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

RrC21682_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: 378aa MW: 42279.7 Da PI: 10.5043

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC21682_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	17.7	1e-05	6	28	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H RrC21682_p1 6 FVCEICNKGFQRDQNLQLHRRGH 28 89*******************88 PP
2	zf-C2H2	16.2	3e-05	83	105	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ykC++C+k + +s+ k H +t+ RrC21682_p1 83 YKCEKCSKKYAVQSDWKAHAKTC 105 9*******************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.2E-5	5	28	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.7E-8	5	28	No hit	No description
SMART	SM00355	0.017	6	28	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	5.7E-5	6	28	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.949	6	28	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	8	28	IPR007087	Zinc finger, C2H2
SMART	SM00355	73	48	78	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.9E-6	71	104	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.7E-8	78	103	No hit	No description
SMART	SM00355	74	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: 378 aa Download sequence Send to blast
MATNRFVCEI CNKGFQRDQN LQLHRRGHNL PWKLKQRSNK EVIKKKVYIC PIKTCVHHDS 60 SRALGDLTGI KKHYSRKHGE KKYKCEKCSK KYAVQSDWKA HAKTCGTREY KCDCGTLFSR 120 AFCDALTEEG ARMSLLSNNP AISTTTMMTT SLNFANDSHV HPKWYKWPPP GTTTSSLCLR 180 HHSSLISPTT NTTNNSKFPR LPQTLISPYH HPQHHNKPQL HSHHYIRKTL LSPHSSPPPP 240 PTTNKTSLYL QSAQMGSTRS NSTTAPSLFA GPTMTSSSSA ASPPPRSSSP MMIQQQLNNN 300 FNTSVSRENH NFAPPNSGVS TSSVGNDYPF QSNRSGLNPA QQMGLTRDFL GVSNENHARQ 360 TGSRPFFPQE LPRFAPLG

Sequence ? help Back to Top

Protein Sequence Length: 378 aa Download sequence Send to blast

MATNRFVCEI CNKGFQRDQN LQLHRRGHNL PWKLKQRSNK EVIKKKVYIC PIKTCVHHDS  60
SRALGDLTGI KKHYSRKHGE KKYKCEKCSK KYAVQSDWKA HAKTCGTREY KCDCGTLFSR  120
AFCDALTEEG ARMSLLSNNP AISTTTMMTT SLNFANDSHV HPKWYKWPPP GTTTSSLCLR  180
HHSSLISPTT NTTNNSKFPR LPQTLISPYH HPQHHNKPQL HSHHYIRKTL LSPHSSPPPP  240
PTTNKTSLYL QSAQMGSTRS NSTTAPSLFA GPTMTSSSSA ASPPPRSSSP MMIQQQLNNN  300
FNTSVSRENH NFAPPNSGVS TSSVGNDYPF QSNRSGLNPA QQMGLTRDFL GVSNENHARQ  360
TGSRPFFPQE LPRFAPLG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-33	79	139	3	71	Zinc finger protein JACKDAW
5b3h_F	1e-33	79	139	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}.

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-130	AB005240.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MOK16.
GenBank	AJ621494	1e-130	AJ621494.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 3 (idz3 gene).
GenBank	AJ630493	1e-130	AJ630493.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g03150.
GenBank	AK228895	1e-130	AK228895.1 Arabidopsis thaliana mRNA for hypothetical protein, partial cds, clone: RAFL16-21-B02.
GenBank	AL163002	1e-130	AL163002.1 Arabidopsis thaliana DNA chromosome 5, BAC clone F15A17 (ESSA project).
GenBank	CP002688	1e-130	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009122730.1	1e-167	PREDICTED: zinc finger protein JACKDAW isoform X2
Swissprot	Q700D2	8e-98	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A397XP91	1e-164	A0A397XP91_BRACM; Uncharacterized protein
STRING	Bra009549.1-P	1e-163	(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	5e-87	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]