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

ONIVA04G00640.1

Organism

Oryza nivara

Taxonomic ID

4536

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

Family

C3H

Protein Properties

Length: 1130aa MW: 123014 Da PI: 6.5716

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
ONIVA04G00640.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	18.4	3.8e-06	104	116	14	26
--TTTTT-SS-SS CS zf-CCCH 14 tCkyGdrCkFaHg 26 CkyGd+C+F+H+ ONIVA04G00640.1 104 SCKYGDSCRFSHD 116 7***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	10.53	87	118	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:3.20.20.70	7.2E-74	329	572	IPR013785	Aldolase-type TIM barrel
SuperFamily	SSF51395	3.3E-64	333	644	No hit	No description
CDD	cd02801	1.25E-91	333	568	No hit	No description
Pfam	PF01207	1.5E-53	336	569	IPR001269	tRNA-dihydrouridine synthase
PROSITE pattern	PS01136	0	417	435	IPR018517	tRNA-dihydrouridine synthase, conserved site
Gene3D	G3DSA:3.90.1300.10	4.7E-89	706	1119	IPR023631	Amidase signature domain
Pfam	PF01425	8.6E-61	719	1110	IPR023631	Amidase signature domain
SuperFamily	SSF75304	1.7E-86	722	1116	IPR023631	Amidase signature domain
PROSITE pattern	PS00571	0	808	839	IPR020556	Amidase, 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

Sequence ? help Back to Top
Protein Sequence Length: 1130 aa Download sequence Send to blast
MAAAAAAAAA APPADPPDSS PAASSPPRPS PEELVARAVA PVKPAFLRPP PVRDAPKDEG 60 KANDGGAVVA EKKSKRQLKR ERKQEQKSSS HLCIEVGKSG NVSSCKYGDS CRFSHDIDAY 120 LAQKPADLEG TCPFTNLDQL CPYGLTCRFL GTHKDIHAAS GNLSEKHEIN ALNKDIQKLL 180 WKNKYKFPKA SAQIKLLGLK EVIKSKPDAA NDDKKVNHDN LDGNDDENKE PLCNPPVNAE 240 CDSTLCEELD RSEGEPLIDN SIPCVEPRPT KKSKVESDEI DKHGAGTLNT NTESEDPNLS 300 NGLEPSNNAS SCRTDLITTP HLREKKIIDF REKLYLAPLT TVGNLPFRRL CKTLGADITC 360 GEMAMCTNLL QGQASEWALL RRHSSEDLFG VQICGAYPDT VARTVELVDN ECSIDFIDIN 420 MGCPIDIVVN KGAGSSLLTK PMRIKSIVQA ASTVTEKPLT VKVRTAFFEG RNRADSIVSD 480 IYDWGASAIT VHGRSRQQRY SKLADWDYIY QCAQKAPDQL HVVGNGDVFS FTDWNKHVSG 540 CSKISTCMIA RGALIKPWIF TEVKEQRHWD ITSGERFNIL KDFVSFGLEH WGSDSKGVET 600 TRYFLLEWLS YTCRYIPVGL LDVIPQRLNW RPPSYCGRDD LETLMISDSA ADWIRISEML 660 LGKVPEGHTV PIFCCFANWA SICRRRAAQA QPLCRLNKLS RGGGVEDQRF VLPPPPPPSS 720 QQLPLHGLTF AIKDIFDIAG RVTGFGNPDW ARTHAPAAAT SPVVLAALAA GATSLGTTIM 780 DEMAYSINGE NTHYGTPTNP CAPGRVPGGS SSGSAVAVAA NLVDFSLGTD TGGSVRVPAA 840 YCGIFGLRPS HGLVSAENVI PMAQMFDTVG WFSRDLSTLS RVTKVLLPLP DDIVKQPTQV 900 TIPMDCFQIL GSLNDRTYQI INASVAKRFD SQIIDNRNLG DFISDNVPSI GKFITDFSES 960 ELPSVPALSV ISHVMRGLQR SQFKANHAEW VNTVKPNLGP GLRERILEAI ASGDNESLED 1020 FQAIRAEFKS ALAALLKDHG ILAIPTVPGP PPKVGMEAAP LENFRARAFS LLSIAGLSGF 1080 CQVSIPLGMR NGLPVSVSLV ARHGADHFLL NVVEELYQTL IDEATKTWSS

Sequence ? help Back to Top

Protein Sequence Length: 1130 aa Download sequence Send to blast

MAAAAAAAAA APPADPPDSS PAASSPPRPS PEELVARAVA PVKPAFLRPP PVRDAPKDEG  60
KANDGGAVVA EKKSKRQLKR ERKQEQKSSS HLCIEVGKSG NVSSCKYGDS CRFSHDIDAY  120
LAQKPADLEG TCPFTNLDQL CPYGLTCRFL GTHKDIHAAS GNLSEKHEIN ALNKDIQKLL  180
WKNKYKFPKA SAQIKLLGLK EVIKSKPDAA NDDKKVNHDN LDGNDDENKE PLCNPPVNAE  240
CDSTLCEELD RSEGEPLIDN SIPCVEPRPT KKSKVESDEI DKHGAGTLNT NTESEDPNLS  300
NGLEPSNNAS SCRTDLITTP HLREKKIIDF REKLYLAPLT TVGNLPFRRL CKTLGADITC  360
GEMAMCTNLL QGQASEWALL RRHSSEDLFG VQICGAYPDT VARTVELVDN ECSIDFIDIN  420
MGCPIDIVVN KGAGSSLLTK PMRIKSIVQA ASTVTEKPLT VKVRTAFFEG RNRADSIVSD  480
IYDWGASAIT VHGRSRQQRY SKLADWDYIY QCAQKAPDQL HVVGNGDVFS FTDWNKHVSG  540
CSKISTCMIA RGALIKPWIF TEVKEQRHWD ITSGERFNIL KDFVSFGLEH WGSDSKGVET  600
TRYFLLEWLS YTCRYIPVGL LDVIPQRLNW RPPSYCGRDD LETLMISDSA ADWIRISEML  660
LGKVPEGHTV PIFCCFANWA SICRRRAAQA QPLCRLNKLS RGGGVEDQRF VLPPPPPPSS  720
QQLPLHGLTF AIKDIFDIAG RVTGFGNPDW ARTHAPAAAT SPVVLAALAA GATSLGTTIM  780
DEMAYSINGE NTHYGTPTNP CAPGRVPGGS SSGSAVAVAA NLVDFSLGTD TGGSVRVPAA  840
YCGIFGLRPS HGLVSAENVI PMAQMFDTVG WFSRDLSTLS RVTKVLLPLP DDIVKQPTQV  900
TIPMDCFQIL GSLNDRTYQI INASVAKRFD SQIIDNRNLG DFISDNVPSI GKFITDFSES  960
ELPSVPALSV ISHVMRGLQR SQFKANHAEW VNTVKPNLGP GLRERILEAI ASGDNESLED  1020
FQAIRAEFKS ALAALLKDHG ILAIPTVPGP PPKVGMEAAP LENFRARAFS LLSIAGLSGF  1080
CQVSIPLGMR NGLPVSVSLV ARHGADHFLL NVVEELYQTL IDEATKTWSS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2dc0_A	1e-31	724	1112	64	425	probable amidase
2dc0_B	1e-31	724	1112	64	425	probable amidase
Search in ModeBase

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}.

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	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	A0A0E0GX68	0.0	A0A0E0GX68_ORYNI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRING	ONIVA04G00640.1	0.0	(Oryza nivara)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP10322	25	27

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]