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

XP_010543388.1

Organism

Tarenaya hassleriana

Taxonomic ID

28532

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya

Family

C2H2

Protein Properties

Length: 515aa MW: 56608.5 Da PI: 10.0283

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010543388.1	genome	NCBI	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	83	105	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H XP_010543388.1 83 FVCEICNKGFQRDQNLQLHRRGH 105 89*******************88 PP
2	zf-C2H2	13.9	0.00016	160	182	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ XP_010543388.1 160 WKCEKCSKKYAVQSDWKAHTKTC 182 58*******************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	3.86E-7	82	105	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.7E-5	82	105	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	8.2E-5	83	105	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.017	83	105	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.949	83	105	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	85	105	IPR007087	Zinc finger, C2H2
SMART	SM00355	68	125	155	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.6E-5	148	181	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.86E-7	155	180	No hit	No description
SMART	SM00355	130	160	180	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: 515 aa Download sequence Send to blast
MQMIPGDPFS LSSSMAGFAH HQEPQLHHLQ QQNPDLNPNP NPNLNPNPNA KPNPSSKKKR 60 NQPDPDAEVI ALSPKTLMAT NRFVCEICNK GFQRDQNLQL HRRGHNLPWK LRQRTNKEAV 120 RKKVYICPIK TCVHHDPSRA LGDLTGIKKH YSRKHGEKKW KCEKCSKKYA VQSDWKAHTK 180 TCGTREYKCD CGTLFSRKDS FITHRAFCDA LTEESARMSS LGNNNSGSTN LNFGNDSNNN 240 NNNMNSVPHG FINRSVHHPD ISSAINHQFG LGFGHDLTGM HAHGLSEMVQ MSSAGNHHLF 300 PPPPSSSSSI PEFAGHHHHF QIPATSTNPN LTLSSSSSAS LPVLQNQQTL KDASPSPLFS 360 SSDKQQPNKP ISPMSATALL QKAAQMGSTR STATAAPSFF AGSMTSSSAA SPSSSSPPPP 420 PRNPIMIHHQ MFNPNPRSIN HQEHHNLAPP PPPPNMSTAT SYAAAAAPNP NPGYYPIQQM 480 GMTRDFLGVS SEHHLHHQMG RQFLPQELTR FAPLG

Sequence ? help Back to Top

Protein Sequence Length: 515 aa Download sequence Send to blast

MQMIPGDPFS LSSSMAGFAH HQEPQLHHLQ QQNPDLNPNP NPNLNPNPNA KPNPSSKKKR  60
NQPDPDAEVI ALSPKTLMAT NRFVCEICNK GFQRDQNLQL HRRGHNLPWK LRQRTNKEAV  120
RKKVYICPIK TCVHHDPSRA LGDLTGIKKH YSRKHGEKKW KCEKCSKKYA VQSDWKAHTK  180
TCGTREYKCD CGTLFSRKDS FITHRAFCDA LTEESARMSS LGNNNSGSTN LNFGNDSNNN  240
NNNMNSVPHG FINRSVHHPD ISSAINHQFG LGFGHDLTGM HAHGLSEMVQ MSSAGNHHLF  300
PPPPSSSSSI PEFAGHHHHF QIPATSTNPN LTLSSSSSAS LPVLQNQQTL KDASPSPLFS  360
SSDKQQPNKP ISPMSATALL QKAAQMGSTR STATAAPSFF AGSMTSSSAA SPSSSSPPPP  420
PRNPIMIHHQ MFNPNPRSIN HQEHHNLAPP PPPPNMSTAT SYAAAAAPNP NPGYYPIQQM  480
GMTRDFLGVS SEHHLHHQMG RQFLPQELTR FAPLG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-43	156	225	3	72	Zinc finger protein JACKDAW
5b3h_F	4e-43	156	225	3	72	Zinc finger protein JACKDAW
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	109	122	KLRQRTNKEAVRKK

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	XP_010543388.1

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010543388.1	0.0	PREDICTED: zinc finger protein JACKDAW-like isoform X2
Swissprot	Q700D2	0.0	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A3P6D0B7	0.0	A0A3P6D0B7_BRAOL; Uncharacterized protein
STRING	XP_010543387.1	0.0	(Tarenaya hassleriana)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G03150.1	1e-168	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]