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

AMDW01006074.1_FGP001

Organism

Oryza longistaminata

Taxonomic ID

4528

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

C3H

Protein Properties

Length: 48aa MW: 5601.35 Da PI: 8.0592

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AMDW01006074.1_FGP001	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	53.3	4.5e-17	7	32	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 +ktelC+ + +tG C+yGd+C+FaHg AMDW01006074.1_FGP001 7 FKTELCNKWEETGACPYGDQCQFAHG 32 79***********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1000.10	2.5E-20	2	39	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.83E-12	3	38	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	7.2E-10	6	33	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.601	6	34	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	3.3E-14	7	32	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 48 aa Download sequence Send to blast
VYNQGMFKTE LCNKWEETGA CPYGDQCQFA HGVAELRPVI RHPRYKTQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1rgo_A	1e-14	7	48	4	45	Butyrate response factor 2
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AMDW01006074.1_FGP001

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC098571	1e-74	AC098571.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1126_B10, complete sequence.
GenBank	AC098832	1e-74	AC098832.3 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1268_B08, complete sequence.
GenBank	AK106354	1e-74	AK106354.1 Oryza sativa Japonica Group cDNA clone:002-102-A03, full insert sequence.
GenBank	AP014961	1e-74	AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
GenBank	CP012613	1e-74	CP012613.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025816734.1	2e-30	zinc finger CCCH domain-containing protein 9-like isoform X2
Swissprot	Q6L5G1	4e-30	C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBL	A0A2T8IL21	5e-29	A0A2T8IL21_9POAL; Uncharacterized protein
STRING	Si002050m	2e-29	(Setaria italica)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G68200.2	3e-29	C3H family protein

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Cheng CH, et al. A fine physical map of the rice chromosome 5. Mol. Genet. Genomics, 2005. 274(4): p. 337-45 [PMID:16261349]