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

905682

Common Name

ARALYDRAFT_905682

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

C2H2

Protein Properties

Length: 451aa MW: 50431.5 Da PI: 10.0202

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
905682	genome	JGI	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	68	90	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F+r nL+ H r H 905682 68 FICEICNKGFKRDQNLQLHRRGH 90 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.19E-7	67	90	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.2E-6	67	90	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
Pfam	PF12171	1.7E-5	68	90	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE profile	PS50157	10.866	68	90	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.011	68	90	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	70	90	IPR007087	Zinc finger, C2H2
SMART	SM00355	120	110	140	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.3E-4	133	166	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.19E-7	140	165	No hit	No description
SMART	SM00355	200	145	165	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 451 aa Download sequence Send to blast
MMMPDDHHHL SFPSYVLHQE HITPNPNPNP NPTSSNSAKR KRNLPGNPDP DAEVIALSPN 60 SLMATNRFIC EICNKGFKRD QNLQLHRRGH NLPWKLKQRT NKEQVKKKVY ICPEKSCVHH 120 DPARALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVMSDW KAHSKICGTR EYRCDCGTLF 180 SRKDSFITHR AFCDALAEEN ARFVSVPPAP AAPAPAYLNN PLDGEVNLGN INQNHQQRQV 240 NTTSSQLDQP GFNIHRNNIA FLGQTLPTNV FASSSSPSPR SASDSLQNLW HLQGQSSHQW 300 LLNENKNNNI LQRGISKNQE EREIKNVISN GSLFSTEARN NTNNYNQDCG HIASMSATAL 360 LQKAAQMGSK RSSSSSSNNS KTFGLMTSIF NNKQGENIKT KEVDERGFTR DFLGVGSQHR 420 PWPLLMVNHN LPNSSPSATI DGTPTADRNQ *

Sequence ? help Back to Top

Protein Sequence Length: 451 aa Download sequence Send to blast

MMMPDDHHHL SFPSYVLHQE HITPNPNPNP NPTSSNSAKR KRNLPGNPDP DAEVIALSPN  60
SLMATNRFIC EICNKGFKRD QNLQLHRRGH NLPWKLKQRT NKEQVKKKVY ICPEKSCVHH  120
DPARALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVMSDW KAHSKICGTR EYRCDCGTLF  180
SRKDSFITHR AFCDALAEEN ARFVSVPPAP AAPAPAYLNN PLDGEVNLGN INQNHQQRQV  240
NTTSSQLDQP GFNIHRNNIA FLGQTLPTNV FASSSSPSPR SASDSLQNLW HLQGQSSHQW  300
LLNENKNNNI LQRGISKNQE EREIKNVISN GSLFSTEARN NTNNYNQDCG HIASMSATAL  360
LQKAAQMGSK RSSSSSSNNS KTFGLMTSIF NNKQGENIKT KEVDERGFTR DFLGVGSQHR  420
PWPLLMVNHN LPNSSPSATI DGTPTADRNQ *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-35	141	206	3	68	Zinc finger protein JACKDAW
5b3h_F	2e-35	141	206	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	905682

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	AF428302	0.0	AF428302.1 Arabidopsis thaliana AT3g45260/F18N11_20 mRNA, complete cds.
GenBank	AJ621493	0.0	AJ621493.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 1 (idz1 gene).
GenBank	AY143936	0.0	AY143936.1 Arabidopsis thaliana At3g45260/F18N11_20 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002877396.1	0.0	protein indeterminate-domain 9
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	D7LNN7	0.0	D7LNN7_ARALL; Zinc finger family protein
STRING	scaffold_501386.1	0.0	(Arabidopsis lyrata)

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	0.0	C2H2-like zinc finger protein

Link Out ? help Back to Top
Phytozome	905682
Entrez Gene	9311794

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]