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

AT1G25560.1

Common Name

AtTEM1, EDF1, F2J7.3, TEM1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

RAV

Protein Properties

Length: 361aa MW: 40557.7 Da PI: 9.7148

Description

RAV family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G25560.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	37.9	4.5e-12	70	118	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 s+ykGV + +grW A+I++ ++r++lg+f +eeAa ++ a ++++g AT1G25560.1 70 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAASSYDIAVRRFRG 118 89**9888.8*****3.....5**********************998 PP
2	B3	104.7	4.8e-33	195	302	1	96
EEEE-..-HHHHTT-EE--HHH.HTT............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+ tpsdv+k++rlv+pk++ae+h + ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F+++ AT1G25560.1 195 FEKTVTPSDVGKLNRLVIPKQHAEKHfplpamttamgmNPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFERST 292 99*******************************988666789*************************************************886 PP SSEE..EEEE CS B3 87 rsefelvvkv 96 +++l++++ AT1G25560.1 293 GPDRQLYIHW 302 6888888876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	1.51E-24	70	125	No hit	No description
SuperFamily	SSF54171	3.86E-16	70	126	IPR016177	DNA-binding domain
Pfam	PF00847	3.4E-6	70	118	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	19.678	71	126	IPR001471	AP2/ERF domain
SMART	SM00380	6.1E-28	71	132	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	8.3E-20	71	126	IPR001471	AP2/ERF domain
Gene3D	G3DSA:2.40.330.10	1.1E-40	190	307	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.77E-30	194	301	No hit	No description
SuperFamily	SSF101936	1.44E-32	194	303	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS50863	14.212	195	306	IPR003340	B3 DNA binding domain
SMART	SM01019	1.3E-26	195	306	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.9E-30	195	302	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009873	Biological Process	ethylene-activated signaling pathway
GO:0048573	Biological Process	photoperiodism, flowering
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 361 aa Download sequence Send to blast
MEYSCVDDSS TTSESLSIST TPKPTTTTEK KLSSPPATSM RLYRMGSGGS SVVLDSENGV 60 ETESRKLPSS KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEEEAASSYD IAVRRFRGRD 120 AVTNFKSQVD GNDAESAFLD AHSKAEIVDM LRKHTYADEF EQSRRKFVNG DGKRSGLETA 180 TYGNDAVLRA REVLFEKTVT PSDVGKLNRL VIPKQHAEKH FPLPAMTTAM GMNPSPTKGV 240 LINLEDRTGK VWRFRYSYWN SSQSYVLTKG WSRFVKEKNL RAGDVVCFER STGPDRQLYI 300 HWKVRSSPVQ TVVRLFGVNI FNVSNEKPND VAVECVGKKR SREDDLFSLG CSKKQAIINI 360 L

Sequence ? help Back to Top

Protein Sequence Length: 361 aa Download sequence Send to blast

MEYSCVDDSS TTSESLSIST TPKPTTTTEK KLSSPPATSM RLYRMGSGGS SVVLDSENGV  60
ETESRKLPSS KYKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEEEAASSYD IAVRRFRGRD  120
AVTNFKSQVD GNDAESAFLD AHSKAEIVDM LRKHTYADEF EQSRRKFVNG DGKRSGLETA  180
TYGNDAVLRA REVLFEKTVT PSDVGKLNRL VIPKQHAEKH FPLPAMTTAM GMNPSPTKGV  240
LINLEDRTGK VWRFRYSYWN SSQSYVLTKG WSRFVKEKNL RAGDVVCFER STGPDRQLYI  300
HWKVRSSPVQ TVVRLFGVNI FNVSNEKPND VAVECVGKKR SREDDLFSLG CSKKQAIINI  360
L

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wid_A	7e-57	192	306	11	118	DNA-binding protein RAV1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.17318	0.0	flower\| leaf\| root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	255742_at	0.0
Expression Atlas	AT1G25560	-
AtGenExpress	AT1G25560	-
ATTED-II	AT1G25560	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in leaves. {ECO:0000269\|PubMed:18718758}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of the RAV transcription factor family that contains AP2 and B3 binding domains. Involved in the regulation of flowering under long days. Loss of function results in early flowering. Overexpression causes late flowering and repression of expression of FT. Novel transcriptional regulator involved in ethylene signaling. Promoter bound by EIN3. EDF1 in turn, binds to promoter elements in ethylene responsive genes.
UniProt	Transcriptional repressor of flowering time on long day plants. Acts directly on FT expression by binding 5'-CAACA-3' and 5'-CACCTG-3 sequences. Functionally redundant with TEM2. {ECO:0000269\|PubMed:18718758}.

Function -- GeneRIF ? help Back to Top
TEMPRANILLO genes (TEM1 and TEM2) act as novel direct Flowering locus T repressors. [PMID: 18718758] TEMPRANILLO genes link photoperiod and gibberellin pathways to control flowering. [PMID: 22549837] Data show that FOREVER YOUNG FLOWER UP-REGULATING FACTOR1 (FUF1; At1g71450) acts as an activator in suppressing ETHYLENE RESPONSE DNA BINDING FACTORs EDF1/2/3/4 function and senescence/abscission of the flowers. [PMID: 26063506] Data show that TEMPRANILLO (TEM) acts as a link between gibberellins (GAs) and cytokinin signaling in the epidermis by negatively regulating downstream genes of both trichome formation pathways. [PMID: 26802039]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00024	PBM	25215497	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G25560.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expressed with a circadian rhythm showing a peak at dawn. {ECO:0000269\|PubMed:18718758}.

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G65480(R)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G25560

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC079281	0.0	AC079281.4 Arabidopsis thaliana chromosome 1 BAC F2J7 genomic sequence, complete sequence.
GenBank	AY091069	0.0	AY091069.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBank	AY122941	0.0	AY122941.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBank	CP002684	0.0	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_173927.1	0.0	AP2/B3 transcription factor family protein
Swissprot	Q9C6M5	0.0	RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBL	A0A178W8G8	0.0	A0A178W8G8_ARATH; TEM1
STRING	AT1G25560.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM848	27	121
Representative plant	OGRP365	16	108

Link Out ? help Back to Top
Phytozome	AT1G25560.1
Entrez Gene	839143
iHOP	AT1G25560
wikigenes	AT1G25560

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Hu YX,Wang YX,Liu XF,Li JY Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell Res., 2004. 14(1): p. 8-15 [PMID:15040885] Teige M, et al. The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol. Cell, 2004. 15(1): p. 141-52 [PMID:15225555] Hampton CR, et al. Cesium toxicity in Arabidopsis. Plant Physiol., 2004. 136(3): p. 3824-37 [PMID:15489280] Stepanova AN,Hoyt JM,Hamilton AA,Alonso JM A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Plant Cell, 2005. 17(8): p. 2230-42 [PMID:15980261] Nakano T,Suzuki K,Fujimura T,Shinshi H Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol., 2006. 140(2): p. 411-32 [PMID:16407444] Mandaokar A, et al. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. Plant J., 2006. 46(6): p. 984-1008 [PMID:16805732] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] Ma S,Bohnert HJ Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol., 2007. 8(4): p. R49 [PMID:17408486] Usadel B, et al. Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes. Plant Physiol., 2008. 146(4): p. 1834-61 [PMID:18305208] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Castillejo C,Pelaz S The balance between CONSTANS and TEMPRANILLO activities determines FT expression to trigger flowering. Curr. Biol., 2008. 18(17): p. 1338-43 [PMID:18718758] Swaminathan K,Peterson K,Jack T The plant B3 superfamily. Trends Plant Sci., 2008. 13(12): p. 647-55 [PMID:18986826] Ikeda M,Ohme-Takagi M A novel group of transcriptional repressors in Arabidopsis. Plant Cell Physiol., 2009. 50(5): p. 970-5 [PMID:19324928] Yant L,Mathieu J,Schmid M Just say no: floral repressors help Arabidopsis bide the time. Curr. Opin. Plant Biol., 2009. 12(5): p. 580-6 [PMID:19695946] Hanada K, et al. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol. Biol. Evol., 2011. 28(1): p. 377-82 [PMID:20736450] Chen MK, et al. The MADS box gene, FOREVER YOUNG FLOWER, acts as a repressor controlling floral organ senescence and abscission in Arabidopsis. Plant J., 2011. 68(1): p. 168-85 [PMID:21689171] Causier B,Ashworth M,Guo W,Davies B The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol., 2012. 158(1): p. 423-38 [PMID:22065421] Osnato M,Castillejo C,Mat TEMPRANILLO genes link photoperiod and gibberellin pathways to control flowering in Arabidopsis. Nat Commun, 2012. 3: p. 808 [PMID:22549837] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Choi D, et al. iNID: an analytical framework for identifying network models for interplays among developmental signaling in Arabidopsis. Mol Plant, 2014. 7(5): p. 792-813 [PMID:24380880] Sgamma T,Jackson A,Muleo R,Thomas B,Massiah A TEMPRANILLO is a regulator of juvenility in plants. Sci Rep, 2014. 4: p. 3704 [PMID:24424565] Matías-Hernández L,Aguilar-Jaramillo AE,Marín-González E,Suárez-López P,Pelaz S RAV genes: regulation of floral induction and beyond. Ann. Bot., 2014. 114(7): p. 1459-70 [PMID:24812253] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Chen WH,Li PF,Chen MK,Lee YI,Yang CH FOREVER YOUNG FLOWER Negatively Regulates Ethylene Response DNA-Binding Factors by Activating an Ethylene-Responsive Factor to Control Arabidopsis Floral Organ Senescence and Abscission. Plant Physiol., 2015. 168(4): p. 1666-83 [PMID:26063506] Marín-González E, et al. SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures. Plant Physiol., 2015. 169(2): p. 1214-24 [PMID:26243615] Matías-Hernández L, et al. TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation. Plant Physiol., 2016. 170(3): p. 1624-39 [PMID:26802039]