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

Rsa1.0_18041.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

Protein Properties

Length: 243aa MW: 27269.8 Da PI: 10.1032

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_18041.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	104.1	7.3e-33	81	181	1	96
EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvv 81 f+k+ tpsdv+k++rlv+pk++ae+h ++++ + led++g++W+++++y+++s++yvltkGW++Fvk++gL++gD v Rsa1.0_18041.1_g00001.1 81 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpaTTTAAKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKGLRAGDAVC 166 89***********************99986666799******************************************** PP EEE-SSSEE..EEEE CS B3 82 Fkldgrsefelvvkv 96 F+++ +++l++ + Rsa1.0_18041.1_g00001.1 167 FERSTGPDRQLYIDW 181 8766777777765 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	2.0E-42	74	187	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.96E-32	78	179	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.43E-30	80	170	No hit	No description
Pfam	PF02362	9.2E-30	81	181	IPR003340	B3 DNA binding domain
SMART	SM01019	8.3E-26	81	185	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	14.692	81	185	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 243 aa Download sequence Send to blast
KFRGRDAAVT NFKSPADDSE SAFLEAHSKA EIVDMLRKHT YADELRQSER KFLDGDGNNG 60 KRRKTATAVN ENDGVSRELL FEKAVTPSDV GKLNRLVIPK QHAEKHFPLP ATTTAAKGVL 120 INLEDRTGKV WRFRYSYWNS SQSYVLTKGW SRFVKEKGLR AGDAVCFERS TGPDRQLYID 180 WKVRSGTEVI NPVQNVVRLF GVNIFNAATN AKTNDECGGE KRSREVDLFA LGCSKKQAII 240 NAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wid_A	7e-62	78	189	11	122	DNA-binding protein RAV1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_18041.1_g00001.1

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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC079281	3e-64	AC079281.4 Arabidopsis thaliana chromosome 1 BAC F2J7 genomic sequence, complete sequence.
GenBank	AY056169	3e-64	AY056169.1 Arabidopsis thaliana At1g25560 mRNA sequence.
GenBank	AY091069	3e-64	AY091069.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBank	AY122941	3e-64	AY122941.1 Arabidopsis thaliana putative DNA-binding protein RAV2 (At1g25560) mRNA, complete cds.
GenBank	CP002684	3e-64	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018447844.1	1e-180	PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
Swissprot	Q9C6M5	1e-128	RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBL	A0A397YL50	1e-148	A0A397YL50_BRACM; Uncharacterized protein
STRING	Bo3g138550.1	1e-145	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM848	27	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G25560.1	1e-130	RAV family protein

Publications ? help Back to Top
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] 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]