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

Bradi5g01730.1.p

Common Name

BRADI_5g01730, LOC100840789

Organism

Brachypodium distachyon

Taxonomic ID

15368

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium

Family

C3H

Protein Properties

Length: 682aa MW: 75441.3 Da PI: 6.3134

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bradi5g01730.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	18.4	3.9e-06	99	111	14	26
--TTTTT-SS-SS CS zf-CCCH 14 tCkyGdrCkFaHg 26 CkyG++C+F+H+ Bradi5g01730.1.p 99 ACKYGASCRFSHD 111 7***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	9.967	82	113	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.643	126	151	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:3.20.20.70	1.4E-74	325	568	IPR013785	Aldolase-type TIM barrel
CDD	cd02801	2.28E-95	329	561	No hit	No description
SuperFamily	SSF51395	2.93E-64	329	642	No hit	No description
Pfam	PF01207	6.7E-54	332	586	IPR001269	tRNA-dihydrouridine synthase
PROSITE pattern	PS01136	0	413	431	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:0005829	Cellular Component	cytosol
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: 682 aa Download sequence Send to blast
MAATAPADDR PDNCPSAAAA SSPPQPTPEE LVARAVAPVK PAFLRPPPVR EAPSEENRAT 60 GAVPLEKKSK RQFKRERKQE QESVSRLCIA VGKSGNPDAC KYGASCRFSH DIDAYLAQKP 120 ADLEGSCPFT VQDKLCPYGL NCRFLGTHKD NNALSENHEI NPLNKDVQKL LWKTKYKFPK 180 ASAQIKHLGL KEVIKTKANA QTEDQKADHD NLDVSCELNG DDKTESLSGP PVNLDCDSGL 240 CEEMVKLEGE PLVGNSVPCV EPRASKKSKV EDGGIHKNGA GTHDTTTYSE DSALVNGLEV 300 PSDDPSSCRV DLVETPHLRE RKIIDFREKL YLAPLTTVGN LPFRRLCKTL GADITCGEMA 360 MCTNLMQGQA SEWALLRRHS SEDLFGVQIC GAFPDTVART VELVDNECSF DFIDINMGCP 420 IDVVVNKGAG SQLLTKPMRI KSIVQASSAV TERPLTVKVR TAFFEGRNRA DSLVSDIYDW 480 GASAITIHGR SRQQRYSKLA DWDYIYQCAQ KAPDDLHVIG NGDIFSYTDW NRHVSGCSKI 540 STCMIARGAL IKPWIFTEIK EQKDWDITSG ERFNILKDFA HFGLEHWGSD SKGVETTRHF 600 LLEWLSYTCR YIPVGLLDVV PQRLNWRPPS YCGRDDLETL MASDSAADWV RISEMLLGKV 660 PEGFTFAPKH KSNAYDRAEN G*

Sequence ? help Back to Top

Protein Sequence Length: 682 aa Download sequence Send to blast

MAATAPADDR PDNCPSAAAA SSPPQPTPEE LVARAVAPVK PAFLRPPPVR EAPSEENRAT  60
GAVPLEKKSK RQFKRERKQE QESVSRLCIA VGKSGNPDAC KYGASCRFSH DIDAYLAQKP  120
ADLEGSCPFT VQDKLCPYGL NCRFLGTHKD NNALSENHEI NPLNKDVQKL LWKTKYKFPK  180
ASAQIKHLGL KEVIKTKANA QTEDQKADHD NLDVSCELNG DDKTESLSGP PVNLDCDSGL  240
CEEMVKLEGE PLVGNSVPCV EPRASKKSKV EDGGIHKNGA GTHDTTTYSE DSALVNGLEV  300
PSDDPSSCRV DLVETPHLRE RKIIDFREKL YLAPLTTVGN LPFRRLCKTL GADITCGEMA  360
MCTNLMQGQA SEWALLRRHS SEDLFGVQIC GAFPDTVART VELVDNECSF DFIDINMGCP  420
IDVVVNKGAG SQLLTKPMRI KSIVQASSAV TERPLTVKVR TAFFEGRNRA DSLVSDIYDW  480
GASAITIHGR SRQQRYSKLA DWDYIYQCAQ KAPDDLHVIG NGDIFSYTDW NRHVSGCSKI  540
STCMIARGAL IKPWIFTEIK EQKDWDITSG ERFNILKDFA HFGLEHWGSD SKGVETTRHF  600
LLEWLSYTCR YIPVGLLDVV PQRLNWRPPS YCGRDDLETL MASDSAADWV RISEMLLGKV  660
PEGFTFAPKH KSNAYDRAEN G*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ei9_A	3e-28	326	564	27	261	tRNA-dihydrouridine synthase B
6ei9_B	3e-28	326	564	27	261	tRNA-dihydrouridine synthase B
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Bradi5g01730.1.p

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	KM399227	0.0	KM399227.1 Brachypodium distachyon FMN-linked oxidoreductases superfamily protein mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003580470.1	0.0	tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like isoform X1
Swissprot	Q7XT07	0.0	DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBL	I1IVR6	0.0	I1IVR6_BRADI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRING	BRADI5G01730.1	0.0	(Brachypodium distachyon)

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	Bradi5g01730.1.p
Entrez Gene	100840789

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] Zeng L, et al. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nat Commun, 2014. 5: p. 4956 [PMID:25249442]