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

LOC_Os04g02730.1

Common Name

Os04g0117600, OSNPB_040117600

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

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: 697aa MW: 77529.9 Da PI: 7.7844

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os04g02730.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	19.2	2.2e-06	115	127	14	26
--TTTTT-SS-SS CS zf-CCCH 14 tCkyGdrCkFaHg 26 CkyGd+C+F+H+ LOC_Os04g02730.1 115 SCKYGDSCRFSHD 127 7***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	10.53	98	129	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:3.20.20.70	4.0E-74	340	583	IPR013785	Aldolase-type TIM barrel
CDD	cd02801	6.42E-95	344	579	No hit	No description
SuperFamily	SSF51395	2.14E-64	344	655	No hit	No description
Pfam	PF01207	7.1E-54	347	581	IPR001269	tRNA-dihydrouridine synthase
PROSITE pattern	PS01136	0	428	446	IPR018517	tRNA-dihydrouridine synthase, conserved site

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0002943	Biological Process	tRNA dihydrouridine synthesis
GO:0055114	Biological Process	oxidation-reduction process
GO:0017150	Molecular Function	tRNA dihydrouridine synthase activity
GO:0046872	Molecular Function	metal ion binding
GO:0050660	Molecular Function	flavin adenine dinucleotide binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0009049	anatomy	inflorescence
PO:0001083	developmental stage	inflorescence development stage
PO:0007006	developmental stage	IL.00 inflorescence just visible stage

Sequence ? help Back to Top
Protein Sequence Length: 697 aa Download sequence Send to blast
MPHCLLTAPQ PWPPPPPPPP RRLPPTRRTP PRPLPPLRGP ARRSWSPVQW PPSSPPSSAR 60 PLSATPPKDE GKANGGGAVV AEKKSKRQLK RERKQEQKSS SHLCIEVGKS GNVSSCKYGD 120 SCRFSHDIDA YLAQKPADLE GTCPFTNLDQ LCPYGLTCRF LGTHKDIHAA SGNLSEKHEI 180 NALNKDIQKL LWKNKYKFPK ASAQIKLLGL KEVIKSKPDA ANDDKKVNHD NLDGNDDENK 240 EPLCNPPVNA ECDSTLCEEL DRSEGEPLID NSIPCVEPRP TKKSKVESDE IDKHGAGTLN 300 TNTESEDPNL SNGLEPSNNS SSCRTDLITT PHLREKKIID FREKLYLAPL TTVGNLPFRR 360 LCKTLGADIT CGEMAMCTNL LQGQASEWAL LRRHSSEDLF GVQICGAYPD TVARTVELVD 420 NECSVDFIDI NMGCPIDIVV NKGAGSSLLT KPMRIKSIVQ AASTVTEKPL TVKVRTAFFE 480 GRNRADSIVS DIYDWGASAI TVHGRSRQQR YSKLADWDYI YQCAQKAPDQ LHVVGNGDVF 540 SFTDWNKHVS GCSKISTSMI ARGALIKPWI FTEVKEQRHW DITSGERFNI LKDFVSFGLE 600 HWGSDSKGVE TTRYFLLEWL SYTCRYIPVG LLDVIPQRLN WRPPSYCGRD DLETLMISDS 660 AADWIRISEM LLGKVPEGFT FTPKHKSNAY DRAENG*

Sequence ? help Back to Top

Protein Sequence Length: 697 aa Download sequence Send to blast

MPHCLLTAPQ PWPPPPPPPP RRLPPTRRTP PRPLPPLRGP ARRSWSPVQW PPSSPPSSAR  60
PLSATPPKDE GKANGGGAVV AEKKSKRQLK RERKQEQKSS SHLCIEVGKS GNVSSCKYGD  120
SCRFSHDIDA YLAQKPADLE GTCPFTNLDQ LCPYGLTCRF LGTHKDIHAA SGNLSEKHEI  180
NALNKDIQKL LWKNKYKFPK ASAQIKLLGL KEVIKSKPDA ANDDKKVNHD NLDGNDDENK  240
EPLCNPPVNA ECDSTLCEEL DRSEGEPLID NSIPCVEPRP TKKSKVESDE IDKHGAGTLN  300
TNTESEDPNL SNGLEPSNNS SSCRTDLITT PHLREKKIID FREKLYLAPL TTVGNLPFRR  360
LCKTLGADIT CGEMAMCTNL LQGQASEWAL LRRHSSEDLF GVQICGAYPD TVARTVELVD  420
NECSVDFIDI NMGCPIDIVV NKGAGSSLLT KPMRIKSIVQ AASTVTEKPL TVKVRTAFFE  480
GRNRADSIVS DIYDWGASAI TVHGRSRQQR YSKLADWDYI YQCAQKAPDQ LHVVGNGDVF  540
SFTDWNKHVS GCSKISTSMI ARGALIKPWI FTEVKEQRHW DITSGERFNI LKDFVSFGLE  600
HWGSDSKGVE TTRYFLLEWL SYTCRYIPVG LLDVIPQRLN WRPPSYCGRD DLETLMISDS  660
AADWIRISEM LLGKVPEGFT FTPKHKSNAY DRAENG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ei9_A	3e-27	341	575	27	257	tRNA-dihydrouridine synthase B
6ei9_B	3e-27	341	575	27	257	tRNA-dihydrouridine synthase B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Os.7618	0.0	callus\| flower\| leaf\| panicle\| root\| stem\| vegetative meristem

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	37988362	0.0
Expression Atlas	A0A0P0W652	-

Functional Description ? help Back to Top
Source	Description
UniProt	Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	LOC_Os04g02730.1

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

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os04g02730

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK111699	0.0	AK111699.1 Oryza sativa Japonica Group cDNA clone:J023009K15, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015635918.1	0.0	LOW QUALITY PROTEIN: tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
Swissprot	Q7XT07	0.0	DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBL	A0A0P0W652	0.0	A0A0P0W652_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRING	OS04T0117600-01	0.0	(Oryza sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10322	25	27
Representative plant	OGRP5751	12	13

Link Out ? help Back to Top
Phytozome	LOC_Os04g02730.1

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]