PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

C3H

Protein Properties

Length: 141aa MW: 16107.3 Da PI: 11.8064

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00083668001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	33.4	7.9e-11	14	38	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C+f+ ++G C++GdrC+++H GSBRNA2T00083668001 14 DRVNCPFYNKMGACRHGDRCSRIHN 38 6899********************7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.479	12	40	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.1E-4	13	39	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.3E-8	14	38	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	3.1E-15	18	37	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	3.1E-15	37	57	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	7.6E-4	70	99	IPR012677	Nucleotide-binding alpha-beta plait domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000398	Biological Process	mRNA splicing, via spliceosome
GO:0089701	Cellular Component	U2AF
GO:0000166	Molecular Function	nucleotide binding
GO:0003723	Molecular Function	RNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 141 aa Download sequence Send to blast
MAEHLASIYG TEKDRVNCPF YNKMGACRHG DRCSRIHNRP AISPTLLLSN MRRPAQDPRA 60 FRGSIRGAQE FKEEDQAAAA LQALQGRSYL GRPIIGEFSP IVSREKRRKL FGRRSYRRGS 120 RSRSISPRGR REYGRRDRDS *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	1e-22	1	102	1	142	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Necessary for the splicing of pre-mRNA. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00083668001

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	AC189555	7e-70	AC189555.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH006E24, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018447245.1	8e-42	PREDICTED: splicing factor U2af small subunit A
Refseq	XP_018447246.1	8e-42	PREDICTED: splicing factor U2af small subunit A
Swissprot	Q9ZQW8	3e-37	U2AFA_ORYSJ; Splicing factor U2af small subunit A
TrEMBL	A0A078I8T3	6e-96	A0A078I8T3_BRANA; BnaC05g21650D protein
STRING	Bo5g054590.1	2e-64	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G44785.1	2e-27	C3H family protein

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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Domon C,Lorković ZJ,Valcárcel J,Filipowicz W Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants. J. Biol. Chem., 1998. 273(51): p. 34603-10 [PMID:9852132]