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

Solyc09g007550.2.1

Common Name

LOC101250621

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: 460aa MW: 51314.6 Da PI: 9.7749

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc09g007550.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.7e-05	61	83	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Solyc09g007550.2.1 61 FICEICNKGFQRDQNLQLHRRGH 83 89*******************88 PP
2	zf-C2H2	14.1	0.00014	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Solyc09g007550.2.1 138 WKCEKCSKKYAVQSDWKAHTKTC 160 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.2E-5	60	83	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.65E-7	60	83	No hit	No description
SMART	SM00355	0.022	61	83	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.845	61	83	IPR007087	Zinc finger, C2H2
Pfam	PF12171	5.4E-5	61	83	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	63	83	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	103	133	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.3E-4	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.65E-7	133	158	No hit	No description
SMART	SM00355	130	138	158	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: 460 aa Download sequence Send to blast
MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPGT PDPDAEVIAI SPKTLMATNR 60 FICEICNKGF QRDQNLQLHR RGHNLPWKLK QRNKQEIVKK KVYICPEKSC VHHDPSRALG 120 DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHTKTC GTREYKCDCG TLFSRKDSFI 180 THRAFCDALA EESARITTTN NLNFNQQQQQ PVGVSQIGTS FAQDFTSMTT VNPLHQHQQK 240 PRLSLWLNQA NNNMSSQSSN LFGLPDHHMV QIPSHNMFGT NQILNPTPTT TTTTNTNTNT 300 NTPATPNPPI PMSATALLQK AAQMGSTKST PNYFSNTFGV MHSSSSPSSN NTTQIFNNNE 360 IHQAFAKQTE DYNQTENILI NGCPNMNSSV NSKAINLDQA LLQTGGMHNQ NVHFNLHNSL 420 TRDFLGMGNE GGQPFLPQEL AKFASINSAM GLSHYSTGH*

Sequence ? help Back to Top

Protein Sequence Length: 460 aa Download sequence Send to blast

MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPGT PDPDAEVIAI SPKTLMATNR  60
FICEICNKGF QRDQNLQLHR RGHNLPWKLK QRNKQEIVKK KVYICPEKSC VHHDPSRALG  120
DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHTKTC GTREYKCDCG TLFSRKDSFI  180
THRAFCDALA EESARITTTN NLNFNQQQQQ PVGVSQIGTS FAQDFTSMTT VNPLHQHQQK  240
PRLSLWLNQA NNNMSSQSSN LFGLPDHHMV QIPSHNMFGT NQILNPTPTT TTTTNTNTNT  300
NTPATPNPPI PMSATALLQK AAQMGSTKST PNYFSNTFGV MHSSSSPSSN NTTQIFNNNE  360
IHQAFAKQTE DYNQTENILI NGCPNMNSSV NSKAINLDQA LLQTGGMHNQ NVHFNLHNSL  420
TRDFLGMGNE GGQPFLPQEL AKFASINSAM GLSHYSTGH*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-38	134	203	3	72	Zinc finger protein JACKDAW
5b3h_F	6e-38	134	203	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.14244	0.0	flower\| fruit\| leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269\|PubMed:17785527}.
Uniprot	TISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269\|PubMed:17785527}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc09g007550.2.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

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	EF576813	0.0	Solanum lycopersicum chromosome 9 clone C09HBa0072G22, complete sequence

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004246670.1	0.0	zinc finger protein JACKDAW isoform X1
Swissprot	Q700D2	1e-129	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A3Q7HWE3	0.0	A0A3Q7HWE3_SOLLC; Uncharacterized protein
STRING	Solyc09g007550.2.1	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
AT5G03150.1	1e-101	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	Solyc09g007550.2.1
Entrez Gene	101250621

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] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]