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

Tp57577_TGAC_v2_mRNA28021

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium

Family

FAR1

Protein Properties

Length: 881aa MW: 100751 Da PI: 6.2188

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA28021	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	88.4	1.1e-27	119	205	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleH 85 fY+eYAk++GF++++++s++sk+++e+++++f Cs++g + e+++ ++r+ ++++t+Cka+++vkk+ dgkw ++++ ++H Tp57577_TGAC_v2_mRNA28021 119 FYQEYAKSMGFTTSIKNSRRSKKTKEFIDAKFACSRYGVTPESDSG---SSRRPSVKKTDCKACMHVKKKPDGKWTIHEFIKDH 199 **************************************999888...7788889************************ PP FAR1 86 nHelap 91 nHel p Tp57577_TGAC_v2_mRNA28021 200 NHELLP 205 *975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	7.3E-25	119	205	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	4.1E-29	326	418	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.285	605	641	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	5.0E-7	607	640	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.4E-8	616	643	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: 881 aa Download sequence Send to blast
LQSGYNFDNF DCGSYSEWND GSVVSGGYPG WNDFDDSVVS GGYPGWNDID DCVVSGGYPG 60 WNDDSAVSGS MGDTVHEEHH TASAPVASPK RDIALFEGDK DFEPPNGIEF ESHEAAYTFY 120 QEYAKSMGFT TSIKNSRRSK KTKEFIDAKF ACSRYGVTPE SDSGSSRRPS VKKTDCKACM 180 HVKKKPDGKW TIHEFIKDHN HELLPALAYH FRIHRNVKLA EKNNIDILHA VSERTRKMYV 240 EMSRQSGGCQ NIGSIVGDMN YQFDRGQFLA LDEGDAQVML EYFKHIQKDN PNFFYSIDLN 300 DEQRLRNLFW IDSKSIDDYL SFNDAVSFDT TYIKSNEKLP FAPFIGVNHH SQPILLGCAL 360 IADETKPTFV WLLKTWLRAM RGKAPKVIVT DQDKALKEAI EEVFPNVRHC FSLWHILEKI 420 PENLSFVIKQ YKNFLPKFNN CIFKSWTDEQ FDLSWWEMVT IFELHDDVWF HSLYEDRKKW 480 VPTYMGDVFL AGMSTPQRSE SMNSFFDKYI HKKITLKEFV KQYGLILQNR YDEEAIADFD 540 TLHKQPALKS PSPWEKQMST VYTHAIFKKF QVEVLGVAGC QSRIEVGDGT VAKFIVQDYE 600 KDEEFLVTWN ELSSEVTCFC RLFEYKGFLC RHALSVLQRC GCSSVPSQYI KKRWTKDAKI 660 REPIITDSTR RVQTRAQRYN DLCKRAIELS EEGSLSEESY NVAIRTLVSC LKNCVLVNNS 720 NDNGAEAGNN GYSLREAEES QSTLALKPSK KRNTTRKRKM QQEQNPVLVD AQDSLQQMDN 780 LTSDAMNLNG YYGTQQNVQG LHVQLNLMEP PQDGYYVNQQ SMQGLGPLNS MGPSHDGFFG 840 TQQSIHGMGG QLEYRPTTTF GYSLQDEHDP HFHSNNSRNT *

Sequence ? help Back to Top

Protein Sequence Length: 881 aa Download sequence Send to blast

LQSGYNFDNF DCGSYSEWND GSVVSGGYPG WNDFDDSVVS GGYPGWNDID DCVVSGGYPG  60
WNDDSAVSGS MGDTVHEEHH TASAPVASPK RDIALFEGDK DFEPPNGIEF ESHEAAYTFY  120
QEYAKSMGFT TSIKNSRRSK KTKEFIDAKF ACSRYGVTPE SDSGSSRRPS VKKTDCKACM  180
HVKKKPDGKW TIHEFIKDHN HELLPALAYH FRIHRNVKLA EKNNIDILHA VSERTRKMYV  240
EMSRQSGGCQ NIGSIVGDMN YQFDRGQFLA LDEGDAQVML EYFKHIQKDN PNFFYSIDLN  300
DEQRLRNLFW IDSKSIDDYL SFNDAVSFDT TYIKSNEKLP FAPFIGVNHH SQPILLGCAL  360
IADETKPTFV WLLKTWLRAM RGKAPKVIVT DQDKALKEAI EEVFPNVRHC FSLWHILEKI  420
PENLSFVIKQ YKNFLPKFNN CIFKSWTDEQ FDLSWWEMVT IFELHDDVWF HSLYEDRKKW  480
VPTYMGDVFL AGMSTPQRSE SMNSFFDKYI HKKITLKEFV KQYGLILQNR YDEEAIADFD  540
TLHKQPALKS PSPWEKQMST VYTHAIFKKF QVEVLGVAGC QSRIEVGDGT VAKFIVQDYE  600
KDEEFLVTWN ELSSEVTCFC RLFEYKGFLC RHALSVLQRC GCSSVPSQYI KKRWTKDAKI  660
REPIITDSTR RVQTRAQRYN DLCKRAIELS EEGSLSEESY NVAIRTLVSC LKNCVLVNNS  720
NDNGAEAGNN GYSLREAEES QSTLALKPSK KRNTTRKRKM QQEQNPVLVD AQDSLQQMDN  780
LTSDAMNLNG YYGTQQNVQG LHVQLNLMEP PQDGYYVNQQ SMQGLGPLNS MGPSHDGFFG  840
TQQSIHGMGG QLEYRPTTTF GYSLQDEHDP HFHSNNSRNT *

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	754	759	TRKRKM

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp57577_TGAC_v2_mRNA28021

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}.

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	AC235177	0.0	AC235177.1 Glycine max strain Williams 82 clone GM_WBb0007H11, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004496891.1	0.0	protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	A0A2K3MUT3	0.0	A0A2K3MUT3_TRIPR; Protein far-red impaired response 1-like (Fragment)
STRING	XP_004496891.1	0.0	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF40	30	530

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

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA28021

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]