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

Neem_6747_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

C2H2

Protein Properties

Length: 593aa MW: 64501.8 Da PI: 9.4792

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_6747_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.2	3.1e-05	52	74	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Neem_6747_f_1 52 FICEVCNKGFQREQNLQLHRRGH 74 89*******************88 PP
2	zf-C2H2	13.1	0.00028	128	150	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Neem_6747_f_1 128 WKCEKCSKRYAVQSDWKAHSKTC 150 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12171	2.2E-5	51	74	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	52	74	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.5E-5	52	74	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.99	52	74	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.43E-7	52	74	No hit	No description
PROSITE pattern	PS00028	0	54	74	IPR007087	Zinc finger, C2H2
SMART	SM00355	130	93	123	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	2.2E-5	116	149	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.43E-7	123	148	No hit	No description
SMART	SM00355	130	128	148	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: 593 aa Download sequence Send to blast
MSASSSAPFF EIREEDQNQM KQQHSATPTS SSAPAPPPQK KKRNQPGTPS KFICEVCNKG 60 FQREQNLQLH RRGHNLPWKL KQKTTKEVKR KVYLCPEPTC VHHDPSRALG DLTGIKKHYS 120 RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYRCDCG TLFSRRDSFI THRAFCDALA 180 QESARQPPSL SAISSHLYGS SNMGLGLSQV GPQLSSIKDQ NSQSNDILRL GGGSRSTAFD 240 HLLPPSMGSS SSFRPPQNMA STGFFMQESN QNYHEEHPSQ QGLLPNKTFH GLMQFPDLQN 300 NTSNTPSAAN LFNLSFLSNS SSSSSISNSN NANTTNSNLQ SSNLLISGHF NSDQNGTTTG 360 GVEGSNLFSN NLINDQISSG VPSLFSSSVQ NENMVPHMSA TALLQKAAQM GSTSSNNNTA 420 SLLRSFGSSS SGGTKPNFGG IFGAPENDSN LQDLMNTFAS GNSSIFGTGS VEVNAYNSPH 480 GQENPYAGYN TNRTNLEQEK RNHGQSFGNI DERKLHQNLN ISNIGGSDRM TRDFLGVGQI 540 VRSVSGGFSQ REKQQQQQQH RHGIDVSSLD SERNVAAPTS QSFGGAGGGG SFQ

Sequence ? help Back to Top

Protein Sequence Length: 593 aa Download sequence Send to blast

MSASSSAPFF EIREEDQNQM KQQHSATPTS SSAPAPPPQK KKRNQPGTPS KFICEVCNKG  60
FQREQNLQLH RRGHNLPWKL KQKTTKEVKR KVYLCPEPTC VHHDPSRALG DLTGIKKHYS  120
RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYRCDCG TLFSRRDSFI THRAFCDALA  180
QESARQPPSL SAISSHLYGS SNMGLGLSQV GPQLSSIKDQ NSQSNDILRL GGGSRSTAFD  240
HLLPPSMGSS SSFRPPQNMA STGFFMQESN QNYHEEHPSQ QGLLPNKTFH GLMQFPDLQN  300
NTSNTPSAAN LFNLSFLSNS SSSSSISNSN NANTTNSNLQ SSNLLISGHF NSDQNGTTTG  360
GVEGSNLFSN NLINDQISSG VPSLFSSSVQ NENMVPHMSA TALLQKAAQM GSTSSNNNTA  420
SLLRSFGSSS SGGTKPNFGG IFGAPENDSN LQDLMNTFAS GNSSIFGTGS VEVNAYNSPH  480
GQENPYAGYN TNRTNLEQEK RNHGQSFGNI DERKLHQNLN ISNIGGSDRM TRDFLGVGQI  540
VRSVSGGFSQ REKQQQQQQH RHGIDVSSLD SERNVAAPTS QSFGGAGGGG SFQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	9e-34	124	185	3	64	Zinc finger protein JACKDAW
5b3h_F	9e-34	124	185	3	64	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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:22898356, ECO:0000269\|PubMed:24821766}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00255	DAP	Transfer from AT2G02070	Download

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC208494	1e-137	AC208494.1 Populus trichocarpa clone JGIACSB265-L05, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011014313.1	0.0	PREDICTED: zinc finger protein NUTCRACKER-like
Refseq	XP_011014314.1	0.0	PREDICTED: zinc finger protein NUTCRACKER-like
Refseq	XP_011014315.1	0.0	PREDICTED: zinc finger protein NUTCRACKER-like
Swissprot	Q9ZUL3	1e-141	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	A0A2K1ZH36	0.0	A0A2K1ZH36_POPTR; Uncharacterized protein
STRING	POPTR_0008s14180.4	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4373	26	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	1e-102	indeterminate(ID)-domain 5

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]