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

904432

Common Name

ARALYDRAFT_904432

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 516aa MW: 55750.8 Da PI: 9.4781

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
904432	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15.8	4.1e-05	83	105	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H 904432 83 FICDVCNKGFQREQNLQLHRRGH 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+ 904432 159 WKCEKCSKRYAVQSDWKAHSKTC 181 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	2.02E-7	82	105	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.0E-5	82	105	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0061	83	105	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	7.2E-5	83	105	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.928	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	2.02E-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: 516 aa Download sequence Send to blast
MSSSSYNTSV IPSSSSSAQP FFITSSGTGD NDFNRKDTFM SMIQQPNSSA PPPKKRRNQP 60 GNPNPDAEVV ALSPKTLMAT NRFICDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK 120 RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT 180 CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMAAASS GVGSGGIYGR 240 LGGGSALSHH HLSDHPSSGF SPLAGYNLNI ATSENRRDFL PQSSNPNFLI QCASSQGMST 300 TMPNNNDQSF MNQHGLIQFD PVDNINLKNS NTNNSFFNLG FFQENTKNSE TTFPSLYSTD 360 VLVHHREENL NTGSNVSATA LLQKATQMGS VTSNDPSALF RGLASSSNSS SVIANHFGGG 420 RIMENDNNGN LQGLMNSLAA VNGGGGSGGS IFDVQFGDNG NMSGSDKLTL DFLGVGGMVR 480 NVNRGGGGGR GSGRGGVSLD GEVKFPEQNH PFGRG*

Sequence ? help Back to Top

Protein Sequence Length: 516 aa Download sequence Send to blast

MSSSSYNTSV IPSSSSSAQP FFITSSGTGD NDFNRKDTFM SMIQQPNSSA PPPKKRRNQP  60
GNPNPDAEVV ALSPKTLMAT NRFICDVCNK GFQREQNLQL HRRGHNLPWK LKQKSTKEVK  120
RKVYLCPEPT CVHHDPSRAL GDLTGIKKHY YRKHGEKKWK CEKCSKRYAV QSDWKAHSKT  180
CGTKEYRCDC GTIFSRRDSY ITHRAFCDAL IQETARNPTV SFTSMAAASS GVGSGGIYGR  240
LGGGSALSHH HLSDHPSSGF SPLAGYNLNI ATSENRRDFL PQSSNPNFLI QCASSQGMST  300
TMPNNNDQSF MNQHGLIQFD PVDNINLKNS NTNNSFFNLG FFQENTKNSE TTFPSLYSTD  360
VLVHHREENL NTGSNVSATA LLQKATQMGS VTSNDPSALF RGLASSSNSS SVIANHFGGG  420
RIMENDNNGN LQGLMNSLAA VNGGGGSGGS IFDVQFGDNG NMSGSDKLTL DFLGVGGMVR  480
NVNRGGGGGR GSGRGGVSLD GEVKFPEQNH PFGRG*

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
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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	904432

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_002876795.1	0.0	protein indeterminate-domain 4, chloroplastic isoform X2
Refseq	XP_020881176.1	0.0	protein indeterminate-domain 4, chloroplastic isoform X2
Refseq	XP_020881177.1	0.0	protein indeterminate-domain 4, chloroplastic isoform X2
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	D7LPZ5	0.0	D7LPZ5_ARALL; ATIDD4-DOMAIN 4
STRING	scaffold_500136.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3678	17	59

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	904432
Entrez Gene	9311181

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]