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_36204_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: 170aa MW: 19642.5 Da PI: 10.4829

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_36204_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	18.4	6.1e-06	52	74	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Neem_36204_f_1 52 FICEVCNKGFQREQNLQLHRRGH 74 89*******************88 PP
2	zf-C2H2	15.3	5.7e-05	128	150	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ Neem_36204_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	4.4E-6	51	74	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	52	74	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	52	74	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.0E-6	52	74	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.77E-8	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	4.3E-6	116	149	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	4.77E-8	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: 170 aa Download sequence Send to blast
MSASSSAPFF EIREEDQNQM KQQHSATPTS SSAPAPPPQK KKRNQPGTPS KFICEVCNKG 60 FQREQNLQLH RRGHNLPWKL KQKTTKEVKR KVYLCPEPTC VHHDPSRALG DLTGIKKHYS 120 RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYRCDCG TLFSRIIMSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-23	124	165	3	44	Zinc finger protein JACKDAW
5b3h_F	4e-23	124	165	3	44	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). 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:0000305\|PubMed:19726569}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000305\|PubMed:17933900}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC208494	1e-138	AC208494.1 Populus trichocarpa clone JGIACSB265-L05, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006379802.2	1e-110	protein indeterminate-domain 5, chloroplastic
Refseq	XP_006379803.2	1e-110	protein indeterminate-domain 5, chloroplastic
Refseq	XP_006379804.2	1e-110	protein indeterminate-domain 5, chloroplastic
Refseq	XP_024463340.1	1e-110	protein indeterminate-domain 5, chloroplastic
Refseq	XP_024463341.1	1e-110	protein indeterminate-domain 5, chloroplastic
Swissprot	Q8GYC1	2e-85	IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBL	A0A2K1ZH36	1e-108	A0A2K1ZH36_POPTR; Uncharacterized protein
STRING	POPTR_0008s14180.4	1e-109	(Populus trichocarpa)

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
AT2G02080.1	4e-85	indeterminate(ID)-domain 4

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]