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_00308.1_g00009.1

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: 221aa MW: 25567.4 Da PI: 7.3232

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00308.1_g00009.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	103.3	1.3e-32	37	142	1	99
EEEE-..-HHHHTT-EE--HHH.HTT........---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh........ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegD 78 f+k ltpsdv+k++rlv+pk++ae++ + + e++ l +ede+g+ W+++++y+++s++yvltkGW+++vk+++L++gD Rsa1.0_00308.1_g00009.1 37 FEKPLTPSDVGKLNRLVIPKQHAERYfplaaavvDAV-EKGLLLCFEDEEGKPWRFRYSYWNSSQSYVLTKGWSRYVKEKQLDAGD 121 99***************************997555.5778**************************************** PP EEEEEE-SSSEE..EEEEE-S CS B3 79 fvvFkldgrsefelvvkvfrk 99 +v+F++++ ++++++++++r+ Rsa1.0_00308.1_g00009.1 122 VVIFHRHRADGGRFFIGWRRR 142 *88779999****97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	4.7E-41	31	150	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.01E-30	34	142	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.19E-28	36	132	No hit	No description
SMART	SM01019	8.4E-24	37	143	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.3E-29	37	142	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	14.099	37	143	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: 221 aa Download sequence Send to blast
MSINQYSSEF HYHSLMWQQQ QQRHHQNEVV EEKEALFEKP LTPSDVGKLN RLVIPKQHAE 60 RYFPLAAAVV DAVEKGLLLC FEDEEGKPWR FRYSYWNSSQ SYVLTKGWSR YVKEKQLDAG 120 DVVIFHRHRA DGGRFFIGWR RRGDSSSSSD SYRHLQSNAY PHAVNRIAGA QAVENQRGNS 180 KTLRLFGVNM ECQIDSDCSE PSTPDGFTTC PTNHDQFSYL T

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5os9_A	2e-49	30	142	1	113	B3 domain-containing transcription factor NGA1
5os9_B	2e-49	30	142	1	113	B3 domain-containing transcription factor NGA1
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00308.1_g00009.1

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	AK117587	0.0	AK117587.1 Arabidopsis thaliana At2g36080 mRNA for putative RAV2-like DNA binding protein, complete cds, clone: RAFL17-23-G02.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018481378.1	1e-168	PREDICTED: B3 domain-containing protein At2g36080 isoform X1
Swissprot	Q8GYJ2	1e-123	Y2608_ARATH; B3 domain-containing protein At2g36080
TrEMBL	A0A397ZPZ0	1e-135	A0A397ZPZ0_BRACM; Uncharacterized protein
STRING	Bra017262.1-P	1e-135	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1220	28	100

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G36080.1	1e-112	B3 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] Tanaka M, et al. The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation. Plant Cell, 2016. 28(11): p. 2830-2849 [PMID:27760805]