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; Brassicaceae incertae sedis; Schrenkiella

Family

C3H

Protein Properties

Length: 774aa MW: 90848.7 Da PI: 7.6279

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp1g08920	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	23.1	1.3e-07	237	256	6	25
-SGGGGTS--TTTTT-SS-S CS zf-CCCH 6 CrffartGtCkyGdrCkFaH 25 C+f+++tG C++G+rC++ H Tp1g08920 237 CPFHLKTGACRFGPRCSRVH 256 ******************99 PP
2	zf-CCCH	28.9	1.9e-09	335	362	1	26
--S---SGGGGTS..--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartG..tCkyGdrCkFaHg 26 +k ++C ++++ tC++G+ C+F+H+ Tp1g08920 335 WKVAICGEYMKSRlkTCSRGSACNFIHC 362 899************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	12.681	231	259	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.1	232	258	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.6E-5	236	256	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	9.3E-12	237	256	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	9.3E-12	256	276	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	1.2E-11	284	330	IPR012677	Nucleotide-binding alpha-beta plait domain
SuperFamily	SSF54928	3.42E-9	285	332	IPR012677	Nucleotide-binding alpha-beta plait domain
SMART	SM00356	0.021	334	363	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	11.319	334	364	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	3.8E-7	335	362	IPR000571	Zinc finger, CCCH-type

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: 774 aa Download sequence Send to blast
MEPQNEKKEG ERPEEAVGGK EWLDENKEKA AEMSRKEKRK AMKKLKRKQV RKEIAAKERE 60 EAEAKLNDPA EQEKLKAIEE EEARKREKEL KEFEESERAW REAMEIKRKK EEEEEAEREE 120 EERRWKDQEE SRKLEASRND ECGEDEDGEY EYIEEGPPEI IFQGNEIILR KNKVKVPKKS 180 VTQVEGNEIA DRPTSNPLPP GTEAFPKCQN VSSAQQILNN VAQEVPNFGT EQDKAHCPFH 240 LKTGACRFGP RCSRVHFYPD KSCTILMKNM YNGPGIAWEQ DEGLEVCRNG SLHLKGNVYV 300 HYRSLELAIL AYQSINGRYF AGKQVKCEFV NISRWKVAIC GEYMKSRLKT CSRGSACNFI 360 HCFRNPGGDY EWADQDKPPP RFWIHKMTAL FGYSDEYLKH MEHEYSGSLN DCRSDQPTDS 420 HRQPSRRSRW RDHDHVNVGS KPCYRSLKNH GDTQDRTCGH KFSSHEEKRH GGDESPSSTR 480 GGSLERDLCK ERRYAKDTLR HESKWSEHSP GHRVMRKRIH GRYSDDDSPD GDDDCRGATG 540 LKRNSSRRYG RRDSDSEIQE WLEDEEDTKT HWSSSDRRSR YENHREGSSA DQEESHAHDR 600 VHAVDDKSHR ERSKHRHERS SSRYSHVGDT TESRRRPHRR SESSDLRDNG ENDMKRSAET 660 SLTVYQSDKD KDKSKQRHRY KIRDPDSDRS RKGKRRRRCS RDGVSVQKSP EVNENGKREN 720 VCGLSSDEES SEREETHKER SYRHEKRRRP QHSHDQTPKE SEEFEGETER WRPM

Sequence ? help Back to Top

Protein Sequence Length: 774 aa Download sequence Send to blast

MEPQNEKKEG ERPEEAVGGK EWLDENKEKA AEMSRKEKRK AMKKLKRKQV RKEIAAKERE  60
EAEAKLNDPA EQEKLKAIEE EEARKREKEL KEFEESERAW REAMEIKRKK EEEEEAEREE  120
EERRWKDQEE SRKLEASRND ECGEDEDGEY EYIEEGPPEI IFQGNEIILR KNKVKVPKKS  180
VTQVEGNEIA DRPTSNPLPP GTEAFPKCQN VSSAQQILNN VAQEVPNFGT EQDKAHCPFH  240
LKTGACRFGP RCSRVHFYPD KSCTILMKNM YNGPGIAWEQ DEGLEVCRNG SLHLKGNVYV  300
HYRSLELAIL AYQSINGRYF AGKQVKCEFV NISRWKVAIC GEYMKSRLKT CSRGSACNFI  360
HCFRNPGGDY EWADQDKPPP RFWIHKMTAL FGYSDEYLKH MEHEYSGSLN DCRSDQPTDS  420
HRQPSRRSRW RDHDHVNVGS KPCYRSLKNH GDTQDRTCGH KFSSHEEKRH GGDESPSSTR  480
GGSLERDLCK ERRYAKDTLR HESKWSEHSP GHRVMRKRIH GRYSDDDSPD GDDDCRGATG  540
LKRNSSRRYG RRDSDSEIQE WLEDEEDTKT HWSSSDRRSR YENHREGSSA DQEESHAHDR  600
VHAVDDKSHR ERSKHRHERS SSRYSHVGDT TESRRRPHRR SESSDLRDNG ENDMKRSAET  660
SLTVYQSDKD KDKSKQRHRY KIRDPDSDRS RKGKRRRRCS RDGVSVQKSP EVNENGKREN  720
VCGLSSDEES SEREETHKER SYRHEKRRRP QHSHDQTPKE SEEFEGETER WRPM

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yh8_A	2e-19	228	361	9	167	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp1g08920

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_013657757.1	0.0	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	Bostr.13671s0457.1.p	0.0	(Boechera stricta)

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]