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

XP_009115732.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

C2H2

Protein Properties

Length: 438aa MW: 46600 Da PI: 9.9547

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009115732.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.4	1.2e-05	64	86	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H XP_009115732.1 64 FVCEICNKGFQRDQNLQLHRRGH 86 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.4E-5	63	86	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.55E-7	63	86	No hit	No description
SMART	SM00355	0.017	64	86	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	6.8E-5	64	86	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.949	64	86	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	66	86	IPR007087	Zinc finger, C2H2
SMART	SM00355	250	105	135	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.8E-4	128	161	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.55E-7	135	160	No hit	No description
SMART	SM00355	180	140	160	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: 438 aa Download sequence Send to blast
MKMPVDLDKS STVSGEASVS STGNQQNPLP KSAAKKKRNL PGMPDPNSEV IALSPKTLLA 60 TNRFVCEICN KGFQRDQNLQ LHRRGHNLPW KLRQKSSQEV KKKVYVCPET SCVHHDPSRA 120 LGDLTGIKKH FCRKHGEKKW KCDKCSKRYA VVSDWKAHSK ICGTKEYKCD CGTLFSRRDS 180 FMTHRAFCDA LAEESVRSHT HGKKQSPEIL TRKKPVPDPK PSLAAAPVET QPAIAIKRPE 240 SPKTPREVLQ ETQEPTGLNG VYFDSSSASP SIYASSCSQS LFAPSSSIEP ISLGLSTSHG 300 PSFLCSPRFP SQPAMSATAL LQKAAQMGAA SSGGSLLRGL GIVSSTSPSM DSIVPNGLAL 360 GLPCGGESSS GLKELMMGNS SVFGPKQTTL DFLGLGRAVG NGGGPGSTLA GPRGGSIDAL 420 ATFGSGEFSG NDIGRRTS

Sequence ? help Back to Top

Protein Sequence Length: 438 aa Download sequence Send to blast

MKMPVDLDKS STVSGEASVS STGNQQNPLP KSAAKKKRNL PGMPDPNSEV IALSPKTLLA  60
TNRFVCEICN KGFQRDQNLQ LHRRGHNLPW KLRQKSSQEV KKKVYVCPET SCVHHDPSRA  120
LGDLTGIKKH FCRKHGEKKW KCDKCSKRYA VVSDWKAHSK ICGTKEYKCD CGTLFSRRDS  180
FMTHRAFCDA LAEESVRSHT HGKKQSPEIL TRKKPVPDPK PSLAAAPVET QPAIAIKRPE  240
SPKTPREVLQ ETQEPTGLNG VYFDSSSASP SIYASSCSQS LFAPSSSIEP ISLGLSTSHG  300
PSFLCSPRFP SQPAMSATAL LQKAAQMGAA SSGGSLLRGL GIVSSTSPSM DSIVPNGLAL  360
GLPCGGESSS GLKELMMGNS SVFGPKQTTL DFLGLGRAVG NGGGPGSTLA GPRGGSIDAL  420
ATFGSGEFSG NDIGRRTS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-32	136	197	3	64	Zinc finger protein JACKDAW
5b3h_F	2e-32	136	197	3	64	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.13742	0.0	root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Observed in vegetative tissues. Mainly expressed in hypocotyls, petioles, shoot apices, root tips, and trichomes, and, at low levels, in leaves, stems and flowers. {ECO:0000269\|PubMed:25035403}.

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00403	DAP	Transfer from AT3G50700	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009115732.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353210	0.0	AK353210.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-27-D18.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009115732.1	0.0	PREDICTED: protein indeterminate-domain 2
Swissprot	Q9SCQ6	0.0	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	M4F4U4	0.0	M4F4U4_BRARP; Uncharacterized protein
STRING	Bra036098.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G50700.1	0.0	indeterminate(ID)-domain 2

Publications ? help Back to Top
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]