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; Raphanus

Family

C3H

Protein Properties

Length: 131aa MW: 14835.8 Da PI: 4.633

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1891_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	31.4	3.3e-10	14	38	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C+f+++ G C++GdrC++ H RrC1891_p1 14 DRVNCPFYFKIGACRHGDRCSRLHN 38 6899********************7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.065	12	40	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0068	13	39	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.5E-8	14	38	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	8.11E-5	16	41	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	8.7E-43	18	37	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	8.7E-43	37	57	IPR009145	U2 auxiliary factor small subunit
PROSITE profile	PS50102	8.74	44	131	IPR000504	RNA recognition motif domain
Gene3D	G3DSA:3.30.70.330	8.3E-20	44	131	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	8.7E-43	75	90	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	4.34E-10	77	131	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	8.7E-43	103	125	IPR009145	U2 auxiliary factor small subunit

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: 131 aa Download sequence Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHNRP TISPTLLLSN MYQRPDMITP 60 GVDPQGQPLD PSKIQAHFED FYEDIFEELD KFGEMESLNV CDNLADHMIG NVYVLFKEED 120 QAAAALKALQ G

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	7e-45	1	131	1	126	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 (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013606215.1	2e-95	PREDICTED: splicing factor U2af small subunit B
Swissprot	Q9FMY5	4e-85	U2AFB_ARATH; Splicing factor U2af small subunit B
TrEMBL	A0A0D3E643	5e-94	A0A0D3E643_BRAOL; Uncharacterized protein
STRING	Bo9g058670.1	8e-95	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM21123	4	4

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G44785.1	1e-31	C3H family protein

Publications ? help Back to Top
Day IS, et al. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing. Plant J., 2012. 71(6): p. 936-47 [PMID:22563826] Kim DW,Jeon SJ,Hwang SM,Hong JC,Bahk JD The C3H-type zinc finger protein GDS1/C3H42 is a nuclear-speckle-localized protein that is essential for normal growth and development in Arabidopsis. Plant Sci., 2016. 250: p. 141-153 [PMID:27457991] Park HY, et al. The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. Plant Cell Rep., 2017. 36(7): p. 1113-1123 [PMID:28432478]