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

Csa00456s130.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 515aa MW: 55337.3 Da PI: 9.4783

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa00456s130.1	genome	CSGP	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	84	106	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C C+k F r nL+ H r H Csa00456s130.1 84 FICDVCNKGFQREQNLQLHRRGH 106 89*******************88 PP
2	zf-C2H2	13.3	0.00024	160	182	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Csa00456s130.1 160 WKCEKCSKRYAVQSDWKAHSKTC 182 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF13912	6.4E-5	83	106	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.0E-5	83	106	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.02E-7	83	106	No hit	No description
PROSITE profile	PS50157	10.928	84	106	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0061	84	106	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	86	106	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	125	155	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.3E-5	148	181	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.02E-7	155	180	No hit	No description
SMART	SM00355	130	160	180	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: 515 aa Download sequence Send to blast
MSSSSYNTSV IPSSSSSAQP FFITSSGAGD NDFNRKDTFM SSMIQQPNSS APPPKKRRNQ 60 PGNPNPDAEV VALSPKTLMA TNRFICDVCN KGFQREQNLQ LHRRGHNLPW KLKQKSTKEV 120 KRKVYLCPEP TCVHHDPSRA LGDLTGIKKH YYRKHGEKKW KCEKCSKRYA VQSDWKAHSK 180 TCGTKEYRCD CGTIFSRRDS YITHRAFCDA LIQETARNPA VSFTSMAAAS SGAGSGGIYG 240 RLGGASALSH HHMSGHPSSG FSPLAGYNLN IASSENRRDF VPQSSNPNFL LQCSSSQGML 300 TTTPNNNDQS FMNQHGLIQF DPVDNINLKS SSTNNSFFNL GFFQENTKNS ETSLPSLYST 360 DVLVQHREEN LNAGSNVSAT ALLQKATQMG SVTSNDSALF RGLASSSNPS SVIGNHFGGG 420 QILENDNGNL QGLMNSFAAV NGGSSGSGGN IFDVHFGNNG NMSGSDKLTL DFLGVGGMVR 480 NVNRGGGGGG SSRGGVSLDG EAKFPEQNHP FGRG*

Sequence ? help Back to Top

Protein Sequence Length: 515 aa Download sequence Send to blast

MSSSSYNTSV IPSSSSSAQP FFITSSGAGD NDFNRKDTFM SSMIQQPNSS APPPKKRRNQ  60
PGNPNPDAEV VALSPKTLMA TNRFICDVCN KGFQREQNLQ LHRRGHNLPW KLKQKSTKEV  120
KRKVYLCPEP TCVHHDPSRA LGDLTGIKKH YYRKHGEKKW KCEKCSKRYA VQSDWKAHSK  180
TCGTKEYRCD CGTIFSRRDS YITHRAFCDA LIQETARNPA VSFTSMAAAS SGAGSGGIYG  240
RLGGASALSH HHMSGHPSSG FSPLAGYNLN IASSENRRDF VPQSSNPNFL LQCSSSQGML  300
TTTPNNNDQS FMNQHGLIQF DPVDNINLKS SSTNNSFFNL GFFQENTKNS ETSLPSLYST  360
DVLVQHREEN LNAGSNVSAT ALLQKATQMG SVTSNDSALF RGLASSSNPS SVIGNHFGGG  420
QILENDNGNL QGLMNSFAAV NGGSSGSGGN IFDVHFGNNG NMSGSDKLTL DFLGVGGMVR  480
NVNRGGGGGG SSRGGVSLDG EAKFPEQNHP FGRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-33	156	222	3	69	Zinc finger protein JACKDAW
5b3h_F	3e-33	156	222	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	Csa00456s130.1

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_010495967.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like isoform X1
Refseq	XP_010495968.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like isoform X2
Refseq	XP_010495969.1	0.0	PREDICTED: protein indeterminate-domain 4, chloroplastic-like isoform X2
Swissprot	Q8GYC1	0.0	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	R0HIV8	0.0	R0HIV8_9BRAS; Uncharacterized protein
STRING	XP_010495968.1	0.0	(Camelina sativa)

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

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]