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

Zmw_sc00848.1.g00120.1

Organism

Zoysia matrella

Taxonomic ID

38722

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Zoysieae; Zoysiinae; Zoysia

Family

C3H

Protein Properties

Length: 75aa MW: 8368.62 Da PI: 7.9002

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zmw_sc00848.1.g00120.1	genome	ZGD	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	31	4.3e-10	27	51	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C+f+++ G C++GdrC++ H Zmw_sc00848.1.g00120.1.sm.mk 27 DRVNCPFYFKIGACHHGDRCSRLHN 51 689*********************7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	12.436	25	53	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.1E-7	27	51	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.22E-5	29	54	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	1.5E-20	31	50	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	1.5E-20	50	70	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:0003723	Molecular Function	RNA binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 75 aa Download sequence Send to blast
MGCCASSHYQ EGIMAEHLAS IFGTEKDRVN CPFYFKIGAC HHGDRCSRLH NRPTISPTLV 60 LVNMYQRPDM ITPGG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	2e-20	14	68	1	55	Splicing factor U2AF 23 kDa subunit
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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}.
UniProt	Necessary for the splicing of pre-mRNA (By similarity). Probably active at the 3' splice sites. {ECO:0000250}.
UniProt	Necessary for the splicing of pre-mRNA. {ECO:0000250}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002458285.1	2e-37	splicing factor U2af small subunit B
Refseq	XP_021313023.1	2e-37	splicing factor U2af small subunit B
Refseq	XP_021313024.1	2e-37	splicing factor U2af small subunit B
Refseq	XP_021313025.1	2e-37	splicing factor U2af small subunit B
Refseq	XP_021313026.1	2e-37	splicing factor U2af small subunit B
Refseq	XP_025816779.1	2e-37	splicing factor U2af small subunit B-like
Refseq	XP_025816780.1	2e-37	splicing factor U2af small subunit B-like
Refseq	XP_025816781.1	2e-37	splicing factor U2af small subunit B-like
Refseq	XP_025816782.1	2e-37	splicing factor U2af small subunit B-like
Swissprot	Q6AUG0	3e-37	U2AFB_ORYSJ; Splicing factor U2af small subunit B
Swissprot	Q9FMY5	2e-37	U2AFB_ARATH; Splicing factor U2af small subunit B
Swissprot	Q9S709	2e-37	U2AFA_ARATH; Splicing factor U2af small subunit A
TrEMBL	A0A3L6QYH7	5e-37	A0A3L6QYH7_PANMI; Uncharacterized protein
STRING	ONIVA05G27760.1	1e-37	(Oryza nivara)

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] Cheng CH, et al. A fine physical map of the rice chromosome 5. Mol. Genet. Genomics, 2005. 274(4): p. 337-45 [PMID:16261349] 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] 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]