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

RrC3747_p3

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

C3H

Protein Properties

Length: 384aa MW: 42539 Da PI: 7.8975

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3747_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	33.7	6.4e-11	126	149	3	26
S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHg 26 e C+ f+r+G C++Gd C FaHg RrC3747_p3 126 GEVCPEFRRGGDCSRGDDCEFAHG 149 689********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	8.4E-6	123	150	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.535	123	151	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.4E-6	123	153	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.0E-6	127	151	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.9E-8	127	149	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5	159	182	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 384 aa Download sequence Send to blast
MDVVRPTVEI PPRKLLSSSK SFQAESSPRS SPRKHNWNNK INKISISEQE EDSFNEDNNN 60 NTTKDTKEYC YDSDTDDPYA SDHFRMFEFK IRRCTRSRSH DWTDCPFAHP GEKARRRDPR 120 RFQYSGEVCP EFRRGGDCSR GDDCEFAHGV FECWLHPIRY RTEACKDGKH CKRKVCFFAH 180 SPRQLRVLPP EGSSASASPG KNPCCLFCSS SPTSTLLGNL SHLSRSPSSS PPLSPANKAA 240 AFSRLRSCAA AGSINYKDVL SELVNSLDSI SLAEALQVSS SSPVSTPVSA AAAAFASSCG 300 LSNQRLHLQQ QQQQSSPLQF ALSPSTPSYL ASSPRSNFFS DDFTPRQRQM NDVTPHAAGR 360 DKTSSFEDGS CGDPDIGWVN DLLT

Sequence ? help Back to Top

Protein Sequence Length: 384 aa Download sequence Send to blast

MDVVRPTVEI PPRKLLSSSK SFQAESSPRS SPRKHNWNNK INKISISEQE EDSFNEDNNN  60
NTTKDTKEYC YDSDTDDPYA SDHFRMFEFK IRRCTRSRSH DWTDCPFAHP GEKARRRDPR  120
RFQYSGEVCP EFRRGGDCSR GDDCEFAHGV FECWLHPIRY RTEACKDGKH CKRKVCFFAH  180
SPRQLRVLPP EGSSASASPG KNPCCLFCSS SPTSTLLGNL SHLSRSPSSS PPLSPANKAA  240
AFSRLRSCAA AGSINYKDVL SELVNSLDSI SLAEALQVSS SSPVSTPVSA AAAAFASSCG  300
LSNQRLHLQQ QQQQSSPLQF ALSPSTPSYL ASSPRSNFFS DDFTPRQRQM NDVTPHAAGR  360
DKTSSFEDGS CGDPDIGWVN DLLT

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription repressor that functions as negative regulator of phytochrome-mediated promotion of seed germination. Inhibits seed germination by regulating the expression of gibberellic acid (GA) and abscisic acid (ABA) metabolic genes. Does not regulate the expression of the DELLA genes RGA and RGA1. Activated by PIL5, a phytochrome-interacting basic helix-loop-helix transcription factor. {ECO:0000269\|PubMed:18487351}.

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	AC003027	1e-166	AC003027.1 Arabidopsis thaliana chromosome I BAC F21M11 genomic sequence, complete sequence.
GenBank	AK117219	1e-166	AK117219.1 Arabidopsis thaliana At1g03790 mRNA for unknown protein, complete cds, clone: RAFL16-76-P06.
GenBank	BT005342	1e-166	BT005342.1 Arabidopsis thaliana At1g03790 mRNA, complete cds.
GenBank	CP002684	1e-166	CP002684.1 Arabidopsis thaliana chromosome 1 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018450188.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 2-like
Swissprot	Q9ZWA1	0.0	C3H2_ARATH; Zinc finger CCCH domain-containing protein 2
TrEMBL	V4MW89	0.0	V4MW89_EUTSA; Uncharacterized protein
STRING	XP_006418203.1	0.0	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2987	27	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03790.1	1e-160	C3H 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] Chang G, et al. AFP2 as the novel regulator breaks high-temperature-induced seeds secondary dormancy through ABI5 and SOM in Arabidopsis thaliana. Biochem. Biophys. Res. Commun., 2018. 501(1): p. 232-238 [PMID:29723526]