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_016439111.1

Organism

Nicotiana tabacum

Taxonomic ID

4097

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

C2H2

Protein Properties

Length: 472aa MW: 52168.3 Da PI: 9.4524

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016439111.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.3	2.8e-05	68	90	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H XP_016439111.1 68 FICEICNKGFQRDQNLQLHRRGH 90 89*******************88 PP
2	zf-C2H2	11.8	0.00074	144	166	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H + + XP_016439111.1 144 WKCEKCSKQYAVQSDWKAHSKIC 166 58*****************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	1.2E-5	67	90	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.85E-7	67	90	No hit	No description
PROSITE profile	PS50157	10.845	68	90	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.022	68	90	IPR015880	Zinc finger, C2H2-like
Pfam	PF12171	5.6E-5	68	90	IPR022755	Zinc finger, double-stranded RNA binding
PROSITE pattern	PS00028	0	70	90	IPR007087	Zinc finger, C2H2
SMART	SM00355	100	109	139	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	9.2E-5	132	165	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	3.85E-7	139	164	No hit	No description
SMART	SM00355	140	144	164	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: 472 aa Download sequence Send to blast
MMSDNGLPSL PSSIRDFIQQ DPNPSSNIPN PNSNPASNKR KRNLPGNPDP DAEVIALSPK 60 SLMATNRFIC EICNKGFQRD QNLQLHRRGH NLPWKLKQRT NKEVKKKVYI CPEKTCVHHD 120 PSRALGDLTG IKKHFSRKHG EKKWKCEKCS KQYAVQSDWK AHSKICGTRE YKCDCGTLFS 180 RKDSFITHRA FCDALAEESA RFTSVPNTAN LNLRNQLMNS GMANLQQHNG NSQFGSLFRP 240 ELMGLGLDPS SQLNLDGQKP RLPLWLDNAN SGNPDDFLAT PSSTTSSLPH DLVQMASHNS 300 NNQWFINGNS ASASSSSMQQ PRVVLKEEEE INRRNLSEST INSSMYYNNS HQETTPQVAH 360 MSATALLQRA AQMGSTRSSN SALFSSSGFG LSSNFASTLA THDNIHGNNG LLLGDTNANS 420 LMMMQNKGKQ VNIPSGNTEG SLTRDFLGVG GNENRPFLQQ SELAKFGNSA IF

Sequence ? help Back to Top

Protein Sequence Length: 472 aa Download sequence Send to blast

MMSDNGLPSL PSSIRDFIQQ DPNPSSNIPN PNSNPASNKR KRNLPGNPDP DAEVIALSPK  60
SLMATNRFIC EICNKGFQRD QNLQLHRRGH NLPWKLKQRT NKEVKKKVYI CPEKTCVHHD  120
PSRALGDLTG IKKHFSRKHG EKKWKCEKCS KQYAVQSDWK AHSKICGTRE YKCDCGTLFS  180
RKDSFITHRA FCDALAEESA RFTSVPNTAN LNLRNQLMNS GMANLQQHNG NSQFGSLFRP  240
ELMGLGLDPS SQLNLDGQKP RLPLWLDNAN SGNPDDFLAT PSSTTSSLPH DLVQMASHNS  300
NNQWFINGNS ASASSSSMQQ PRVVLKEEEE INRRNLSEST INSSMYYNNS HQETTPQVAH  360
MSATALLQRA AQMGSTRSSN SALFSSSGFG LSSNFASTLA THDNIHGNNG LLLGDTNANS  420
LMMMQNKGKQ VNIPSGNTEG SLTRDFLGVG GNENRPFLQQ SELAKFGNSA IF

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	1e-36	140	207	3	70	Zinc finger protein JACKDAW
5b3h_F	1e-36	140	207	3	70	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}.

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	AC231670	1e-126	AC231670.1 Solanum tuberosum chromosome 11 clone RH121D01, complete sequence.
GenBank	HG975450	1e-126	HG975450.1 Solanum pennellii chromosome ch11, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009612448.1	0.0	PREDICTED: protein indeterminate-domain 9-like
Refseq	XP_016439111.1	0.0	PREDICTED: protein indeterminate-domain 9-like
Swissprot	Q944L3	1e-120	IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBL	A0A1S3XGQ3	0.0	A0A1S3XGQ3_TOBAC; protein indeterminate-domain 9-like
STRING	XP_009612448.1	0.0	(Nicotiana tomentosiformis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA103	24	350

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G45260.1	1e-119	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]