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

Itr_sc000189.1_g00038.1

Organism

Ipomoea trifida

Taxonomic ID

35884

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea

Family

C3H

Protein Properties

Length: 798aa MW: 87816.4 Da PI: 7.052

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Itr_sc000189.1_g00038.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	32.5	1.4e-10	750	771	6	27
-SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 6 CrffartGtCkyGdrCkFaHgp 27 C+++ +tGtCkyG++CkF+H+p Itr_sc000189.1_g00038.1 750 CPYYTKTGTCKYGATCKFNHPP 771 ********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00582	3.9E-11	1	123	IPR006569	CID domain
PROSITE profile	PS51391	21.529	1	126	IPR006569	CID domain
Gene3D	G3DSA:1.25.40.90	5.4E-23	46	126	IPR008942	ENTH/VHS
SuperFamily	SSF48464	3.66E-19	48	126	IPR008942	ENTH/VHS
Pfam	PF04818	7.8E-7	54	107	IPR006903	RNA polymerase II-binding domain
PROSITE pattern	PS00028	0	542	562	IPR007087	Zinc finger, C2H2
PROSITE profile	PS50103	15.272	744	772	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.7E-5	744	771	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.44E-5	748	771	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	4.6E-8	750	771	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.4E-5	750	769	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: 798 aa Download sequence Send to blast
MSNDTSAGAS KSAPPSILDR FKAMLKERDE EVRVSSEDGV ISPPTMDEAP VEQKLPSLYL 60 LDSIVKNIGR EYIRHFSARL PEVFCETYRQ VQPNMFAALR HLFGTWSTVF PSSVLRKIEA 120 CLQFSPSTSH QSSGLTNLRA SESPRPGHGI HVNPKYLEAR RQLAGHSTIN AVGAEKLSST 180 GRAGLISSDI DAVKLLPTAA ARTVRSSSPF GVGRARSLSP PVDDFAVEST PQISERPSPS 240 HSRIDYGLNG VMAGDDETID WHRNLLHDGS SQRLENSVAC SVKKGVDLQG PRALIDAYGI 300 DEREKAFNYH HHKLGQPDAN GIGKRVGVKT WQNTEEEEFN WEDMSPTLGD PSRRNDFSSS 360 MPPSGRFITG PCVGSLQALS AINDSRRSLS DQAQHSLVKV SSNVDDIDFI VSGREITSKI 420 PGFYEEASLI SAPSYSQEPQ FLPQDFPHQS HLRIRVEGGG RAPSMRLSGT GLSTKVGEQK 480 LHLVGNLTTA DGKFWRPPSV ASRVNPGFNS SDSVGTEFNM ELLKERHEST ITALYSALPR 540 QCTTCGLRFK SQDAHSSHMD WHVTKNRLSK NRKHNPSRKW FVSLSMWLSS AEALGTDAVP 600 GFLPLEDVVE KKDDDELAVP ADDEQNACAL CGEPFDDFYS DETEEWMFRG AVYMNAPTGS 660 TTGMDRSESS SSCIEASKKH DEDYTDDGGL RKRMRSTCTV RIVPVRFSCT KRFQHPLDRS 720 PPVTSSMEGQ QQNVKPSLAG LPRREGAIHC PYYTKTGTCK YGATCKFNHP PPGVVMCIPS 780 QQQSRGFGLL PLLALTTL

Sequence ? help Back to Top

Protein Sequence Length: 798 aa Download sequence Send to blast

MSNDTSAGAS KSAPPSILDR FKAMLKERDE EVRVSSEDGV ISPPTMDEAP VEQKLPSLYL  60
LDSIVKNIGR EYIRHFSARL PEVFCETYRQ VQPNMFAALR HLFGTWSTVF PSSVLRKIEA  120
CLQFSPSTSH QSSGLTNLRA SESPRPGHGI HVNPKYLEAR RQLAGHSTIN AVGAEKLSST  180
GRAGLISSDI DAVKLLPTAA ARTVRSSSPF GVGRARSLSP PVDDFAVEST PQISERPSPS  240
HSRIDYGLNG VMAGDDETID WHRNLLHDGS SQRLENSVAC SVKKGVDLQG PRALIDAYGI  300
DEREKAFNYH HHKLGQPDAN GIGKRVGVKT WQNTEEEEFN WEDMSPTLGD PSRRNDFSSS  360
MPPSGRFITG PCVGSLQALS AINDSRRSLS DQAQHSLVKV SSNVDDIDFI VSGREITSKI  420
PGFYEEASLI SAPSYSQEPQ FLPQDFPHQS HLRIRVEGGG RAPSMRLSGT GLSTKVGEQK  480
LHLVGNLTTA DGKFWRPPSV ASRVNPGFNS SDSVGTEFNM ELLKERHEST ITALYSALPR  540
QCTTCGLRFK SQDAHSSHMD WHVTKNRLSK NRKHNPSRKW FVSLSMWLSS AEALGTDAVP  600
GFLPLEDVVE KKDDDELAVP ADDEQNACAL CGEPFDDFYS DETEEWMFRG AVYMNAPTGS  660
TTGMDRSESS SSCIEASKKH DEDYTDDGGL RKRMRSTCTV RIVPVRFSCT KRFQHPLDRS  720
PPVTSSMEGQ QQNVKPSLAG LPRREGAIHC PYYTKTGTCK YGATCKFNHP PPGVVMCIPS  780
QQQSRGFGLL PLLALTTL

Functional Description ? help Back to Top
Source	Description
UniProt	Promotes flowering by suppressing FLC-mediated inhibition of flowering through the regulation of FCA pre-mRNA alternative processing (PubMed:18298670). Regulates mRNA maturation including alternative polyadenylation, splicing or transcription initiation of stress-associated genes (PubMed:21364912). {ECO:0000269\|PubMed:18298670, ECO:0000269\|PubMed:21364912}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_019173654.1	0.0	PREDICTED: polyadenylation and cleavage factor homolog 4-like isoform X1
Swissprot	Q0WPF2	2e-74	PCFS4_ARATH; Polyadenylation and cleavage factor homolog 4
TrEMBL	A0A328DG70	0.0	A0A328DG70_9ASTE; Uncharacterized protein
STRING	XP_009793882.1	1e-150	(Nicotiana sylvestris)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G12680.1	9e-22	floral homeotic protein (HUA1)

Publications ? help Back to Top
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] 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] Zheng J, et al. Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray. PLoS ONE, 2011. 6(2): p. e14719 [PMID:21364912] Xing D, et al. The regulatory role of Pcf11-similar-4 (PCFS4) in Arabidopsis development by genome-wide physical interactions with target loci. BMC Genomics, 2013. 14: p. 598 [PMID:24004414] Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE Research progress on the autonomous flowering time pathway in Arabidopsis. Physiol Mol Biol Plants, 2017. 23(3): p. 477-485 [PMID:28878488]