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_18666.1_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: 217aa MW: 24937.2 Da PI: 9.6975

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_18666.1_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	52.3	1.1e-16	120	213	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 f vl ps+ + ++++lp fae++ g+ ++ ++ ++ ++W v++ k gr +++GW eF +n++ egD++vF+l Rsa1.0_18666.1_g00001.1 120 FRVVLRPSYLYRGCIMYLPSGFAEKYlTGI-AGF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELL 199 678899******************8444.344..44.34677***..666666779******************** PP SSSEE..EEEEE-S CS B3 86 grsefelvvkvfrk 99 ++++f l+v++fr Rsa1.0_18666.1_g00001.1 200 KTRDFILKVTAFRV 213 99*999999985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	3.7E-23	112	213	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	3.53E-22	113	214	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.12E-20	118	212	No hit	No description
SMART	SM01019	1.8E-18	120	214	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.435	120	214	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.3E-15	120	213	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: 217 aa Download sequence Send to blast
MDSAHDVFNN KRARLFEDRQ IEGTRDTQPL IPESNEGYDG SNPTQSLFTD SKPEETPKVP 60 KKRGRKKKNP NPEDMSSSTT PENSSKFYKS ASDRKRTVTA EERERAISAA KTYEPTNPFF 120 RVVLRPSYLY RGCIMYLPSG FAEKYLTGIA GFIKLQLGEK QWPVRCLYKA GRAKFSQGWY 180 EFTLENNIGE GDVCVFELLK TRDFILKVTA FRVNQYV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4i1k_A	1e-88	86	217	15	146	B3 domain-containing transcription factor VRN1
4i1k_B	1e-88	86	217	15	146	B3 domain-containing transcription factor VRN1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the regulation of vernalization (By similarity). Binds to DNA in vitro in a non-sequence-specific manner. XLG2 promotes the DNA binding activity of RTV1 specifically to promoter regions of FT and SOC1 in vivo and thus leads to the activation of floral integrator genes. {ECO:0000250, ECO:0000269\|PubMed:22232549}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_18666.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By cold. {ECO:0000269\|PubMed:22232549}.

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	AK353236	1e-175	AK353236.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-N21.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018492716.1	1e-162	PREDICTED: B3 domain-containing protein REM19-like
Swissprot	Q9XIB5	1e-121	REM19_ARATH; B3 domain-containing protein REM19
TrEMBL	A0A078J4Z6	1e-140	A0A078J4Z6_BRANA; BnaC05g51360D protein
TrEMBL	A0A0D3CFU5	1e-140	A0A0D3CFU5_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6EJG7	1e-140	A0A3P6EJG7_BRAOL; Uncharacterized protein
STRING	Bo5g076230.1	1e-141	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1124	28	103

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G49480.1	1e-110	related to vernalization1 1

Publications ? help Back to Top
Conte MG,Gaillard S,Droc G,Perin C Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics, 2008. 9: p. 183 [PMID:18426584] Mantegazza O, et al. Analysis of the arabidopsis REM gene family predicts functions during flower development. Ann. Bot., 2014. 114(7): p. 1507-15 [PMID:25002525]