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

RrC14337_p1

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: 376aa MW: 42085.3 Da PI: 9.5224

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC14337_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	19.4	2.9e-06	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F+r nL+ H r H RrC14337_p1 6 FICEVCNKGFKRDQNLQLHRRGH 28 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	9.09E-8	5	28	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.7E-6	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	1.6E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.887	6	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.013	6	28	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	48	78	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.4E-4	71	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.09E-8	78	103	No hit	No description
SMART	SM00355	200	83	103	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 376 aa Download sequence Send to blast
MATNRFICEV CNKGFKRDQN LQLHRRGHNL PCKLKQRTNK EQVKKKVYIC PEKTCVHYDP 60 ARALGDLTGI KKHFSRKHGE KKWKCDKCSK KYAVMSDWKA HSKICGTREY RCDCGTLFSR 120 KDSFITHRAF CDALAEKSAR CASVPPATAS YLNNAPEAEV NIRNVKANHQ QPSLNIDHYN 180 IDGFMGVSFT NQLPLPANVF ASSSSPSPRK ASDSLQNLWH GQSSHQWLLN ENNNINILQR 240 GISNNQEDHD TKKGISNGYL LSSDARTNYD QNDGQVISSM SATALLQKAA QMGSKTSSSS 300 SNNCTAFGLV TSSTFNSKHT ENDIKTKEVD ERGFTRDFLG VGNQNRPWPL LMVNHNLPNM 360 TQPVTTDGTP IADMNL

Sequence ? help Back to Top

Protein Sequence Length: 376 aa Download sequence Send to blast

MATNRFICEV CNKGFKRDQN LQLHRRGHNL PCKLKQRTNK EQVKKKVYIC PEKTCVHYDP  60
ARALGDLTGI KKHFSRKHGE KKWKCDKCSK KYAVMSDWKA HSKICGTREY RCDCGTLFSR  120
KDSFITHRAF CDALAEKSAR CASVPPATAS YLNNAPEAEV NIRNVKANHQ QPSLNIDHYN  180
IDGFMGVSFT NQLPLPANVF ASSSSPSPRK ASDSLQNLWH GQSSHQWLLN ENNNINILQR  240
GISNNQEDHD TKKGISNGYL LSSDARTNYD QNDGQVISSM SATALLQKAA QMGSKTSSSS  300
SNNCTAFGLV TSSTFNSKHT ENDIKTKEVD ERGFTRDFLG VGNQNRPWPL LMVNHNLPNM  360
TQPVTTDGTP IADMNL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-34	79	144	3	68	Zinc finger protein JACKDAW
5b3h_F	3e-34	79	144	3	68	Zinc finger protein JACKDAW
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). 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:0000269\|PubMed:25829440}.

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_009150182.1	0.0	PREDICTED: protein indeterminate-domain 9-like isoform X2
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	M4EYE8	0.0	M4EYE8_BRARP; Uncharacterized protein
STRING	Bra033840.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM155	28	306

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G45260.1	1e-164	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]