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

BGIOSGA023330-PA

Organism

Oryza sativa subsp. indica

Taxonomic ID

39946

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; Oryza sativa

Family

C3H

Protein Properties

Length: 632aa MW: 71348.4 Da PI: 10.1077

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
BGIOSGA023330-PA	genome	RIS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	17.6	6.6e-06	479	500	4	26
---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 4 elCrffartGtCkyGdrCkFaHg 26 + C +f++ G+C yGd C+ H+ BGIOSGA023330-PA 479 PVCEDFLK-GYCAYGDECHKKHS 500 67****.*******97776 PP
2	zf-CCCH	18.8	2.8e-06	503	524	6	27
-SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 6 CrffartGtCkyGdrCkFaHgp 27 C+ f +tG+C+ G+rCk +H++ BGIOSGA023330-PA 503 CPVFEATGECPQGSRCKLHHPK 524 *****************99985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.037	393	422	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.9	393	421	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	14	422	446	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.859	426	447	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	11.235	448	474	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0094	448	473	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.76	475	502	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	7.7E-5	475	501	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.1	502	524	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	8.437	503	525	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0043484	Biological Process	regulation of RNA splicing
GO:0060149	Biological Process	negative regulation of posttranscriptional gene silencing
GO:0016607	Cellular Component	nuclear speck
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 632 aa Download sequence Send to blast
MNFVRKADTK DLANSNISVE RPKTPPLPLH TKSSCPTTLL EPLSQTLQKQ HGHDAEKEDL 60 TGQPKSGVDN SSIKSAQKSE PSDPSKVVYV RPKSNQLVAA QRQHPIDLVN SPTDKILSLQ 120 APIASDLYLK KRKNQIVLSS CSPSDGLSTK ETLPAENSNS EEKKDLMIAC SISGIPGVKD 180 RPQKALQTTN NVGRFSHVWT LNGQQPQRKG FMGSSHMNAF PRILPWKRKI FCKNFRSSHM 240 SNVSSIRIVR KLLQTRKRDM IYTVSTDGFS LRKSGVLSVG GSSLKWSRSL EKRSQKVNKE 300 ATLALAEVER RKREKRKRQS LHDKGDHQFE SVTGNQLRNS CQSSSDLRKP STCNEYVRVS 360 KGNQLVRNPK NVIRMLASDK VRWSLHTVRS RLAKKQQYCQ FFTRFGECKK PRGKCPYIHD 420 RAKVTICTKF LKGLCSNTSC KLTHKVLPER MPDCSYFLRG LCTNIACPYR HVKVNLNAPV 480 CEDFLKGYCA YGDECHKKHS YVCPVFEATG ECPQGSRCKL HHPKSKVKSK SRRPDFLQNS 540 SWGRYFDASI DHQDETRKVS LDEDEREKPQ RVFSDGDLGF ISLDDDADED VTALDASDDI 600 PLMELDSGDL SAQTDNLDAL IKPLRIMRTA RV

Sequence ? help Back to Top

Protein Sequence Length: 632 aa Download sequence Send to blast

MNFVRKADTK DLANSNISVE RPKTPPLPLH TKSSCPTTLL EPLSQTLQKQ HGHDAEKEDL  60
TGQPKSGVDN SSIKSAQKSE PSDPSKVVYV RPKSNQLVAA QRQHPIDLVN SPTDKILSLQ  120
APIASDLYLK KRKNQIVLSS CSPSDGLSTK ETLPAENSNS EEKKDLMIAC SISGIPGVKD  180
RPQKALQTTN NVGRFSHVWT LNGQQPQRKG FMGSSHMNAF PRILPWKRKI FCKNFRSSHM  240
SNVSSIRIVR KLLQTRKRDM IYTVSTDGFS LRKSGVLSVG GSSLKWSRSL EKRSQKVNKE  300
ATLALAEVER RKREKRKRQS LHDKGDHQFE SVTGNQLRNS CQSSSDLRKP STCNEYVRVS  360
KGNQLVRNPK NVIRMLASDK VRWSLHTVRS RLAKKQQYCQ FFTRFGECKK PRGKCPYIHD  420
RAKVTICTKF LKGLCSNTSC KLTHKVLPER MPDCSYFLRG LCTNIACPYR HVKVNLNAPV  480
CEDFLKGYCA YGDECHKKHS YVCPVFEATG ECPQGSRCKL HHPKSKVKSK SRRPDFLQNS  540
SWGRYFDASI DHQDETRKVS LDEDEREKPQ RVFSDGDLGF ISLDDDADED VTALDASDDI  600
PLMELDSGDL SAQTDNLDAL IKPLRIMRTA RV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6fbs_C	6e-16	399	524	41	168	Cleavage and polyadenylation specificity factor subunit 4
6fuw_C	6e-16	399	524	41	168	Cleavage and polyadenylation specificity factor subunit 4
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	309	314	RRKREK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.18758	0.0	leaf\| root

Functional Description ? help Back to Top
Source	Description
UniProt	Possesses RNA-binding and ribonuclease activities in vitro. {ECO:0000269\|PubMed:18582464}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	CP012614	0.0	CP012614.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 6 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015643043.1	0.0	uncharacterized protein LOC4341610 isoform X2
Swissprot	Q3ED78	1e-126	C3H7_ARATH; Zinc finger CCCH domain-containing protein 7
TrEMBL	A0A0E0HTX7	0.0	A0A0E0HTX7_ORYNI; Uncharacterized protein
STRING	ONIVA06G26100.1	0.0	(Oryza nivara)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6703	10	10

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G04990.2	4e-06	C3H family protein

Publications ? help Back to Top
Hématy K, et al. The Zinc-Finger Protein SOP1 Is Required for a Subset of the Nuclear Exosome Functions in Arabidopsis. PLoS Genet., 2016. 12(2): p. e1005817 [PMID:26828932]