPSPWEKQM SIVYTHAIFK RFQVEVLGVV  540
GCHPKRENEN QGTIPFRVQD CEKDENFMVI WNEEKSEVSC SCRLFEYRGF LCRHAMIVLQ  600
MCGRTSIPPR YILKRWTKDA KSGQSTTEGT DRVQTRVQRY NDLCKHAIEL SEEGSLSEES  660
YNIAFCVLVE ALKNCVNVNN SCISAVESTG HAQGLREAEE KNQGSLASKS SKKKSTSRKR  720
KGQSEPALMF VDTQDSLQPM ENLSSDGITL NGYYGAQQNV QGLVQLNLME PPHDGYYVNQ  780
QSMQGLGQLN SMAPGHDSFF GTQQSMHGLG QLDYRPSASF TYALQDESQL RSTQLHGGVS  840
RHP

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:12753585, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:22634759}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00434	DAP	Transfer from AT4G15090	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated after exposure to far-red light. Subject to a negative feedback regulation by PHYA signaling. {ECO:0000269\|PubMed:18033885}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017630930.1	0.0	PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1
Refseq	XP_017630931.1	0.0	PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1
Refseq	XP_017630932.1	0.0	PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	A0A1U8L5X4	0.0	A0A1U8L5X4_GOSHI; protein FAR-RED IMPAIRED RESPONSE 1-like
STRING	Gorai.007G173400.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM118	26	253

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G15090.1	0.0	FAR1 family protein

Publications ? help Back to Top
Domergue F, et al. Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiol., 2010. 153(4): p. 1539-54 [PMID:20571114] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Wang C, et al. SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes. J Genet Genomics, 2015. 42(4): p. 161-8 [PMID:25953354] Wang W, et al. A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis. J Integr Plant Biol, 2016. 58(1): p. 91-103 [PMID:25989254] Ma L, et al. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. Mol Plant, 2016. 9(4): p. 541-57 [PMID:26714049] Siddiqui H,Khan S,Rhodes BM,Devlin PF FHY3 and FAR1 Act Downstream of Light Stable Phytochromes. Front Plant Sci, 2016. 7: p. 175 [PMID:26941752] Liu L,Li B,Liu X FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis. Plant Signal Behav, 2016. 11(10): p. e1238545 [PMID:27660915] Ma L,Xue N,Fu X,Zhang H,Li G Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar. New Phytol., 2017. 213(4): p. 1682-1696 [PMID:27859295] Liu Y, et al. Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1. Plant Cell, 2017. 29(9): p. 2269-2284 [PMID:28842534] Joly-Lopez Z, et al. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. Front Plant Sci, 2017. 8: p. 2027 [PMID:29250089]