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

fgenesh1_pg.C_Chr_05.0001000049

Organism

Ostreococcus tauri

Taxonomic ID

70448

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Chlorophyta; prasinophytes; Mamiellophyceae; Mamiellales; Bathycoccaceae; Ostreococcus

Family

C3H

Protein Properties

Length: 209aa MW: 23362.6 Da PI: 6.9113

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
fgenesh1_pg.C_Chr_05.0001000049	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	17.2	8.9e-06	67	89	3	26
S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHg 26 ++ Crf+a++G+Ck + C++ H+ fgenesh1_pg.C_Chr_05.0001000049 67 MPTCRFYAKYGECKE-PDCPYKHS 89 789*********9.*****8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1000.10	7.8E-5	35	63	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.97E-6	35	66	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.981	36	63	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0044	36	62	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.803	64	91	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	7.2E-5	64	90	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.28	92	116	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	9.967	95	117	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006979	Biological Process	response to oxidative stress
GO:0034052	Biological Process	positive regulation of plant-type hypersensitive response
GO:1900363	Biological Process	regulation of mRNA polyadenylation
GO:2000031	Biological Process	regulation of salicylic acid mediated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
GO:0003723	Molecular Function	RNA binding
GO:0004521	Molecular Function	endoribonuclease activity
GO:0005516	Molecular Function	calmodulin binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 209 aa Download sequence Send to blast
MDDDADLDFD FEDKLDANDT QPQAPPPELN ERGRKNYRQT VCRHWLRNLC MKGNACGFLH 60 QFDKSRMPTC RFYAKYGECK EPDCPYKHSL EDVKDCNMFK LGFCIHGNLC RFRHVKLPGP 120 PPPVEEMALV GQPGHLHGAK SFKQREREKA MAMAMQPREA PDATFKAPPL PPGPPPKHLA 180 RKEERCGIQD GMPGADEEAG ADGFPGAA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6dnh_C	1e-22	38	116	65	145	Cleavage and polyadenylation specificity factor subunit 4
6fbs_C	5e-23	38	116	64	144	Cleavage and polyadenylation specificity factor subunit 4
6fuw_C	5e-23	38	116	64	144	Cleavage and polyadenylation specificity factor subunit 4
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Functional Description ? help Back to Top
Source	Description
UniProt	Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation. May interact with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition (By similarity). Mediates poly(A) site selection (PubMed:23136375). Binds RNA in a calcium-dependent manner (PubMed:16500995, PubMed:17576667, PubMed:20214900). Exhibits endonuclease activity with an ability to nick and degrade linear as well as circular single-stranded RNA that leaves RNA 3' ends with hydroxyl groups, thus mediating processing of the pre-mRNA as a prelude to the polyadenylation (PubMed:17576667). Involved in the post-transcriptional control, probably via poly(A) addition, of the responses of plants to stress, especially genes mediating tolerance to oxidative stress (PubMed:18545667). Plays a role in the regulation of salicylic acid (SA) production via the control of messenger RNA 3' end processing, thus being a key component of programmed cell death and plant immune responses required for resistance to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550). {ECO:0000250\|UniProtKB:O95639, ECO:0000269\|PubMed:16500995, ECO:0000269\|PubMed:17576667, ECO:0000269\|PubMed:18545667, ECO:0000269\|PubMed:20214900, ECO:0000269\|PubMed:23136375, ECO:0000269\|PubMed:24706550}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Isoform 2 is up-regulated by exposure to the oxidative agent methyl viologen (MV). {ECO:0000269\|PubMed:18545667}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022838922.1	1e-115	Zinc finger, CCCH-type
Swissprot	A9LNK9	3e-42	CPSF_ARATH; 30-kDa cleavage and polyadenylation specificity factor 30
TrEMBL	A0A090M0Y8	1e-114	A0A090M0Y8_OSTTA; Zinc finger, CCCH-type
STRING	A0A090M0Y8	1e-115	(Ostreococcus tauri)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Chlorophytae	OGCP3492	7	7

Publications ? help Back to Top
Forbes KP,Addepalli B,Hunt AG An Arabidopsis Fip1 homolog interacts with RNA and provides conceptual links with a number of other polyadenylation factor subunits. J. Biol. Chem., 2006. 281(1): p. 176-86 [PMID:16282318] Xu R, et al. The 73 kD subunit of the cleavage and polyadenylation specificity factor (CPSF) complex affects reproductive development in Arabidopsis. Plant Mol. Biol., 2006. 61(4-5): p. 799-815 [PMID:16897494] Addepalli B,Hunt AG A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor. Nucleic Acids Res., 2007. 35(13): p. 4453-63 [PMID:17576667] Addepalli B,Hunt AG Redox and heavy metal effects on the biochemical activities of an Arabidopsis polyadenylation factor subunit. Arch. Biochem. Biophys., 2008. 473(1): p. 88-95 [PMID:18331819] Hunt AG, et al. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling. BMC Genomics, 2008. 9: p. 220 [PMID:18479511] Zhang J, et al. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS ONE, 2008. 3(6): p. e2410 [PMID:18545667] Qi X,Bao FS,Xie Z Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. PLoS ONE, 2009. 4(3): p. e4971 [PMID:19308254] Rao S,Dinkins RD,Hunt AG Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biol., 2009. 10: p. 51 [PMID:19573236] Zhao H,Xing D,Li QQ Unique features of plant cleavage and polyadenylation specificity factor revealed by proteomic studies. Plant Physiol., 2009. 151(3): p. 1546-56 [PMID:19748916] Bell SA,Hunt AG The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett., 2010. 584(8): p. 1449-54 [PMID:20214900] Addepalli B,Limbach PA,Hunt AG A disulfide linkage in a CCCH zinc finger motif of an Arabidopsis CPSF30 ortholog. FEBS Lett., 2010. 584(21): p. 4408-12 [PMID:20888817] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Thomas PE, et al. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell, 2012. 24(11): p. 4376-88 [PMID:23136375] Bruggeman Q, et al. The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis. Plant Physiol., 2014. 165(2): p. 732-746 [PMID:24706550] Hunt AG The Arabidopsis polyadenylation factor subunit CPSF30 as conceptual link between mRNA polyadenylation and cellular signaling. Curr. Opin. Plant Biol., 2014. 21: p. 128-132 [PMID:25104048] Liu M, et al. Integration of developmental and environmental signals via a polyadenylation factor in Arabidopsis. PLoS ONE, 2014. 9(12): p. e115779 [PMID:25546057] Chakrabarti M,Hunt AG CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants. Biomolecules, 2015. 5(2): p. 1151-68 [PMID:26061761] Li QQ,Liu Z,Lu W,Liu M Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene. Sci Rep, 2017. 7(1): p. 2052 [PMID:28515442] Li Z, et al. The Arabidopsis CPSF30-L gene plays an essential role in nitrate signaling and regulates the nitrate transceptor gene NRT1.1. New Phytol., 2017. 216(4): p. 1205-1222 [PMID:28850721] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478]