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

RrC15946_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 225aa MW: 25018.4 Da PI: 10.4905

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC15946_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	104.4	6.1e-33	49	160	1	97
EEEE-..-HHHHTT-EE--HHH.HTT...............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh...............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 f+k+ tpsdv+k++rlv+pk++ae+h ++++++ + led++g++W+++++y+++s++yvltkGW++Fvk+++L++gD+v F+ RrC15946_p2 49 FEKAVTPSDVGKLNRLVIPKQHAEKHfplpamttavtvtamAPSPTKGVLINLEDRTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLRAGDVVCFE 146 89****************************999999999667789************************************************* PP E-SSSEE..EEEEE CS B3 84 ldgrsefelvvkvf 97 ++ +++l++ ++ RrC15946_p2 147 RSTGPDRQLYIDWR 160 88778888988887 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.9E-40	43	163	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.28E-31	47	152	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.17E-30	48	148	No hit	No description
PROSITE profile	PS50863	13.944	49	163	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-29	49	160	IPR003340	B3 DNA binding domain
SMART	SM01019	2.4E-25	49	163	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: 225 aa Download sequence Send to blast
MLRKHTYADE LQQSRRKFLD GDGNGKSGTA TMSSSHGNDG VSRAREVLFE KAVTPSDVGK 60 LNRLVIPKQH AEKHFPLPAM TTAVTVTAMA PSPTKGVLIN LEDRTGKVWR FRYSYWNSSQ 120 SYVLTKGWSR FVKEKNLRAG DVVCFERSTG PDRQLYIDWR VQSGTEEITP VRSVVRLFGV 180 NISNATSNAK SNDVAAEYGG GKKRSREVDL FALGCSKKQT MINAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wid_A	6e-60	46	166	11	121	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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013637910.1	1e-145	PREDICTED: AP2/ERF and B3 domain-containing transcription repressor TEM1-like
Swissprot	Q9C6M5	1e-119	RAVL1_ARATH; AP2/ERF and B3 domain-containing transcription repressor TEM1
TrEMBL	A0A0D3CD61	1e-143	A0A0D3CD61_BRAOL; Uncharacterized protein
STRING	Bo5g043120.1	1e-144	(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-115	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]