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_48400.1_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: 85aa MW: 9766.08 Da PI: 6.2294

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_48400.1_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	43	8e-14	2	67	23	95
.HTT.---..--SEEEEEE.TTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEE CS B3 23 aeeh.ggkkeesktltled.esgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvk 95 +++h +gk+ ++ t tl++ + ++W+v + ++ lt+GWkeF++a++L+ gD+v+Fkl+g++ f +v+ Rsa1.0_48400.1_g00001.1 2 FSKHiQGKT-NGNTWTLTSdATDQTWQVIQ--EERR----LTRGWKEFAEAHDLRIGDIVIFKLEGSMVF--HVT 67 556645554.55577777658889999999..7777....************************998888..666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01019	2.3E-5	1	72	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.872	1	72	IPR003340	B3 DNA binding domain
CDD	cd10017	6.82E-12	2	69	No hit	No description
Pfam	PF02362	5.8E-9	7	64	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	1.57E-15	8	79	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.5E-18	11	81	IPR015300	DNA-binding pseudobarrel 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: 85 aa Download sequence Send to blast
FFSKHIQGKT NGNTWTLTSD ATDQTWQVIQ EERRLTRGWK EFAEAHDLRI GDIVIFKLEG 60 SMVFHVTPFG PSCCDIQYTS MLVVT

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_48400.1_g00001.1

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	AC189599	1e-125	AC189599.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH014H10, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018438527.1	9e-59	PREDICTED: B3 domain-containing protein REM7-like
Refseq	XP_018461325.1	9e-59	PREDICTED: B3 domain-containing protein REM7-like
Refseq	XP_018483785.1	9e-59	PREDICTED: B3 domain-containing protein REM7-like
Swissprot	O81778	5e-32	REM9_ARATH; B3 domain-containing protein REM9
Swissprot	Q8H2D0	1e-32	REM7_ARATH; B3 domain-containing protein REM7
TrEMBL	A0A3P5YBE8	2e-51	A0A3P5YBE8_BRACM; Uncharacterized protein
TrEMBL	A0A3P5YP81	5e-51	A0A3P5YP81_BRACM; Uncharacterized protein
TrEMBL	M4F5X8	2e-50	M4F5X8_BRARP; Uncharacterized protein
STRING	Bra016772.1-P	5e-51	(Brassica rapa)
STRING	Bra036483.1-P	8e-51	(Brassica rapa)
STRING	Bra036486.1-P	4e-51	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM204	22	261

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G31660.1	4e-35	B3 family protein

Publications ? help Back to Top
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] Wang S, et al. Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis. PLoS Genet., 2016. 12(5): p. e1006027 [PMID:27138552]