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; Sisymbrieae; Sisymbrium

Family

C3H

Protein Properties

Length: 787aa MW: 92616.5 Da PI: 7.1742

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676723302	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	22.3	2.3e-07	238	257	6	25
-SGGGGTS--TTTTT-SS-S CS zf-CCCH 6 CrffartGtCkyGdrCkFaH 25 C+f+++tG C++G rC++ H 676723302 238 CPFHLKTGACRFGLRCSRVH 257 ******************99 PP
2	zf-CCCH	27.7	4.6e-09	367	394	1	26
--S---SGGGGTS..--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartG..tCkyGdrCkFaHg 26 +k ++C ++++ tC++G+ C+F H+ 676723302 367 WKVAICGEYMKSRlkTCSRGSACNFLHC 394 899************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	11.779	232	260	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.2	233	259	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.9E-5	237	257	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	7.1E-37	238	257	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	7.1E-37	257	277	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	1.4E-26	263	362	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	9.695	264	364	IPR000504	RNA recognition motif domain
CDD	cd12540	1.25E-46	265	363	No hit	No description
SMART	SM00361	4.4E-6	284	360	IPR003954	RNA recognition motif domain, eukaryote
PRINTS	PR01848	7.1E-37	293	308	IPR009145	U2 auxiliary factor small subunit
SuperFamily	SSF54928	1.24E-16	296	364	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	7.1E-37	321	343	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	7.1E-37	348	372	IPR009145	U2 auxiliary factor small subunit
PROSITE profile	PS50103	11.441	366	396	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.018	366	395	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.5E-7	367	394	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	7.1E-37	386	398	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: 787 aa Download sequence Send to blast
MEPQDEKEEV ERPEEAMEGK ERLEENKEKA AEMSRKEKRK AMKKLKRKQV RKEIASKERE 60 EAEAKLNDPV EQEKLKAIEE EEARKREKEL KEFEESERAW IEAMEIKMKK EEEEAAKREE 120 EERRWKDLEE SRKLLEASRN DECGEDEDGE YEYIEEGPPE IIFQGNEIIL RKNKVKVPKK 180 SVAQLDANEI ADRPSSNPLP PGTEDFPKYQ NASSAQQILD NVAQEAPNFG TEQDKAHCPF 240 HLKTGACRFG LRCSRVHFYP DKSCTILMKN MYNGPGIAWE QDEVLEYTDE EAEQCYEEFY 300 EDVHTEFLKY GELINFKVCR NGSFHLKGNV YVHFRSLDSA FLAYQSINGR YFAGKQVTCE 360 FVNISRWKVA ICGEYMKSRL KTCSRGSACN FLHCFRNPGG DYEWADHDRP PPRFWIHKMT 420 ALFGYPDEYL KHMEREYSGS LNDFRSEQPA DSHRQLSRRS RSRDHDHENV RSKPCYRSLK 480 NHGDTQDSTR GHKLSRHAEK RHVEDESTNN TRDGSSERDM YKERRYAKET WRQESKWSEH 540 SPGHRVMRKR IHGRYSDDDD SGDDDAKGET GHKAKSSRRY GRRGSDSEIS ERLDGDVDTR 600 THRSSSDRRS RKEDNREGSS ADKEERHAQD KVQAVGDKSQ RERWKHGHER SSSRYSHERD 660 STGSDRKTSV ETSPREYQSD KDREKSKQRH TRYKTRDDDS DGSRKAKHRR RSSGNGVSVR 720 ESQEVNRNGK RENVSSSSGD EECSDRGETH KERPHRRGKR RRSQHSHEQT PKESDEFERE 780 IERWRPM

Sequence ? help Back to Top

Protein Sequence Length: 787 aa Download sequence Send to blast

MEPQDEKEEV ERPEEAMEGK ERLEENKEKA AEMSRKEKRK AMKKLKRKQV RKEIASKERE  60
EAEAKLNDPV EQEKLKAIEE EEARKREKEL KEFEESERAW IEAMEIKMKK EEEEAAKREE  120
EERRWKDLEE SRKLLEASRN DECGEDEDGE YEYIEEGPPE IIFQGNEIIL RKNKVKVPKK  180
SVAQLDANEI ADRPSSNPLP PGTEDFPKYQ NASSAQQILD NVAQEAPNFG TEQDKAHCPF  240
HLKTGACRFG LRCSRVHFYP DKSCTILMKN MYNGPGIAWE QDEVLEYTDE EAEQCYEEFY  300
EDVHTEFLKY GELINFKVCR NGSFHLKGNV YVHFRSLDSA FLAYQSINGR YFAGKQVTCE  360
FVNISRWKVA ICGEYMKSRL KTCSRGSACN FLHCFRNPGG DYEWADHDRP PPRFWIHKMT  420
ALFGYPDEYL KHMEREYSGS LNDFRSEQPA DSHRQLSRRS RSRDHDHENV RSKPCYRSLK  480
NHGDTQDSTR GHKLSRHAEK RHVEDESTNN TRDGSSERDM YKERRYAKET WRQESKWSEH  540
SPGHRVMRKR IHGRYSDDDD SGDDDAKGET GHKAKSSRRY GRRGSDSEIS ERLDGDVDTR  600
THRSSSDRRS RKEDNREGSS ADKEERHAQD KVQAVGDKSQ RERWKHGHER SSSRYSHERD  660
STGSDRKTSV ETSPREYQSD KDREKSKQRH TRYKTRDDDS DGSRKAKHRR RSSGNGVSVR  720
ESQEVNRNGK RENVSSSSGD EECSDRGETH KERPHRRGKR RRSQHSHEQT PKESDEFERE  780
IERWRPM

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	6e-30	226	393	6	167	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	676723302

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_009144452.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 5-like
Swissprot	Q9SY74	0.0	C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBL	M4DPK5	0.0	M4DPK5_BRARP; Uncharacterized protein
STRING	Bra018446.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5975	20	25

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G10320.1	0.0	C3H family protein

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]