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_6347_f_3

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: 467aa MW: 50791.4 Da PI: 9.2247

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_6347_f_3	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	15.7	4.2e-05	64	84	3	23
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H Neem_6347_f_3 64 CEICGKGFQRDQNLQLHRRGH 84 *******************88 PP
2	zf-C2H2	13.5	0.00021	138	160	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Neem_6347_f_3 138 WKCEKCSKRYAVQSDWKAHSKTC 160 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	4.0E-5	61	84	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.97E-6	61	84	No hit	No description
PROSITE profile	PS50157	11.489	62	84	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.076	62	84	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	64	84	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.5E-4	126	159	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.97E-6	133	158	No hit	No description
SMART	SM00355	130	138	158	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0044212	Molecular Function	transcription regulatory region DNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 467 aa Download sequence Send to blast
MAEETIPNGF VQNSAAGSNP PAVKKKRNLP GTPGKQLLYS IIDPEAEVIA LSPKTLMATN 60 RFLCEICGKG FQRDQNLQLH RRGHNLPWKL KQRASKEVRK RVYVCPEKTC VHHHPSRALG 120 DLTGIKKHFC RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYKCDCG TIFSRRDSFI 180 THRAFCDALA EETARVNAAS SMNSLANGTI NYHLMGTPLG PSVAQHFSSI FKPISSSAET 240 IDQTRRGLSI WMAPASQGHE NIVNNLQEIH QVGSMHSGTA VFGDPLASCS NPPPSDDHLN 300 WVFGNKLSSN NAHEALASTS LPLTDVKEAA THQLVSVPSL YSSQQHTHQA ASADMSATAL 360 LQKAAQIGAT STHPSFLGSF GLKCSSNQVQ DGNKFCGLYG STAIANNLGT DVEKSGSDIS 420 TLSQPQMPPA KRRHLLSEES TGGQTRDFLG VGVQAISCHP SSIRGWI

Sequence ? help Back to Top

Protein Sequence Length: 467 aa Download sequence Send to blast

MAEETIPNGF VQNSAAGSNP PAVKKKRNLP GTPGKQLLYS IIDPEAEVIA LSPKTLMATN  60
RFLCEICGKG FQRDQNLQLH RRGHNLPWKL KQRASKEVRK RVYVCPEKTC VHHHPSRALG  120
DLTGIKKHFC RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYKCDCG TIFSRRDSFI  180
THRAFCDALA EETARVNAAS SMNSLANGTI NYHLMGTPLG PSVAQHFSSI FKPISSSAET  240
IDQTRRGLSI WMAPASQGHE NIVNNLQEIH QVGSMHSGTA VFGDPLASCS NPPPSDDHLN  300
WVFGNKLSSN NAHEALASTS LPLTDVKEAA THQLVSVPSL YSSQQHTHQA ASADMSATAL  360
LQKAAQIGAT STHPSFLGSF GLKCSSNQVQ DGNKFCGLYG STAIANNLGT DVEKSGSDIS  420
TLSQPQMPPA KRRHLLSEES TGGQTRDFLG VGVQAISCHP SSIRGWI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	2e-36	134	203	3	72	Zinc finger protein JACKDAW
5b3h_F	2e-36	134	203	3	72	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). 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). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269\|PubMed:17785527, ECO:0000269\|PubMed:21935722, ECO:0000269\|PubMed:24821766, ECO:0000269\|PubMed:25829440}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00125	DAP	Transfer from AT1G03840	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269\|PubMed:21935722}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007043706.2	0.0	PREDICTED: zinc finger protein MAGPIE isoform X2
Swissprot	Q9ZWA6	1e-150	IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBL	A0A061E4I0	0.0	A0A061E4I0_THECC; C2H2 and C2HC zinc fingers superfamily protein
STRING	EOX99537	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3710	26	60

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G03840.1	1e-153	C2H2 family protein

Publications ? help Back to Top
Muñoz-Strale D,León G Identification of two highly specific pollen promoters using transcriptomic data. Plant Physiol. Biochem., 2014. 83: p. 292-9 [PMID:25208507] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]