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

Phvul.006G221300.1

Common Name

PHAVU_006G221300g

Organism

Phaseolus vulgaris

Taxonomic ID

3885

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 548aa MW: 64680.9 Da PI: 6.4794

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Phvul.006G221300.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	19	2.6e-06	169	188	6	25
-SGGGGTS--TTTTT-SS-S CS zf-CCCH 6 CrffartGtCkyGdrCkFaH 25 C+f+++tG C++G rC++ H Phvul.006G221300.1 169 CPFHLKTGACRFGMRCSRVH 188 ******************99 PP
2	zf-CCCH	28.9	2e-09	300	327	1	26
--S---SGGGGTS..--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartG..tCkyGdrCkFaHg 26 +k ++C ++++G tC++G C+F+H+ Phvul.006G221300.1 300 WKVAICGEYMKSGfkTCSHGTACNFIHC 327 899************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	11.76	163	191	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.5	164	190	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.6E-4	168	188	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	9.9E-38	169	188	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	9.9E-38	188	208	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	7.4E-27	195	295	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	10.582	195	297	IPR000504	RNA recognition motif domain
CDD	cd12540	7.00E-49	196	296	No hit	No description
SMART	SM00361	5.6E-5	212	293	IPR003954	RNA recognition motif domain, eukaryote
PRINTS	PR01848	9.9E-38	226	241	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	4.75E-16	229	297	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	9.9E-38	254	276	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	9.9E-38	281	305	IPR009145	U2 auxiliary factor small subunit
PROSITE profile	PS50103	10.465	299	329	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	3.4E-4	299	328	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.2E-6	300	327	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	9.9E-38	319	331	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: 548 aa Download sequence Send to blast
MKRKQTRKEA AERERREEED RLNDPEEQRR IQLLEQEEAD RMQRDTILFQ EREKAFMDII 60 ITRQQQEEEQ QQEQEREHEQ EQSIDQDHEF EYEDGPPEII WQGNEIIFKK KQLRVRVTDT 120 HHDHNRPTSN PLPPESSVSE SESESRTQTL QDVAQQIPNF GTEQDKAHCP FHLKTGACRF 180 GMRCSRVHFY PDKSSTILIK NMYNGPGLAC DRDQDEGLEY TDEEVERCFE EFYEDVHTEF 240 LKFGEIVNFK VCKNGSFHLR GNVYVQYKAL DSALLAYNLV NGRYFAGKQV TCQFVNLTRW 300 KVAICGEYMK SGFKTCSHGT ACNFIHCFRN PGGDYEWADS DKPPPKFWVE KIIALFGYSD 360 YYETSREQGN LSLSKTDSDR YHCTRSRSRE MDKISCGHSG RRKHEDERKQ RTPNEDRNAS 420 FKNTHKRKSL GRTPDTDSDR EWLEKEENRE RRHEYTRNGS FNKNRDDNSG SHEEDSDVDC 480 DTRDNEKQHG RDVRRHRISE SSRHQGGDAS ESDKDLFGRV AMETVHDYSR KSSRHRRSDV 540 YKKKRSK*

Sequence ? help Back to Top

Protein Sequence Length: 548 aa Download sequence Send to blast

MKRKQTRKEA AERERREEED RLNDPEEQRR IQLLEQEEAD RMQRDTILFQ EREKAFMDII  60
ITRQQQEEEQ QQEQEREHEQ EQSIDQDHEF EYEDGPPEII WQGNEIIFKK KQLRVRVTDT  120
HHDHNRPTSN PLPPESSVSE SESESRTQTL QDVAQQIPNF GTEQDKAHCP FHLKTGACRF  180
GMRCSRVHFY PDKSSTILIK NMYNGPGLAC DRDQDEGLEY TDEEVERCFE EFYEDVHTEF  240
LKFGEIVNFK VCKNGSFHLR GNVYVQYKAL DSALLAYNLV NGRYFAGKQV TCQFVNLTRW  300
KVAICGEYMK SGFKTCSHGT ACNFIHCFRN PGGDYEWADS DKPPPKFWVE KIIALFGYSD  360
YYETSREQGN LSLSKTDSDR YHCTRSRSRE MDKISCGHSG RRKHEDERKQ RTPNEDRNAS  420
FKNTHKRKSL GRTPDTDSDR EWLEKEENRE RRHEYTRNGS FNKNRDDNSG SHEEDSDVDC  480
DTRDNEKQHG RDVRRHRISE SSRHQGGDAS ESDKDLFGRV AMETVHDYSR KSSRHRRSDV  540
YKKKRSK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	7e-32	160	354	9	182	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Phvul.006G221300.1

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	AP015038	1e-110	AP015038.1 Vigna angularis var. angularis DNA, chromosome 5, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007148590.1	0.0	hypothetical protein PHAVU_006G221300g
Swissprot	Q9SY74	1e-165	C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBL	V7BRH3	0.0	V7BRH3_PHAVU; Uncharacterized protein
STRING	XP_007148590.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4713	24	33

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G10320.1	1e-140	C3H family protein

Link Out ? help Back to Top
Phytozome	Phvul.006G221300.1
Entrez Gene	18629588

Publications ? help Back to Top
Lorković ZJ,Wieczorek Kirk DA,Lambermon MH,Filipowicz W Pre-mRNA splicing in higher plants. Trends Plant Sci., 2000. 5(4): p. 160-7 [PMID:10740297] 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]