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

RrC417_p8

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

GATA

Protein Properties

Length: 334aa MW: 37313 Da PI: 9.3543

Description

GATA family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC417_p8	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GATA	56.5	3.9e-18	232	266	1	35
GATA 1 CsnCgttkTplWRrgpdgnktLCnaCGlyyrkkgl 35 C+ Cgt+kTplWR+gp g+k+LCnaCG++++kk++ RrC417_p8 232 CAICGTSKTPLWRSGPTGPKSLCNACGIRNKKKKS 266 999*****************************975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51352	12.899	77	187	IPR013766	Thioredoxin domain
SuperFamily	SSF52833	2.76E-24	79	184	IPR012336	Thioredoxin-like fold
Gene3D	G3DSA:3.40.30.10	1.5E-23	80	186	IPR012336	Thioredoxin-like fold
Pfam	PF00085	5.3E-19	81	165	IPR013766	Thioredoxin domain
CDD	cd02947	3.34E-23	86	183	No hit	No description
PRINTS	PR00421	7.1E-5	100	108	No hit	No description
PRINTS	PR00421	7.1E-5	108	117	No hit	No description
PRINTS	PR00421	7.1E-5	148	159	No hit	No description
SuperFamily	SSF57716	3.04E-13	225	277	No hit	No description
SMART	SM00401	3.1E-13	226	279	IPR000679	Zinc finger, GATA-type
PROSITE profile	PS50114	12.967	226	262	IPR000679	Zinc finger, GATA-type
Gene3D	G3DSA:3.30.50.10	2.6E-15	230	265	IPR013088	Zinc finger, NHR/GATA-type
Pfam	PF00320	3.9E-16	232	265	IPR000679	Zinc finger, GATA-type
PROSITE pattern	PS00344	0	232	257	IPR000679	Zinc finger, GATA-type
CDD	cd00202	1.50E-11	232	260	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0045454	Biological Process	cell redox homeostasis
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008270	Molecular Function	zinc ion binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 334 aa Download sequence Send to blast
MALVQSTALA NFNVRLSPVL STLHAPSFLF LRREIRPLTS PLSSSSSTAG SLSFSPLTHQ 60 RKPPLCPPPR GKFVREDYLV RKLSAEELQE LVKGERKVPL IVDFYATWCG PCILMAQELE 120 MLAVEYESNA MIVKVDTDDE YEFARDMQVR GLPTLLFISP DPSKDAIRTE GLIPIQMMRD 180 IIDNDIHPNR GWIMLDHTEK ISDSEAMKSK FTSKYATEEE ISSSSSNEKK SCAICGTSKT 240 PLWRSGPTGP KSLCNACGIR NKKKKSTVKN KKKNHTRSNP KLGDSLKERL LELGREVMMQ 300 RSTAGGDQRR KKLGEEEQAA VLLMALSYAS SVYA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2l5l_A	5e-15	75	158	16	99	Thioredoxin
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Thiol-disulfide oxidoreductase that plays a role in proper chloroplast development, most likely through regulating plastid-encoded polymerase (PEP) dependent chloroplast transcription. Acts as a component of the transcriptionally active plastid chromosome that is required for plastid gene expression. May be involved in cell death and defense responses (By similarity). {ECO:0000250\|UniProtKB:Q9LKW0, ECO:0000269\|PubMed:16326926, ECO:0000269\|PubMed:20133584, ECO:0000269\|PubMed:20511297, ECO:0000269\|PubMed:21949211}.

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	AF370315	1e-150	AF370315.1 Arabidopsis thaliana putative thioredoxin (At3g06730) mRNA, complete cds.
GenBank	AY063100	1e-150	AY063100.1 Arabidopsis thaliana putative thioredoxin (At3g06730) mRNA, complete cds.
GenBank	AY084959	1e-150	AY084959.1 Arabidopsis thaliana clone 12284 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018437106.1	1e-132	PREDICTED: thioredoxin-like protein CITRX, chloroplastic
Refseq	XP_018437113.1	1e-132	PREDICTED: thioredoxin-like protein CITRX, chloroplastic
Swissprot	Q9M7X9	1e-107	CITRX_ARATH; Thioredoxin-like protein CITRX, chloroplastic
TrEMBL	M4FGQ9	1e-110	M4FGQ9_BRARP; Uncharacterized protein
STRING	Bra040287.1-P	1e-111	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM10253	2	2

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G06740.1	6e-52	GATA transcription factor 15

Publications ? help Back to Top
Rivas S, et al. CITRX thioredoxin interacts with the tomato Cf-9 resistance protein and negatively regulates defence. EMBO J., 2004. 23(10): p. 2156-65 [PMID:15131698] Giacomelli L,Rudella A,van Wijk KJ High light response of the thylakoid proteome in arabidopsis wild type and the ascorbate-deficient mutant vtc2-2. A comparative proteomics study. Plant Physiol., 2006. 141(2): p. 685-701 [PMID:16648217] Meyer Y, et al. Evolution of redoxin genes in the green lineage. Photosyn. Res., 2006. 89(2-3): p. 179-92 [PMID:17031546] Chibani K,Wingsle G,Jacquot JP,Gelhaye E,Rouhier N Comparative genomic study of the thioredoxin family in photosynthetic organisms with emphasis on Populus trichocarpa. Mol Plant, 2009. 2(2): p. 308-22 [PMID:19825616] Meng L,Wong JH,Feldman LJ,Lemaux PG,Buchanan BB A membrane-associated thioredoxin required for plant growth moves from cell to cell, suggestive of a role in intercellular communication. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(8): p. 3900-5 [PMID:20133584] Arsova B, et al. Plastidial thioredoxin z interacts with two fructokinase-like proteins in a thiol-dependent manner: evidence for an essential role in chloroplast development in Arabidopsis and Nicotiana benthamiana. Plant Cell, 2010. 22(5): p. 1498-515 [PMID:20511297] Hofmann NR A new thioredoxin is involved in plastid gene expression. Plant Cell, 2010. 22(5): p. 1423 [PMID:20511298] Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis. Plant Physiol., 2011. 155(4): p. 1678-89 [PMID:21139083] Steiner S,Schröter Y,Pfalz J,Pfannschmidt T Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development. Plant Physiol., 2011. 157(3): p. 1043-55 [PMID:21949211] Bohrer AS, et al. New insights into the reduction systems of plastidial thioredoxins point out the unique properties of thioredoxin z from Arabidopsis. J. Exp. Bot., 2012. 63(18): p. 6315-23 [PMID:23096001] Yua QB, et al. AtECB1/MRL7, a thioredoxin-like fold protein with disulfide reductase activity, regulates chloroplast gene expression and chloroplast biogenesis in Arabidopsis thaliana. Mol Plant, 2014. 7(1): p. 206-17 [PMID:23956074] Huang C, et al. The reduced plastid-encoded polymerase-dependent plastid gene expression leads to the delayed greening of the Arabidopsis fln2 mutant. PLoS ONE, 2013. 8(9): p. e73092 [PMID:24019900] Wimmelbacher M,Börnke F Redox activity of thioredoxin z and fructokinase-like protein 1 is dispensable for autotrophic growth of Arabidopsis thaliana. J. Exp. Bot., 2014. 65(9): p. 2405-13 [PMID:24659486] Díaz MG, et al. Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana. Nat Commun, 2018. 9(1): p. 50 [PMID:29298981]