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_009150084.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 450aa MW: 50462.6 Da PI: 9.8766

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009150084.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	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 XP_009150084.1 68 FICEICNKGFKRDQNLQLHRRGH 90 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	5.2E-6	67	90	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	7.4E-8	67	90	No hit	No description
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	97	110	140	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.4E-4	133	166	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	7.4E-8	140	165	No hit	No description
SMART	SM00355	190	145	165	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: 450 aa Download sequence Send to blast
MIIPDDHHHL SFPSYVLHQE HITPNPNPNP NPTASNSNKR KRNLPGNPDP DAEVIALSPN 60 SLMTTNRFIC EICNKGFKRD QNLQLHRRGH NLPWKLKQRT DKEQVKKKVY ICPEKTCVHH 120 DPGRALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVVSDW KAHSKICGTR EYKCDCGTLF 180 SRKDSFITHR AFCDALAEES ARFASVPPAA AAYLNNSSDA EVNLGNIKPN HQQRLLDLTS 240 SQLDRHGFNV NRNNINGFMG QSSTNQLPLA ANVFASSSSP SPHSASALLQ NLWQLQGQSY 300 QQWLLNKNNN NIIQSGMPNN QEDHDTIRRE LVINGSSFSS EARTSYNQNG GQEIASMSAT 360 TLLQMAAQIG SKRSSSSSNN GMAFGLVTSS IFNNKEMENK IKTKEFDERG FTRDFLGVGS 420 QNRHRPILMV NHNLPTTNDG TPTTYMNHKT

Sequence ? help Back to Top

Protein Sequence Length: 450 aa Download sequence Send to blast

MIIPDDHHHL SFPSYVLHQE HITPNPNPNP NPTASNSNKR KRNLPGNPDP DAEVIALSPN  60
SLMTTNRFIC EICNKGFKRD QNLQLHRRGH NLPWKLKQRT DKEQVKKKVY ICPEKTCVHH  120
DPGRALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVVSDW KAHSKICGTR EYKCDCGTLF  180
SRKDSFITHR AFCDALAEES ARFASVPPAA AAYLNNSSDA EVNLGNIKPN HQQRLLDLTS  240
SQLDRHGFNV NRNNINGFMG QSSTNQLPLA ANVFASSSSP SPHSASALLQ NLWQLQGQSY  300
QQWLLNKNNN NIIQSGMPNN QEDHDTIRRE LVINGSSFSS EARTSYNQNG GQEIASMSAT  360
TLLQMAAQIG SKRSSSSSNN GMAFGLVTSS IFNNKEMENK IKTKEFDERG FTRDFLGVGS  420
QNRHRPILMV NHNLPTTNDG TPTTYMNHKT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-35	141	206	3	68	Zinc finger protein JACKDAW
5b3h_F	1e-35	141	206	3	68	Zinc finger protein JACKDAW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, especially in vascular initials, cortex, endodermis, and quiescent center (QC). {ECO:0000269\|PubMed:25829440}.

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	XP_009150084.1

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_009150084.1	0.0	PREDICTED: protein indeterminate-domain 9 isoform X1
Swissprot	Q944L3	0.0	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	A0A397YYN8	0.0	A0A397YYN8_BRACM; Uncharacterized protein
STRING	Bra038293.1-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]