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_48209.1_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: 126aa MW: 14842.3 Da PI: 10.3005

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_48209.1_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	9	31	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Rsa1.0_48209.1_g00001.1 9 FVCEICNKGFQRDQNLQLHRRGH 31 89*******************88 PP
2	zf-C2H2	18.3	6.4e-06	86	108	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ykC++C+k + +s+ k H +t+ Rsa1.0_48209.1_g00001.1 86 YKCEKCSKKYAVQSDWKAHAKTC 108 9*******************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	5.74E-9	8	31	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.5E-6	8	31	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.949	9	31	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.017	9	31	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	1.2E-5	9	31	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	11	31	IPR007087	Zinc finger, C2H2
SMART	SM00355	73	51	81	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.2E-6	74	107	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	5.74E-9	81	106	No hit	No description
SMART	SM00355	74	86	106	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: 126 aa Download sequence Send to blast
TTLMATNRFV CEICNKGFQR DQNLQLHRRG HNLPWKLKQR SNKEVIKKKV YICPIKTCVH 60 HDSSRALGDL TGIKKHYSRK HGEKKYKCEK CSKKYAVQSD WKAHAKTCGT REYKCDCGTL 120 FSRYYI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	5e-23	82	123	3	44	Zinc finger protein JACKDAW
5b3h_F	5e-23	82	123	3	44	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_48209.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

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	AB005240	1e-138	AB005240.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MOK16.
GenBank	AL163002	1e-138	AL163002.1 Arabidopsis thaliana DNA chromosome 5, BAC clone F15A17 (ESSA project).
GenBank	CP002688	1e-138	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018473110.1	3e-88	PREDICTED: zinc finger protein JACKDAW-like
Swissprot	Q700D2	3e-85	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A0D3AZI4	1e-89	A0A0D3AZI4_BRAOL; Uncharacterized protein
TrEMBL	A0A3N6QF84	1e-89	A0A3N6QF84_BRACR; Uncharacterized protein
STRING	Bra005741.1-P	8e-87	(Brassica rapa)
STRING	Bo3g002190.1	2e-90	(Brassica oleracea)

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
AT5G03150.1	1e-75	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] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] 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] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]