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

Sopen09g002420.2

Organism

Solanum pennellii

Taxonomic ID

28526

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: 455aa MW: 51012.2 Da PI: 9.7749

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopen09g002420.2	genome	spenn	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	58	80	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Sopen09g002420.2 58 FICEICNKGFQRDQNLQLHRRGH 80 89*******************88 PP
2	zf-C2H2	14.1	0.00014	135	157	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Sopen09g002420.2 135 WKCEKCSKKYAVQSDWKAHTKTC 157 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	4.11E-7	57	80	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.2E-5	57	80	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.845	58	80	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.022	58	80	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	5.3E-5	58	80	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	60	80	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	100	130	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.3E-4	123	156	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.11E-7	130	155	No hit	No description
SMART	SM00355	130	135	155	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: 455 aa Download sequence Send to blast
MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPDP DAEVIAISPK TLMATNRFIC 60 EICNKGFQRD QNLQLHRRGH NLPWKLKQRN KQEIVKKKVY ICPEKSCVHH DPSRALGDLT 120 GIKKHFSRKH GEKKWKCEKC SKKYAVQSDW KAHTKTCGTR EYKCDCGTLF SRKDSFITHR 180 AFCDALAEES ARITTTNNLN FNQQQQQQPV GVSQIGTSFA QDFTSMTTVN PLHQHQQKPR 240 LSLWLNQANN NMSSQSSNLF GLPDHHMVQI PSHNMFATNQ ILNPTPTTNT NTNTNTNTPA 300 TPNPPIPMSA TALLQKAAQM GSTKSTPNYF SNTFGVMHSS SSPSSNNTTQ IFNNNEIHQA 360 FAKQTEDYNQ TENILINGCP NMNSSVNSKA INLDQALLQT GGMHNQNVHF NLHNSLTRDF 420 LGMGNEGGQP FLPQELAKFA SINSAMGLSH YSTGH

Sequence ? help Back to Top

Protein Sequence Length: 455 aa Download sequence Send to blast

MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPDP DAEVIAISPK TLMATNRFIC  60
EICNKGFQRD QNLQLHRRGH NLPWKLKQRN KQEIVKKKVY ICPEKSCVHH DPSRALGDLT  120
GIKKHFSRKH GEKKWKCEKC SKKYAVQSDW KAHTKTCGTR EYKCDCGTLF SRKDSFITHR  180
AFCDALAEES ARITTTNNLN FNQQQQQQPV GVSQIGTSFA QDFTSMTTVN PLHQHQQKPR  240
LSLWLNQANN NMSSQSSNLF GLPDHHMVQI PSHNMFATNQ ILNPTPTTNT NTNTNTNTPA  300
TPNPPIPMSA TALLQKAAQM GSTKSTPNYF SNTFGVMHSS SSPSSNNTTQ IFNNNEIHQA  360
FAKQTEDYNQ TENILINGCP NMNSSVNSKA INLDQALLQT GGMHNQNVHF NLHNSLTRDF  420
LGMGNEGGQP FLPQELAKFA SINSAMGLSH YSTGH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-38	131	200	3	72	Zinc finger protein JACKDAW
5b3h_F	6e-38	131	200	3	72	Zinc finger protein JACKDAW
Search in ModeBase

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}.

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	HG975448	0.0	HG975448.1 Solanum pennellii chromosome ch09, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015086420.1	0.0	zinc finger protein JACKDAW-like isoform X2
Swissprot	Q700D2	1e-125	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A3Q7HWE3	0.0	A0A3Q7HWE3_SOLLC; Uncharacterized protein
STRING	Solyc09g007550.2.1	0.0	(Solanum lycopersicum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	6e-99	C2H2-like zinc finger protein

Publications ? help Back to Top
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]