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

Bradi5g01730.2.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: 680aa MW: 75184.1 Da PI: 6.4097

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bradi5g01730.2.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	97	109	14	26
--TTTTT-SS-SS CS zf-CCCH 14 tCkyGdrCkFaHg 26 CkyG++C+F+H+ Bradi5g01730.2.p 97 ACKYGASCRFSHD 109 7***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	9.967	80	111	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	6.643	124	149	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:3.20.20.70	1.4E-74	323	566	IPR013785	Aldolase-type TIM barrel
CDD	cd02801	2.17E-95	327	559	No hit	No description
SuperFamily	SSF51395	2.87E-64	327	640	No hit	No description
Pfam	PF01207	6.7E-54	330	584	IPR001269	tRNA-dihydrouridine synthase
PROSITE pattern	PS01136	0	411	429	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: 680 aa Download sequence Send to blast
MAATAPADDR PDNCPSAAAA SSPPQPTPEE LVARAVAPVK PAFLRPPPVR EAPSEENRAT 60 GAVPLEKKSK RQFKRERKQE SVSRLCIAVG KSGNPDACKY GASCRFSHDI DAYLAQKPAD 120 LEGSCPFTVQ DKLCPYGLNC RFLGTHKDNN ALSENHEINP LNKDVQKLLW KTKYKFPKAS 180 AQIKHLGLKE VIKTKANAQT EDQKADHDNL DVSCELNGDD KTESLSGPPV NLDCDSGLCE 240 EMVKLEGEPL VGNSVPCVEP RASKKSKVED GGIHKNGAGT HDTTTYSEDS ALVNGLEVPS 300 DDPSSCRVDL VETPHLRERK IIDFREKLYL APLTTVGNLP FRRLCKTLGA DITCGEMAMC 360 TNLMQGQASE WALLRRHSSE DLFGVQICGA FPDTVARTVE LVDNECSFDF IDINMGCPID 420 VVVNKGAGSQ LLTKPMRIKS IVQASSAVTE RPLTVKVRTA FFEGRNRADS LVSDIYDWGA 480 SAITIHGRSR QQRYSKLADW DYIYQCAQKA PDDLHVIGNG DIFSYTDWNR HVSGCSKIST 540 CMIARGALIK PWIFTEIKEQ KDWDITSGER FNILKDFAHF GLEHWGSDSK GVETTRHFLL 600 EWLSYTCRYI PVGLLDVVPQ RLNWRPPSYC GRDDLETLMA SDSAADWVRI SEMLLGKVPE 660 GFTFAPKHKS NAYDRAENG*

Sequence ? help Back to Top

Protein Sequence Length: 680 aa Download sequence Send to blast

MAATAPADDR PDNCPSAAAA SSPPQPTPEE LVARAVAPVK PAFLRPPPVR EAPSEENRAT  60
GAVPLEKKSK RQFKRERKQE SVSRLCIAVG KSGNPDACKY GASCRFSHDI DAYLAQKPAD  120
LEGSCPFTVQ DKLCPYGLNC RFLGTHKDNN ALSENHEINP LNKDVQKLLW KTKYKFPKAS  180
AQIKHLGLKE VIKTKANAQT EDQKADHDNL DVSCELNGDD KTESLSGPPV NLDCDSGLCE  240
EMVKLEGEPL VGNSVPCVEP RASKKSKVED GGIHKNGAGT HDTTTYSEDS ALVNGLEVPS  300
DDPSSCRVDL VETPHLRERK IIDFREKLYL APLTTVGNLP FRRLCKTLGA DITCGEMAMC  360
TNLMQGQASE WALLRRHSSE DLFGVQICGA FPDTVARTVE LVDNECSFDF IDINMGCPID  420
VVVNKGAGSQ LLTKPMRIKS IVQASSAVTE RPLTVKVRTA FFEGRNRADS LVSDIYDWGA  480
SAITIHGRSR QQRYSKLADW DYIYQCAQKA PDDLHVIGNG DIFSYTDWNR HVSGCSKIST  540
CMIARGALIK PWIFTEIKEQ KDWDITSGER FNILKDFAHF GLEHWGSDSK GVETTRHFLL  600
EWLSYTCRYI PVGLLDVVPQ RLNWRPPSYC GRDDLETLMA SDSAADWVRI SEMLLGKVPE  660
GFTFAPKHKS NAYDRAENG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ei9_A	4e-28	324	562	27	261	tRNA-dihydrouridine synthase B
6ei9_B	4e-28	324	562	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	Bradi5g01730.2.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_010239653.1	0.0	tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like isoform X2
Swissprot	Q7XT07	0.0	DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBL	A0A0Q3I6A5	0.0	A0A0Q3I6A5_BRADI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRING	BRADI5G01730.1	0.0	(Brachypodium distachyon)

Link Out ? help Back to Top
Phytozome	Bradi5g01730.2.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]