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

PGSC0003DMP400020118

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 454aa MW: 50632.5 Da PI: 8.8677

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400020118	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.4	1.3e-05	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H PGSC0003DMP400020118 6 FVCEICNKGFQRDQNLQLHRRGH 28 89*******************88 PP
2	zf-C2H2	15.8	4e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k + +s+ k H++t+ PGSC0003DMP400020118 82 WKCDKCSKKYAVQSDWKAHQKTC 104 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	1.5E-5	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.24E-8	5	28	No hit	No description
Pfam	PF12171	7.1E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.949	6	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.017	6	28	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	88	47	77	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.5E-5	70	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.24E-8	77	103	No hit	No description
SMART	SM00355	94	82	102	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: 454 aa Download sequence Send to blast
MATNRFVCEI CNKGFQRDQN LQLHRRGHNL PWKLRQRTTT EVRKRVYICP EPTCVHHNRA 60 RALGDLTGIK KHYSRKHGEK KWKCDKCSKK YAVQSDWKAH QKTCGTREYK CDCGTIFSRR 120 DSFITHRAFC DALAEENNKV NQGLMNNNIE HNMHSGQMHE LMSSNASLGL SEFNNFDPKN 180 SLKSLPQEFL PFPFKSMTNN MAPGGMFSTT SGNLFGNSPR SVASSSSGLQ LSSNIPSNFN 240 YLQDNGKNGV AQGQGQISSV PMSATALLQK AAQMGATASS SINSPMMQKS FVTSAMAGPD 300 ITITRPSPNY ENFQMQQDNN NHQNQNQNHQ LNLAAVMNDM GIYSGILMSN DQNNDAGYIK 360 NVTEVLDCDN HNHSTNDGVR NQTMMVQNGS NDMLTVDFLG IGGASRTPIS NLQEQQRFEA 420 AINQQRLQAT SSFHHQQNIN NNSGLEKPIW DNV*

Sequence ? help Back to Top

Protein Sequence Length: 454 aa Download sequence Send to blast

MATNRFVCEI CNKGFQRDQN LQLHRRGHNL PWKLRQRTTT EVRKRVYICP EPTCVHHNRA  60
RALGDLTGIK KHYSRKHGEK KWKCDKCSKK YAVQSDWKAH QKTCGTREYK CDCGTIFSRR  120
DSFITHRAFC DALAEENNKV NQGLMNNNIE HNMHSGQMHE LMSSNASLGL SEFNNFDPKN  180
SLKSLPQEFL PFPFKSMTNN MAPGGMFSTT SGNLFGNSPR SVASSSSGLQ LSSNIPSNFN  240
YLQDNGKNGV AQGQGQISSV PMSATALLQK AAQMGATASS SINSPMMQKS FVTSAMAGPD  300
ITITRPSPNY ENFQMQQDNN NHQNQNQNHQ LNLAAVMNDM GIYSGILMSN DQNNDAGYIK  360
NVTEVLDCDN HNHSTNDGVR NQTMMVQNGS NDMLTVDFLG IGGASRTPIS NLQEQQRFEA  420
AINQQRLQAT SSFHHQQNIN NNSGLEKPIW DNV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	5e-35	78	148	3	72	Zinc finger protein JACKDAW
5b3h_F	5e-35	78	148	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that acts as a positive regulator of gibberellin (GA) action, homeostasis and signaling. GA converts the GAF1 complex from transcriptional activator to repressor via the degradation of DELLA proteins. {ECO:0000269\|PubMed:25035403}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	PGSC0003DMP400020118

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	HG975521	0.0	HG975521.1 Solanum lycopersicum chromosome ch09, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006359407.1	0.0	PREDICTED: protein indeterminate-domain 2-like
Swissprot	Q9SCQ6	6e-94	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	M1ASZ9	0.0	M1ASZ9_SOLTU; Uncharacterized protein
STRING	PGSC0003DMT400029550	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA103	24	350

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G50700.1	6e-83	indeterminate(ID)-domain 2

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400020118

Publications ? help Back to Top
Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Khare D, et al. Root avoidance of toxic metals requires the GeBP-LIKE 4 transcription factor in Arabidopsis thaliana. New Phytol., 2017. 213(3): p. 1257-1273 [PMID:27768815]