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

GSBRNA2T00115422001

Common Name

GSBRNA2T00115422001

Organism

Brassica napus

Taxonomic ID

3708

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: 525aa MW: 56356.2 Da PI: 9.9474

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00115422001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.4	2.7e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H GSBRNA2T00115422001 82 FICEVCNKGFQREQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	13.3	0.00025	158	180	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ GSBRNA2T00115422001 158 WKCEKCSKRYAVQSDWKAHSKTC 180 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.08E-7	81	104	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.7E-6	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.99	82	104	IPR007087	Zinc finger, C2H2
Pfam	PF12171	2.5E-5	82	104	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	82	104	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	84	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	123	153	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.3E-5	146	179	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.08E-7	153	178	No hit	No description
SMART	SM00355	130	158	178	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: 525 aa Download sequence Send to blast
MAASSSSAAS FFGVQQDDQS HLLPPNSFAA APPLPTHHQP PQSQQPLDAP PQKKKRNQPR 60 TPNSDAEVIA LSPKTLMATN RFICEVCNKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR 120 KVYLCPEPSC VHHDPSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC 180 GTKEYRCDCG TLFSRRDSFI THRAFCDALA QESARHPTSL TSLPSHHFPY GQNTNNSNNN 240 TSSMILGLPH IGNPQNLDHQ SGDVLRLGSG GGGFLAASNN IKPSPMNFQQ SLMQFSNDNH 300 NSPSSNLFNL SFLSGNNGIA SGTSNPNAAA VPSGNHMISN HFGAGRINSG AVPSLYSSSM 360 QNPNSASHMS ATALLQKAAQ MGSSTSSSNN NTNNASSILR SFGSGMYGEN ESNLHDLMNS 420 FSNPGATGNS ANGVDSQFGT YGGVNKGLSA DKQNMTRDFL GVGQIVRSMS GSAGFQQQQQ 480 QHGNGGRERV GSSSDSADRN SMNVNPGGGG STSSPPYGIH HASF*

Sequence ? help Back to Top

Protein Sequence Length: 525 aa Download sequence Send to blast

MAASSSSAAS FFGVQQDDQS HLLPPNSFAA APPLPTHHQP PQSQQPLDAP PQKKKRNQPR  60
TPNSDAEVIA LSPKTLMATN RFICEVCNKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR  120
KVYLCPEPSC VHHDPSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC  180
GTKEYRCDCG TLFSRRDSFI THRAFCDALA QESARHPTSL TSLPSHHFPY GQNTNNSNNN  240
TSSMILGLPH IGNPQNLDHQ SGDVLRLGSG GGGFLAASNN IKPSPMNFQQ SLMQFSNDNH  300
NSPSSNLFNL SFLSGNNGIA SGTSNPNAAA VPSGNHMISN HFGAGRINSG AVPSLYSSSM  360
QNPNSASHMS ATALLQKAAQ MGSSTSSSNN NTNNASSILR SFGSGMYGEN ESNLHDLMNS  420
FSNPGATGNS ANGVDSQFGT YGGVNKGLSA DKQNMTRDFL GVGQIVRSMS GSAGFQQQQQ  480
QHGNGGRERV GSSSDSADRN SMNVNPGGGG STSSPPYGIH HASF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	8e-34	154	215	3	64	Zinc finger protein JACKDAW
5b3h_F	8e-34	154	215	3	64	Zinc finger protein JACKDAW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305\|PubMed:22898356}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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:22898356, ECO:0000269\|PubMed:24821766}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00115422001

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ621495	0.0	AJ621495.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 2 (idz2 gene).
GenBank	AY056174	0.0	AY056174.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBank	BT001215	0.0	BT001215.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009101276.1	0.0	PREDICTED: LOW QUALITY PROTEIN: protein indeterminate-domain 5, chloroplastic
Swissprot	Q9ZUL3	0.0	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A078FSW9	0.0	A0A078FSW9_BRANA; BnaA06g34340D protein
STRING	Bra024834.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4373	26	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-151	indeterminate(ID)-domain 5

Publications ? help Back to Top
Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]