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_016477042.1

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: 491aa MW: 54124.8 Da PI: 9.5251

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016477042.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	14.1	0.00014	67	87	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++C+k F r nL+ H r H XP_016477042.1 67 CEICNKGFQRDQNLQLHRRGH 87 *******************88 PP
2	zf-C2H2	12.8	0.00036	142	164	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ XP_016477042.1 142 WKCEKCSKKYAVQSDWKAHSKTC 164 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	2.3E-5	64	87	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.81E-7	64	87	No hit	No description
SMART	SM00355	0.11	65	87	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.824	65	87	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	67	87	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	107	137	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.2E-4	130	163	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.81E-7	137	162	No hit	No description
SMART	SM00355	140	142	162	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: 491 aa Download sequence Send to blast
MMSGDVFSFP SSVKAVLPQH ELQTNPNPRP NPSSSKKRRN LPGTPDPDAE VIALSPKSLM 60 ATNRFLCEIC NKGFQRDQNL QLHRRGHNLP WKLKQRNKDE IVKKKVYICP EKTCIHHDAS 120 RALGDLTGIK KHFSRKHGEK KWKCEKCSKK YAVQSDWKAH SKTCGTREYK CDCGTLFSRK 180 DSFITHRAFC DALAEESSRI TSVGANNMNF PNINDTLLNQ QSNLHGISQI GTFYRPEFGN 240 GNSLNQQQQK PRLSLWLDQA NNNPLQMSAN SNLFESTTTS GFVDMMQMPS SNVFGSSSTV 300 ANFSLSSSQG TSMAETLSSL YSDSTQNNHL AKSSTPMSAT ALLQKAAQMG STKSNQSTVF 360 SNSFNLMSSS SSSPSNTPTF SSLHSSETTD QKFPKLSQDY TVSLAEGNGG LILCTNFSSS 420 ANTKAINLDQ AIMQTVGMQT PAVPMNMQQG MNNCLTRDFL GIRNEPFLSQ EMAKFASMSS 480 AMGLSHYSSS H

Sequence ? help Back to Top

Protein Sequence Length: 491 aa Download sequence Send to blast

MMSGDVFSFP SSVKAVLPQH ELQTNPNPRP NPSSSKKRRN LPGTPDPDAE VIALSPKSLM  60
ATNRFLCEIC NKGFQRDQNL QLHRRGHNLP WKLKQRNKDE IVKKKVYICP EKTCIHHDAS  120
RALGDLTGIK KHFSRKHGEK KWKCEKCSKK YAVQSDWKAH SKTCGTREYK CDCGTLFSRK  180
DSFITHRAFC DALAEESSRI TSVGANNMNF PNINDTLLNQ QSNLHGISQI GTFYRPEFGN  240
GNSLNQQQQK PRLSLWLDQA NNNPLQMSAN SNLFESTTTS GFVDMMQMPS SNVFGSSSTV  300
ANFSLSSSQG TSMAETLSSL YSDSTQNNHL AKSSTPMSAT ALLQKAAQMG STKSNQSTVF  360
SNSFNLMSSS SSSPSNTPTF SSLHSSETTD QKFPKLSQDY TVSLAEGNGG LILCTNFSSS  420
ANTKAINLDQ AIMQTVGMQT PAVPMNMQQG MNNCLTRDFL GIRNEPFLSQ EMAKFASMSS  480
AMGLSHYSSS H

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	5e-39	138	207	3	72	Zinc finger protein JACKDAW
5b3h_F	5e-39	138	207	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:20356954, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440, ECO:0000269\|PubMed:28211915}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not regulated by SCR and SHR. {ECO:0000269\|PubMed:21935722}.

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	HG975449	1e-154	HG975449.1 Solanum pennellii chromosome ch10, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009778699.1	0.0	PREDICTED: zinc finger protein JACKDAW-like
Refseq	XP_016477042.1	0.0	PREDICTED: zinc finger protein JACKDAW-like
Swissprot	Q700D2	1e-127	IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBL	A0A1S4AK15	0.0	A0A1S4AK15_TOBAC; zinc finger protein JACKDAW-like
TrEMBL	A0A1U7WVJ0	0.0	A0A1U7WVJ0_NICSY; zinc finger protein JACKDAW-like
STRING	XP_009778699.1	0.0	(Nicotiana sylvestris)

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
AT5G03150.1	1e-108	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] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938]