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

XP_013594212.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 463aa MW: 50521.5 Da PI: 8.5931

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013594212.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	15	6.9e-05	67	87	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C+ Cgk F r nL+ H r H XP_013594212.1 67 CEVCGKGFQRDQNLQLHRRGH 87 *******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	6.99E-6	64	87	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.5E-5	64	87	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.51	65	87	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.089	65	87	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	67	87	IPR007087	Zinc finger, C2H2
SMART	SM00355	240	106	136	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	6.99E-6	136	161	No hit	No description
SMART	SM00355	160	141	161	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010150	Biological Process	leaf senescence
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0048573	Biological Process	photoperiodism, flowering
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 463 aa Download sequence Send to blast
MTGEVLKTVS SGSAAFAPSS STLDHDESLI NPPLVKKKRN LPGNPDPEAE VIALSPKTLM 60 ATNRFLCEVC GKGFQRDQNL QLHRRGHNLP WKLKQRTSKE VRKRVYVCPE KTCVHHDPAR 120 ALGDLTGIKK HFCRKHGEKK WTCEKCAKRY AVHSDYKAHS KTCGTREYRC DCGIIFSRRD 180 SFITHRAFCD ALAEETAKIN AASHLNGLSA AGTVGMNLNY QYLMGTLNPP LQPFEPQPPT 240 NQNHHQHFLP PPPSSSSSLS LWMGQDIAPT SQTQPQDYEW VFANAKAASG CINNNNHNDL 300 ITQTANASST TTATLSVPSL FSSDQTQSPN ANVNMSATAL LQKAAEIGAN STTATTTNPS 360 AFLKSFPQKS SDQTTTSYGG EKFFALFGTN NNIGVVSNSH DQETENVRND VTVASAMDEL 420 QNYPWKRRKV DGGGEGGGGG QTRDFLGVGV QTLCHPSSIN GWI

Sequence ? help Back to Top

Protein Sequence Length: 463 aa Download sequence Send to blast

MTGEVLKTVS SGSAAFAPSS STLDHDESLI NPPLVKKKRN LPGNPDPEAE VIALSPKTLM  60
ATNRFLCEVC GKGFQRDQNL QLHRRGHNLP WKLKQRTSKE VRKRVYVCPE KTCVHHDPAR  120
ALGDLTGIKK HFCRKHGEKK WTCEKCAKRY AVHSDYKAHS KTCGTREYRC DCGIIFSRRD  180
SFITHRAFCD ALAEETAKIN AASHLNGLSA AGTVGMNLNY QYLMGTLNPP LQPFEPQPPT  240
NQNHHQHFLP PPPSSSSSLS LWMGQDIAPT SQTQPQDYEW VFANAKAASG CINNNNHNDL  300
ITQTANASST TTATLSVPSL FSSDQTQSPN ANVNMSATAL LQKAAEIGAN STTATTTNPS  360
AFLKSFPQKS SDQTTTSYGG EKFFALFGTN NNIGVVSNSH DQETENVRND VTVASAMDEL  420
QNYPWKRRKV DGGGEGGGGG QTRDFLGVGV QTLCHPSSIN GWI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	6e-32	137	206	3	72	Zinc finger protein JACKDAW
5b3h_F	6e-32	137	206	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed throughout development. {ECO:0000269\|PubMed:21265895}.
Uniprot	TISSUE SPECIFICITY: Highly expressed in vegetative organs and at lower levels in flowers and siliques. Expressed predominantly in roots. In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269\|PubMed:21265895, ECO:0000269\|PubMed:25829440, ECO:0000305\|PubMed:21265895}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds to the DNA sequence 5'-CTTTTGTCC-3' (PubMed:21265895, PubMed:25929516). Regulates photoperiodic flowering by modulating sugar transport and metabolism (PubMed:21265895, PubMed:25929516). Regulates SUS1 and SUS4 (PubMed:21265895). Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:25829440). {ECO:0000269\|PubMed:21265895, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:25929516}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013594212.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by 'SHORT-ROOT' (SHR)(PubMed:16640459). Strongly down-regulated by sugar deprivation, but not regulated by day-length. {ECO:0000269\|PubMed:16640459}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013594212.1	0.0	PREDICTED: zinc finger protein NUTCRACKER
Swissprot	Q9FFH3	0.0	IDD8_ARATH; Zinc finger protein NUTCRACKER
TrEMBL	A0A0D3D8V0	0.0	A0A0D3D8V0_BRAOL; Uncharacterized protein
STRING	Bo7g067160.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3710	26	60

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G44160.1	0.0	C2H2-like zinc finger protein

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] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306]