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

676708864

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 453aa MW: 50594.6 Da PI: 9.9235

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676708864	genome	VEGI	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	71	93	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F+r nL+ H r H 676708864 71 FICEICNKGFKRDQNLQLHRRGH 93 89*******************88 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.3E-7	70	93	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.3E-6	70	93	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.866	71	93	IPR007087	Zinc finger, C2H2
Pfam	PF12171	1.7E-5	71	93	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.011	71	93	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	73	93	IPR007087	Zinc finger, C2H2
SMART	SM00355	120	113	143	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.3E-4	136	169	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.3E-7	143	168	No hit	No description
SMART	SM00355	200	148	168	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: 453 aa Download sequence Send to blast
MMMPDDHHHL SFPSYVLHQE HITPNPNPNP NPTSSNSNKR KRNLPGNPGM YNPDAEVIAL 60 SPNSLMATNR FICEICNKGF KRDQNLQLHR RGHNLPWKLK QRTNKEQVKK KVYICPEKSC 120 VHHDPARALG DLTGIKKHFS RKHGEKKWKC DKCSKKYAVM SDWKAHSKIC GTREYRCDCG 180 TLFSRKDSFI THRAFCDALA EESARFVSVP PGAAEYLKNA SDAEVNLGNS KPNHQQRLLN 240 STSSQPGYNI NRNSINGFMG QSFTNQLPLS ANIFASSSSP SPRSASDSLQ NLWHLQGQSS 300 HQWLLNENNS NNNILQRGIS NDQEDHDTKK GISNISLFSS EARNSYYQSG GQVIASMSAT 360 ALLQKAAQMG SKRSSSSSNN STGFGLMTSS ILNNKQTENN IKIKEVDERG FTRDFLGVGS 420 QNRPWPLLMV NHNLPDLSPR STTDGTPTAD VNQ

Sequence ? help Back to Top

Protein Sequence Length: 453 aa Download sequence Send to blast

MMMPDDHHHL SFPSYVLHQE HITPNPNPNP NPTSSNSNKR KRNLPGNPGM YNPDAEVIAL  60
SPNSLMATNR FICEICNKGF KRDQNLQLHR RGHNLPWKLK QRTNKEQVKK KVYICPEKSC  120
VHHDPARALG DLTGIKKHFS RKHGEKKWKC DKCSKKYAVM SDWKAHSKIC GTREYRCDCG  180
TLFSRKDSFI THRAFCDALA EESARFVSVP PGAAEYLKNA SDAEVNLGNS KPNHQQRLLN  240
STSSQPGYNI NRNSINGFMG QSFTNQLPLS ANIFASSSSP SPRSASDSLQ NLWHLQGQSS  300
HQWLLNENNS NNNILQRGIS NDQEDHDTKK GISNISLFSS EARNSYYQSG GQVIASMSAT  360
ALLQKAAQMG SKRSSSSSNN STGFGLMTSS ILNNKQTENN IKIKEVDERG FTRDFLGVGS  420
QNRPWPLLMV NHNLPDLSPR STTDGTPTAD VNQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	3e-35	144	209	3	68	Zinc finger protein JACKDAW
5b3h_F	3e-35	144	209	3	68	Zinc finger protein JACKDAW
Search in ModeBase

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	676708864

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
Refseq	XP_009150187.1	0.0	PREDICTED: protein indeterminate-domain 9-like isoform X3
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	M4EYE8	0.0	M4EYE8_BRARP; 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]