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

e_gw1.5.1148.1

Organism

Ostreococcus sp. RCC809

Taxonomic ID

385169

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 114aa MW: 13523.4 Da PI: 7.68

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
e_gw1.5.1148.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	18.5	3.5e-06	65	88	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 +++ Crffa++G+Ck + C++ H+ e_gw1.5.1148.1 65 RMPTCRFFAKYGECKE-PDCPYKHS 88 5789*********9.*****8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF90229	2.55E-6	34	66	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.7E-5	34	62	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0044	35	61	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.981	35	62	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	5.0E-5	63	89	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.896	63	90	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.8	91	114	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	10.587	94	114	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: 114 aa Download sequence Send to blast
MDDLDVDFDF EDKLDANDTQ PQAPPPELNE RGRKNYRQTV CRHWLRNLCM KGNACGFLHQ 60 FDKSRMPTCR FFAKYGECKE PDCPYKHSLE DIKDCNMYKL GFCIHGPKCR FRHV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6dnh_C	2e-23	37	114	65	144	Cleavage and polyadenylation specificity factor subunit 4
6fbs_C	7e-24	37	114	64	143	Cleavage and polyadenylation specificity factor subunit 4
6fuw_C	7e-24	37	114	64	143	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	CP000585	1e-89	CP000585.1 Ostreococcus lucimarinus CCE9901 chromosome 5, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022838922.1	1e-68	Zinc finger, CCCH-type
Swissprot	A9LNK9	1e-42	CPSF_ARATH; 30-kDa cleavage and polyadenylation specificity factor 30
TrEMBL	A0A090M0Y8	2e-67	A0A090M0Y8_OSTTA; Zinc finger, CCCH-type
STRING	A0A090M0Y8	4e-68	(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]