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

Solyc04g008500.2.1

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

C2H2

Protein Properties

Length: 518aa MW: 57519.5 Da PI: 9.23

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc04g008500.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.3	0.00012	53	73	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C+ C+k F r nL+ H r H Solyc04g008500.2.1 53 CEVCNKGFQREQNLQLHRRGH 73 *******************88 PP
2	zf-C2H2	14.6	9.7e-05	128	150	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Solyc04g008500.2.1 128 FKCEKCSKKYAVQSDWKAHTKTC 150 89*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	9.8E-6	50	73	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.95E-7	50	73	No hit	No description
SMART	SM00355	0.025	51	73	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.97	51	73	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	53	73	IPR007087	Zinc finger, C2H2
SMART	SM00355	160	93	123	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.6E-5	116	149	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.95E-7	123	148	No hit	No description
SMART	SM00355	88	128	148	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 518 aa Download sequence Send to blast
MREEELSQNQ QENLLQAQAP SKKRRNQPGT PSPDAEVIAL SPNTLMATNR FLCEVCNKGF 60 QREQNLQLHR RGHNLPWKLK QKNTKEVAKR KVYLCPEPTC VHHEPSRALG DLTGIKKHYF 120 RKHGEKKFKC EKCSKKYAVQ SDWKAHTKTC GTREYRCDCG TLFSRRDSFI THRAFCDALV 180 QENARNILSP NSLMNTLGMN NNQYLYGSSS NINLGTFSKL GNNNNITKTT TTTTTTTSGV 240 QFDHHHHDNN LIGSSTTTTT TTNNPFFLQD TNQDHYNANN NNIKPLMVHG LMQLPNLDHN 300 NNNSSSSTTM FNLNFFQNNL STNSGILGDH HHHHHRHDNN SNISCSIPSL YGVQVLESSN 360 TTFSSGPIMS ATALLQKAAQ MGSSSTSNIS ATASLFKAFG SNTSGSSSSG TKSDHQAFNF 420 GSDITDSGII NAYGGGSHEG YNTTTKLNFE QNQGPPQKKQ LTRDFLGVGE IVRSMNGRFS 480 TQREQQQQNN GLNNMMSSLL DPERNQIQQS FGSATND*

Sequence ? help Back to Top

Protein Sequence Length: 518 aa Download sequence Send to blast

MREEELSQNQ QENLLQAQAP SKKRRNQPGT PSPDAEVIAL SPNTLMATNR FLCEVCNKGF  60
QREQNLQLHR RGHNLPWKLK QKNTKEVAKR KVYLCPEPTC VHHEPSRALG DLTGIKKHYF  120
RKHGEKKFKC EKCSKKYAVQ SDWKAHTKTC GTREYRCDCG TLFSRRDSFI THRAFCDALV  180
QENARNILSP NSLMNTLGMN NNQYLYGSSS NINLGTFSKL GNNNNITKTT TTTTTTTSGV  240
QFDHHHHDNN LIGSSTTTTT TTNNPFFLQD TNQDHYNANN NNIKPLMVHG LMQLPNLDHN  300
NNNSSSSTTM FNLNFFQNNL STNSGILGDH HHHHHRHDNN SNISCSIPSL YGVQVLESSN  360
TTFSSGPIMS ATALLQKAAQ MGSSSTSNIS ATASLFKAFG SNTSGSSSSG TKSDHQAFNF  420
GSDITDSGII NAYGGGSHEG YNTTTKLNFE QNQGPPQKKQ LTRDFLGVGE IVRSMNGRFS  480
TQREQQQQNN GLNNMMSSLL DPERNQIQQS FGSATND*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	8e-33	124	201	3	72	Zinc finger protein JACKDAW
5b3h_F	8e-33	124	201	3	72	Zinc finger protein JACKDAW
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.22759	0.0	callus\| leaf

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:24821766, ECO:0000305\|PubMed:19726569}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00256	DAP	Transfer from AT2G02080	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc04g008500.2.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004236896.1	0.0	protein indeterminate-domain 5, chloroplastic isoform X2
Swissprot	Q8GYC1	1e-125	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A3Q7FW43	0.0	A0A3Q7FW43_SOLLC; Uncharacterized protein
STRING	Solyc04g008500.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA103	24	350
Representative plant	OGRP95	16	242

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	1e-108	indeterminate(ID)-domain 4

Link Out ? help Back to Top
Phytozome	Solyc04g008500.2.1

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] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]