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_00280.1_g00018.1

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: 513aa MW: 56180.9 Da PI: 10.1299

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00280.1_g00018.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.2	1.5e-05	82	104	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Rsa1.0_00280.1_g00018.1 82 FVCEICNKGFQRDQNLQLHRRGH 104 89*******************88 PP
2	zf-C2H2	15	7.1e-05	159	181	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Rsa1.0_00280.1_g00018.1 159 FKCEKCSKKYAVQSDWKAHAKTC 181 89******************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.7E-5	81	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.36E-8	81	104	No hit	No description
PROSITE profile	PS50157	10.949	82	104	IPR007087	Zinc finger, C2H2
Pfam	PF12171	8.2E-5	82	104	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.017	82	104	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	84	104	IPR007087	Zinc finger, C2H2
SMART	SM00355	73	124	154	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.3E-5	147	180	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	9.36E-8	154	179	No hit	No description
SMART	SM00355	92	159	179	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010075	Biological Process	regulation of meristem growth
GO:0045604	Biological Process	regulation of epidermal cell differentiation
GO:0048364	Biological Process	root development
GO:0051302	Biological Process	regulation of cell division
GO:0003676	Molecular Function	nucleic acid binding
GO:0042803	Molecular Function	protein homodimerization activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 513 aa Download sequence Send to blast
MQMIPGDPFS ISSSMGGFVH QEQHLHHIQQ HIPDINPNSS SNPNAKPNSS SAKKKRNQPG 60 TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSSKEVIK 120 KKVYICPIKT CVHHDSSRAL GDLTGIKKHY SRKHGEKKFK CEKCSKKYAV QSDWKAHAKT 180 CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNPATTTMP ANLNFGNDSH 240 VMNNPNLPHG FVHRGVHHPD INAAISQFGL GFGHDLSAMH PQGLSDMVQM NSAGNHHLFP 300 LSSSSVLPDF SGHHHSQQFQ IPTTSTNPNL TLSSSSTSQQ NSASLPSLQH QTLKDSSFSP 360 LFSSSSSESK QNKPLSPMSA TALLQKAAQM GSTRSNSTTA PSIFAGPTMT SISSAASPPP 420 RSSSPMMIQQ QLNNNFNTNA PREIHNLAPP ISGVTTSSVD NNHRFQSNRS GMNPAQQMGL 480 TRDFLGVSNE HHAHQTGHRP FLPQELARFA PSS

Sequence ? help Back to Top

Protein Sequence Length: 513 aa Download sequence Send to blast

MQMIPGDPFS ISSSMGGFVH QEQHLHHIQQ HIPDINPNSS SNPNAKPNSS SAKKKRNQPG  60
TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSSKEVIK  120
KKVYICPIKT CVHHDSSRAL GDLTGIKKHY SRKHGEKKFK CEKCSKKYAV QSDWKAHAKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNPATTTMP ANLNFGNDSH  240
VMNNPNLPHG FVHRGVHHPD INAAISQFGL GFGHDLSAMH PQGLSDMVQM NSAGNHHLFP  300
LSSSSVLPDF SGHHHSQQFQ IPTTSTNPNL TLSSSSTSQQ NSASLPSLQH QTLKDSSFSP  360
LFSSSSSESK QNKPLSPMSA TALLQKAAQM GSTRSNSTTA PSIFAGPTMT SISSAASPPP  420
RSSSPMMIQQ QLNNNFNTNA PREIHNLAPP ISGVTTSSVD NNHRFQSNRS GMNPAQQMGL  480
TRDFLGVSNE HHAHQTGHRP FLPQELARFA PSS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-42	155	223	3	71	Zinc finger protein JACKDAW
5b3h_F	4e-42	155	223	3	71	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00485	DAP	Transfer from AT5G03150	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00280.1_g00018.1

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	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018443047.1	0.0	PREDICTED: zinc finger protein JACKDAW
Swissprot	Q700D2	0.0	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	M4CZA2	0.0	M4CZA2_BRARP; Uncharacterized protein
STRING	Bra009549.1-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
AT5G03150.1	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] 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]