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

Tp5g16040

Organism

Thellungiella parvula

Taxonomic ID

98039

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 431aa MW: 48039.7 Da PI: 9.927

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp5g16040	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	19.9	2e-06	69	91	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F+r nL+ H r H Tp5g16040 69 FICEICNKGFKRDQNLQLHRRGH 91 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	4.9E-6	68	91	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	7.83E-8	68	91	No hit	No description
Pfam	PF12171	1.6E-5	69	91	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.011	69	91	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.866	69	91	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	71	91	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	111	141	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.0E-4	134	167	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	7.83E-8	141	166	No hit	No description
SMART	SM00355	200	146	166	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: 431 aa Download sequence Send to blast
MMMPDDHHHL SFPSYVLHQE QHITSNPNPN PNPTSSNSNK RKRNLPGNPD PDAEVIALSP 60 NSLMATNRFI CEICNKGFKR DQNLQLHRRG HNLPWKLKQR TKNEQVKKKV YICPEKTCVH 120 HDPARALGDL TGIKKHFSRK HGEKKWKCDK CSKKYAVMSD WKAHSKICGT REYRCDCGTL 180 FSRKDSFITH RAFCDALAEE SARFVSVPPA AAAYLNNSPE AEAKLGNINP NLSSTSSQLD 240 QPGFNINSNN INGFMGQSFT NQLPLPANVF ASSSSPSPRS ASDSFQNLWH LQGQSSHQWL 300 LNGNNNNNNI LQRGINNIQE DHDTKKGISN GSLLSSGART DYYQNGGQVI ASMSATALLQ 360 KAAQMGSKRS SPSSNNATAF GLMTSSIFNN KQTENNINTK EVDERGFTRD FLGVGSQNRP 420 WPLLMVNHNH V

Sequence ? help Back to Top

Protein Sequence Length: 431 aa Download sequence Send to blast

MMMPDDHHHL SFPSYVLHQE QHITSNPNPN PNPTSSNSNK RKRNLPGNPD PDAEVIALSP  60
NSLMATNRFI CEICNKGFKR DQNLQLHRRG HNLPWKLKQR TKNEQVKKKV YICPEKTCVH  120
HDPARALGDL TGIKKHFSRK HGEKKWKCDK CSKKYAVMSD WKAHSKICGT REYRCDCGTL  180
FSRKDSFITH RAFCDALAEE SARFVSVPPA AAAYLNNSPE AEAKLGNINP NLSSTSSQLD  240
QPGFNINSNN INGFMGQSFT NQLPLPANVF ASSSSPSPRS ASDSFQNLWH LQGQSSHQWL  300
LNGNNNNNNI LQRGINNIQE DHDTKKGISN GSLLSSGART DYYQNGGQVI ASMSATALLQ  360
KAAQMGSKRS SPSSNNATAF GLMTSSIFNN KQTENNINTK EVDERGFTRD FLGVGSQNRP  420
WPLLMVNHNH V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-35	142	207	3	68	Zinc finger protein JACKDAW
5b3h_F	2e-35	142	207	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	Tp5g16040

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	AK352822	0.0	AK352822.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-07-P14.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009150182.1	0.0	PREDICTED: protein indeterminate-domain 9-like isoform X2
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	A0A398APW3	0.0	A0A398APW3_BRACM; Uncharacterized protein
STRING	Bra033840.1-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
AT3G45260.1	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]