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

Rsa1.0_00921.1_g00013.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 456aa MW: 48272.7 Da PI: 9.9156

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00921.1_g00013.1	genome	RGD	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	62	84	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Rsa1.0_00921.1_g00013.1 62 FVCEICNKGFQRDQNLQLHRRGH 84 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	5.99E-7	61	84	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.5E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.949	62	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.017	62	84	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	7.1E-5	62	84	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	250	103	133	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.1E-4	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.99E-7	133	158	No hit	No description
SMART	SM00355	180	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: 456 aa Download sequence Send to blast
MPVDLDNSST VSGEASVSST GNQQNPLPKS AAKKKRNLPG MPDPDSEVIA LSPKTLLATN 60 RFVCEICNKG FQRDQNLQLH RRGHNLPWKL RQKSSKEVKK KVYVCPETSC VHHDPSRALG 120 DLTGIKKHFC RKHGEKKWKC DKCSKRYAVV SDWKAHSKIC GTKEYKCDCG TLFSRRDSFM 180 THRAFCDALA EESVRNHTHS KKQSPEILTR KKHVPDPESL TGSNPTASSV APVETRSAKI 240 ISPRAINTKR PESPKTPREI LQEAQEPTGG LNGVFFESSS ASPSIYASPS CSQSLFAPSS 300 SIEPIALGLS ASHGPSFLCS TRFPAQPAMS ATALLQKAAQ MGAASSGGSL LRGLGIVSST 360 SPSVDSLVPN GLALGLPCGG ESSSGLKELM MGNSSVFGPK QTTLDFLGLG RAVGNGGGGG 420 GGPGSTLIGP RGSSIDALAT FGSGEFSGHD IGRRTS

Sequence ? help Back to Top

Protein Sequence Length: 456 aa Download sequence Send to blast

MPVDLDNSST VSGEASVSST GNQQNPLPKS AAKKKRNLPG MPDPDSEVIA LSPKTLLATN  60
RFVCEICNKG FQRDQNLQLH RRGHNLPWKL RQKSSKEVKK KVYVCPETSC VHHDPSRALG  120
DLTGIKKHFC RKHGEKKWKC DKCSKRYAVV SDWKAHSKIC GTKEYKCDCG TLFSRRDSFM  180
THRAFCDALA EESVRNHTHS KKQSPEILTR KKHVPDPESL TGSNPTASSV APVETRSAKI  240
ISPRAINTKR PESPKTPREI LQEAQEPTGG LNGVFFESSS ASPSIYASPS CSQSLFAPSS  300
SIEPIALGLS ASHGPSFLCS TRFPAQPAMS ATALLQKAAQ MGAASSGGSL LRGLGIVSST  360
SPSVDSLVPN GLALGLPCGG ESSSGLKELM MGNSSVFGPK QTTLDFLGLG RAVGNGGGGG  420
GGPGSTLIGP RGSSIDALAT FGSGEFSGHD IGRRTS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-32	134	195	3	64	Zinc finger protein JACKDAW
5b3h_F	2e-32	134	195	3	64	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}.

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	Rsa1.0_00921.1_g00013.1

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_018441934.1	0.0	PREDICTED: protein indeterminate-domain 2
Swissprot	Q9SCQ6	0.0	IDD2_ARATH; Zinc finger protein GAI-ASSOCIATED FACTOR 1
TrEMBL	A0A078GDB0	0.0	A0A078GDB0_BRANA; BnaC05g34640D protein
STRING	Bo8g080100.1	0.0	(Brassica oleracea)

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]