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

Carubv10017029m

Common Name

CARUB_v10016990mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 517aa MW: 55705.8 Da PI: 9.5871

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10017029m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.8	1.9e-05	83	105	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C C+k F r nL+ H r H Carubv10017029m 83 FVCDVCNKGFQREQNLQLHRRGH 105 89*******************88 PP
2	zf-C2H2	13.3	0.00024	159	181	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Carubv10017029m 159 WKCEKCSKRYAVQSDWKAHSKTC 181 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.68E-7	82	105	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-5	82	105	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0047	83	105	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.032	83	105	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	85	105	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	124	154	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.3E-5	147	180	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.68E-7	154	179	No hit	No description
SMART	SM00355	130	159	179	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: 517 aa Download sequence Send to blast
MSSSSYNTSV IPSSSSSAQP FFITSSGVGD NDFNRKDPFM SMIQQPNSSA PPLKKRRNQP 60 GNPNPDAEVV ALSPKTLMAT NRFVCDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK 120 RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT 180 CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMAAASS GVGSGGIYGR 240 LGGGSALSHH HMSGHPNSGF NPLAGYNLNI ASSENRRDFV PQSANPNFLL QCSSSQGMLT 300 ATPNNNDQSF MNQHGLIQFD PVDNINLKSS GTNNSFFNLG FFQENTKNSE TSLPSLYSND 360 VLVHHREEEL NTGSNVSATA LLQKATQMGS VTSNDSALFR GLASSSNSTS LIPSHFGGGR 420 IMENDNNGNL QGLMNSLAAV NATGGGSGGN IFDVHFGNNG NMSGSDKLTL DFLGVGGMVR 480 NANRGGGGRG SGSGRGGVSL DGEAKFPEQN HPFGRG*

Sequence ? help Back to Top

Protein Sequence Length: 517 aa Download sequence Send to blast

MSSSSYNTSV IPSSSSSAQP FFITSSGVGD NDFNRKDPFM SMIQQPNSSA PPLKKRRNQP  60
GNPNPDAEVV ALSPKTLMAT NRFVCDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK  120
RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT  180
CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMAAASS GVGSGGIYGR  240
LGGGSALSHH HMSGHPNSGF NPLAGYNLNI ASSENRRDFV PQSANPNFLL QCSSSQGMLT  300
ATPNNNDQSF MNQHGLIQFD PVDNINLKSS GTNNSFFNLG FFQENTKNSE TSLPSLYSND  360
VLVHHREEEL NTGSNVSATA LLQKATQMGS VTSNDSALFR GLASSSNSTS LIPSHFGGGR  420
IMENDNNGNL QGLMNSLAAV NATGGGSGGN IFDVHFGNNG NMSGSDKLTL DFLGVGGMVR  480
NANRGGGGRG SGSGRGGVSL DGEAKFPEQN HPFGRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-33	155	221	3	69	Zinc finger protein JACKDAW
5b3h_F	2e-33	155	221	3	69	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:24821766, ECO:0000305\|PubMed:19726569}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00256	DAP	Transfer from AT2G02080	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10017029m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

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	AK117733	0.0	AK117733.1 Arabidopsis thaliana At2g02080 mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL17-41-L01.
GenBank	BT005897	0.0	BT005897.1 Arabidopsis thaliana At2g02080 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006290880.1	0.0	protein indeterminate-domain 4, chloroplastic
Refseq	XP_023638726.1	0.0	protein indeterminate-domain 4, chloroplastic
Refseq	XP_023638727.1	0.0	protein indeterminate-domain 4, chloroplastic
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	R0HIV8	0.0	R0HIV8_9BRAS; Uncharacterized protein
STRING	XP_006290879.1	0.0	(Capsella rubella)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02080.1	0.0	indeterminate(ID)-domain 4

Link Out ? help Back to Top
Phytozome	Carubv10017029m
Entrez Gene	17886193

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]