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

Pta011901

Organism

Pinus taeda

Taxonomic ID

3352

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pinus; Pinus

Family

C3H

Protein Properties

Length: 177aa MW: 20450.8 Da PI: 6.5037

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
gnl\|UG\|Pta#S26636430	PU_unref	Unigene	View CDS
PUT-157a-Pinus_taeda-176	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	29.7	1.1e-09	14	37	2	25
-S---SGGGGTS--TTTTT-SS-S CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaH 25 ++++C+f+++ G C++GdrC++ H Pta011901 14 DRVNCPFYFKIGACRHGDRCSRVH 37 6899*******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	12.915	12	40	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.022	13	39	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.7E-7	14	37	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	8.9E-63	18	37	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	3.66E-15	32	154	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	8.9E-63	37	57	IPR009145	U2 auxiliary factor small subunit
CDD	cd12539	9.08E-63	44	145	No hit	No description
PROSITE profile	PS50102	9.286	44	146	IPR000504	RNA recognition motif domain
Gene3D	G3DSA:3.30.70.330	2.2E-20	44	145	IPR012677	Nucleotide-binding alpha-beta plait domain
SMART	SM00361	0.0038	67	142	IPR003954	RNA recognition motif domain, eukaryote
PRINTS	PR01848	8.9E-63	75	90	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	8.9E-63	103	125	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	8.9E-63	130	154	IPR009145	U2 auxiliary factor small subunit
SMART	SM00356	1.1	148	174	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	9.61	148	175	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	8.9E-63	165	177	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: 177 aa Download sequence Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRVHTRP SISPTLLLSN MYQRPDIITP 60 GVDLQGHALD PRRVQEHFED FYEDLFEELS KREKXESLNV LDNLADHMVG NVYVQFREEE 120 HAAAALRALT GRFYAGRPII VDFSPVTDFR EASCRQYEEN TCKRAGYCNF MHLKQIS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	4e-66	1	177	1	172	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pta.34508	0.0	root

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010243574.1	1e-117	PREDICTED: splicing factor U2af small subunit B-like
Refseq	XP_010243584.1	1e-117	PREDICTED: splicing factor U2af small subunit B-like
Swissprot	Q6AUG0	1e-106	U2AFB_ORYSJ; Splicing factor U2af small subunit B
TrEMBL	A0A2G5DIL4	1e-118	A0A2G5DIL4_AQUCA; Uncharacterized protein
STRING	Aquca_019_00036.1	1e-118	(Aquilegia coerulea)

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] 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]