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

RrC2816_p4

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

C2H2

Protein Properties

Length: 177aa MW: 20372.1 Da PI: 9.7192

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC2816_p4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	20.2	1.5e-06	66	88	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y+C++C++ F r nL+ H r+H RrC2816_p4 66 YVCEICNQGFQRDQNLQMHRRRH 88 9*********************9 PP
2	zf-C2H2	15.3	5.7e-05	145	166	2	23
EETTTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCpdCgksFsrksnLkrHirtH 23 C+ C+k + +s++k H++t+ RrC2816_p4 145 ICERCSKGYAVQSDYKAHLKTC 166 7*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.4E-5	63	89	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.3E-6	65	88	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0052	66	88	IPR015880	Zinc finger, C2H2-like
Pfam	PF12874	0.0067	66	84	No hit	No description
PROSITE profile	PS50157	10.97	66	88	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	68	88	IPR007087	Zinc finger, C2H2
SMART	SM00355	160	108	138	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.9E-4	135	165	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	110	144	171	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: 177 aa Download sequence Send to blast
MIDYERSKNI NHHQNPPPSS SSSDLLPDGN GAAVTQKRKR RPAGTPDPEA EVVSLSPRTL 60 LESDRYVCEI CNQGFQRDQN LQMHRRRHKV PWKLLKRETT EEVKKRVYVC PEPTCLHHNP 120 CHALGDLVGI KKHFRRKHSN HKQWICERCS KGYAVQSDYK AHLKTCGTRG HSCDCGR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-12	142	176	5	39	Zinc finger protein JACKDAW
5b3h_F	6e-12	142	176	5	39	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor regulating starch metabolism by binding directly to the promoter of QQS (PubMed:21556057). The IDD14beta isoform attenuates the transcription factor activity by competitively forming heterodimers with reduced DNA-binding capacity(PubMed:21556057). Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Has a redundant role with IDD16 in directing leaf and floral organ morphogenesis (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269\|PubMed:21556057, ECO:0000269\|PubMed:24039602}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by auxin. {ECO:0000269\|PubMed:24039602}.

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	AC189489	0.0	AC189489.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB084K02, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018452684.1	1e-132	PREDICTED: protein indeterminate-domain 14 isoform X1
Refseq	XP_018452686.1	1e-132	PREDICTED: protein indeterminate-domain 14 isoform X2
Swissprot	Q9C9X7	1e-114	IDD14_ARATH; Protein indeterminate-domain 14
TrEMBL	V4KMC6	1e-115	V4KMC6_EUTSA; Uncharacterized protein
STRING	Bostr.26959s0085.1.p	1e-118	(Boechera stricta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM693	28	131

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G68130.1	1e-116	indeterminate(ID)-domain 14

Publications ? help Back to Top
Arendsee ZW,Li L,Wurtele ES Coming of age: orphan genes in plants. Trends Plant Sci., 2014. 19(11): p. 698-708 [PMID:25151064] Qu Y, et al. Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis. J. Exp. Bot., 2017. 68(17): p. 4851-4867 [PMID:28992128]