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

Rsa1.0_15979.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 293aa MW: 33484.8 Da PI: 9.874

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_15979.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	19.8	2.1e-06	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F+r nL+ H r H Rsa1.0_15979.1_g00001.1 6 FICEVCNKGFKRDQNLQLHRRGH 28 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	6.37E-8	5	28	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.0E-6	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	1.2E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.013	6	28	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.887	6	28	IPR007087	Zinc finger, C2H2
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	5.6E-4	71	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	6.37E-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:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 293 aa Download sequence Send to blast
MATNRFICEV CNKGFKRDQN LQLHRRGHNL PWKLKQRTNK EQVKKKVYIC PEKTCVHHDP 60 ARALGDLTGI KKHFSRKHGE KKWKCDKCSK KYAVMSDWKA HSKFFGTREY RCDCGILFSR 120 KDSFITHRAF CDALAEESAR CSSVPPTAAS YLNNAPEAEV NLRNVKANHQ QPRQSSHQWL 180 LNENNNINIL QMGISNNQED HDTKKAAQIE SKRSSSSSNN CTAFGLMTST TSNSKHTEND 240 IKTKEVDERG FTRDFLGVGS QNRPWPLLMV NHNLPNMTQP VTTDGTPTPD MNH

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-33	79	144	3	68	Zinc finger protein JACKDAW
5b3h_F	2e-33	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_15979.1_g00001.1

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK352822	1e-158	AK352822.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-07-P14.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009150167.1	1e-178	PREDICTED: protein indeterminate-domain 9-like isoform X1
Refseq	XP_009150175.1	1e-178	PREDICTED: protein indeterminate-domain 9-like isoform X1
Refseq	XP_009150182.1	1e-178	PREDICTED: protein indeterminate-domain 9-like isoform X2
Swissprot	Q944L3	1e-109	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	M4EYE8	1e-177	M4EYE8_BRARP; Uncharacterized protein
STRING	Bra033840.1-P	1e-178	(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-99	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]