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

Solyc06g054620.2.1

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

C3H

Protein Properties

Length: 381aa MW: 40984.8 Da PI: 6.7685

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc06g054620.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	36.7	7e-12	47	71	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 ++ C +++r+G+C yG+rC+F+H++ Solyc06g054620.2.1 47 EPDCIYYLRNGICGYGSRCRFNHPR 71 799********************96 PP
2	zf-CCCH	33.1	9.5e-11	96	117	6	27
-SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 6 CrffartGtCkyGdrCkFaHgp 27 C++++rtG C++G++Ck++H++ Solyc06g054620.2.1 96 CQYYMRTGMCRFGASCKYHHPR 117 ********************96 PP
3	zf-CCCH	30.9	4.8e-10	139	163	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 +++C ++++tG+Ck+G CkF+H++ Solyc06g054620.2.1 139 EKECAHYMKTGHCKFGIICKFNHPQ 163 679********************97 PP
4	zf-CCCH	34.9	2.6e-11	334	360	1	27
--S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHgp 27 +++++C++++++G Ck+G++Ck+ H+p Solyc06g054620.2.1 334 PGQPECHYYMKYGDCKFGSSCKYQHPP 360 5789*********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	7.8E-6	44	71	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.418	44	72	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.4E-9	47	71	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	3.27E-6	48	72	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.0E-5	50	71	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.1E-4	90	117	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.399	90	118	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.83E-6	93	118	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.9E-5	95	117	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.3E-7	96	117	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0048	136	163	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.554	136	164	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.57E-5	137	164	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.7E-7	139	163	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	3.9E-5	333	360	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.352	333	361	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.2E-8	335	360	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.44E-5	337	361	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: 381 aa Download sequence Send to blast
MFRRDQSTDD VPVTEQASSN EETGLEEPMR QLSVGTEAGS YPERPNEPDC IYYLRNGICG 60 YGSRCRFNHP RDRSLAVGER RATGGEYPER AGQYVCQYYM RTGMCRFGAS CKYHHPRQGE 120 ESPSLVIHNI FGYPLRPNEK ECAHYMKTGH CKFGIICKFN HPQPTGVQVP ASAAGPFPLP 180 AVVPPPATYP ELRPLPVDSA EQYGIITGNW PVIGPALLSD SYTPDTYGPM FFPPEVVPVS 240 DWTHYLGSTS PVQYQTTQSA AGAGPVPCQS SHSAAGTGPV PSQTTQSAAG AGPIYGHTGL 300 SASAPAYASP YASLTASRGA SSSIQDGLAF PERPGQPECH YYMKYGDCKF GSSCKYQHPP 360 ESSGSKAALI LRAMGLPPDL *

Sequence ? help Back to Top

Protein Sequence Length: 381 aa Download sequence Send to blast

MFRRDQSTDD VPVTEQASSN EETGLEEPMR QLSVGTEAGS YPERPNEPDC IYYLRNGICG  60
YGSRCRFNHP RDRSLAVGER RATGGEYPER AGQYVCQYYM RTGMCRFGAS CKYHHPRQGE  120
ESPSLVIHNI FGYPLRPNEK ECAHYMKTGH CKFGIICKFN HPQPTGVQVP ASAAGPFPLP  180
AVVPPPATYP ELRPLPVDSA EQYGIITGNW PVIGPALLSD SYTPDTYGPM FFPPEVVPVS  240
DWTHYLGSTS PVQYQTTQSA AGAGPVPCQS SHSAAGTGPV PSQTTQSAAG AGPIYGHTGL  300
SASAPAYASP YASLTASRGA SSSIQDGLAF PERPGQPECH YYMKYGDCKF GSSCKYQHPP  360
ESSGSKAALI LRAMGLPPDL *

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc06g054620.2.1

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_004241158.2	0.0	zinc finger CCCH domain-containing protein 5-like isoform X1
TrEMBL	M1D145	0.0	M1D145_SOLTU; Uncharacterized protein
STRING	Solyc06g054620.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA18578	4	4
Representative plant	OGRP2865	11	31

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G06410.1	5e-86	C3H family protein

Link Out ? help Back to Top
Phytozome	Solyc06g054620.2.1

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505]