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

Lj3g3v1132330.2

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus

Family

C3H

Protein Properties

Length: 351aa MW: 41126.7 Da PI: 7.9225

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj3g3v1132330.2	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	28.6	2.5e-09	14	37	2	25
-S---SGGGGTS--TTTTT-SS-S CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaH 25 ++++C+f+++ G C++GdrC++ H Lj3g3v1132330.2 14 DRVNCPFYFKIGACRHGDRCSRLH 37 6899******************** PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	13.112	12	40	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.0065	13	39	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.2E-7	14	37	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	4.8E-60	18	37	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	4.8E-60	37	57	IPR009145	U2 auxiliary factor small subunit
CDD	cd12539	1.85E-59	44	145	No hit	No description
Gene3D	G3DSA:3.30.70.330	2.7E-21	44	145	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	9.661	44	146	IPR000504	RNA recognition motif domain
PRINTS	PR01848	4.8E-60	75	90	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	1.02E-14	77	149	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	4.8E-60	103	125	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	4.8E-60	130	154	IPR009145	U2 auxiliary factor small subunit
SMART	SM00356	0.48	148	174	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	10.211	148	175	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	4.8E-60	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:0048573	Biological Process	photoperiodism, flowering
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: 351 aa Download sequence Send to blast
MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHTKP SISPTLLLSN MYQRPDIVTP 60 GVDAQGQPID PRKIQTHFDD FYQDLFDELS KYGRLQTLNV CDNLADHMVG NVYAQFREEE 120 HAAEALKNLT GRFYAGNPII VDFSPVTDFR EATCRQYEED SCNRGGYCNF MHLKKISREL 180 RRELFGMDNR GRHGRSRSPD RHRSNEDRSP RGHSRKYDER SHHHESRGRR RRSNSPGHRR 240 GRSRSPRGSR ERRPARDGSE ERRARIEQWN REREEQKHES KVSTEENNAG NNGHVQDSNE 300 QWNREREEQK HESKVSTEEN NDGNNGHVQD GNEHHDYQQQ QQQPLEGGYD Y

Sequence ? help Back to Top

Protein Sequence Length: 351 aa Download sequence Send to blast

MAEHLASIFG TEKDRVNCPF YFKIGACRHG DRCSRLHTKP SISPTLLLSN MYQRPDIVTP  60
GVDAQGQPID PRKIQTHFDD FYQDLFDELS KYGRLQTLNV CDNLADHMVG NVYAQFREEE  120
HAAEALKNLT GRFYAGNPII VDFSPVTDFR EATCRQYEED SCNRGGYCNF MHLKKISREL  180
RRELFGMDNR GRHGRSRSPD RHRSNEDRSP RGHSRKYDER SHHHESRGRR RRSNSPGHRR  240
GRSRSPRGSR ERRPARDGSE ERRARIEQWN REREEQKHES KVSTEENNAG NNGHVQDSNE  300
QWNREREEQK HESKVSTEEN NDGNNGHVQD GNEHHDYQQQ QQQPLEGGYD Y

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	1e-69	1	184	1	179	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	219	231	RSHHHESRGRRRR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Lja.11452	0.0	cell culture\| floral bud\| protoplast

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	Lj3g3v1132330.2

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	AP010455	0.0	AP010455.1 Lotus japonicus genomic DNA, chromosome 3, clone: LjT04F17, TM0701, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_019436316.1	1e-163	PREDICTED: splicing factor U2af small subunit B-like
Refseq	XP_019436317.1	1e-163	PREDICTED: splicing factor U2af small subunit B-like
Refseq	XP_019436319.1	1e-163	PREDICTED: splicing factor U2af small subunit B-like
Refseq	XP_019436320.1	1e-163	PREDICTED: splicing factor U2af small subunit B-like
Swissprot	Q9ZQW8	1e-125	U2AFA_ORYSJ; Splicing factor U2af small subunit A
TrEMBL	A0A4D6N6P7	1e-164	A0A4D6N6P7_VIGUN; Splicing factor U2AF a subunit
STRING	EOY33579	1e-159	(Theobroma cacao)
STRING	evm.model.supercontig_47.49	1e-159	(Carica papaya)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G10320.1	1e-37	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] 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]