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

RrC1188_p3

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

C3H

Protein Properties

Length: 984aa MW: 111749 Da PI: 7.4447

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1188_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	22.7	1.7e-07	222	241	6	25
-SGGGGTS--TTTTT-SS-S CS zf-CCCH 6 CrffartGtCkyGdrCkFaH 25 C+f+++tG C++G+rC++ H RrC1188_p3 222 CPFHLKTGACRFGPRCSRVH 241 ******************99 PP
2	zf-CCCH	28.5	2.6e-09	377	404	1	26
--S---SGGGGTS..--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartG..tCkyGdrCkFaHg 26 +k ++C ++++ tC++G+ C+F+H+ RrC1188_p3 377 WKVAICGEYMKSRlkTCSRGSACNFIHC 404 899************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	12.681	216	244	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.1	217	243	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.1E-5	221	241	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	6.2E-32	222	241	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	6.2E-32	241	261	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.30.70.330	3.8E-24	247	372	IPR012677	Nucleotide-binding alpha-beta plait domain
PROSITE profile	PS50102	9.576	269	374	IPR000504	RNA recognition motif domain
SMART	SM00361	7.6E-5	301	370	IPR003954	RNA recognition motif domain, eukaryote
SuperFamily	SSF54928	2.17E-16	304	374	IPR012677	Nucleotide-binding alpha-beta plait domain
PRINTS	PR01848	6.2E-32	331	353	IPR009145	U2 auxiliary factor small subunit
PRINTS	PR01848	6.2E-32	358	382	IPR009145	U2 auxiliary factor small subunit
PROSITE profile	PS50103	11.319	376	406	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.021	376	405	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.0E-7	377	404	IPR000571	Zinc finger, CCCH-type
PRINTS	PR01848	6.2E-32	396	408	IPR009145	U2 auxiliary factor small subunit
Gene3D	G3DSA:3.40.50.720	2.3E-58	742	934	IPR016040	NAD(P)-binding domain
Pfam	PF00106	8.9E-48	743	929	IPR002347	Short-chain dehydrogenase/reductase SDR
SuperFamily	SSF51735	1.12E-54	743	937	IPR016040	NAD(P)-binding domain
CDD	cd05233	1.73E-57	745	930	No hit	No description
PROSITE pattern	PS00061	0	878	906	IPR020904	Short-chain dehydrogenase/reductase, conserved site

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:0016491	Molecular Function	oxidoreductase activity
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 984 aa Download sequence Send to blast
MTEPQSEKPE EGERLEESME ESKDKSAEMS RKEKRKAMKK LKRKQVRKEI AEKEREEAEA 60 KLNDPAEQEK LKAIEEEEER KREKELREFE ESERAWREAM EIKRKKEEEE ERRWKELEES 120 RKLLEASNDE EDDEYEYIEE GPPEIIFKGN EIILRKNKVR VPKKTVAQVD VNEIADRPTS 180 NPLPPGTEAL SKSQNVSSAQ QILDSVAQEV PNFGTEQDKA HCPFHLKTGA CRFGPRCSRV 240 HFYPDKSCTI LMKNMYNGPG IAWEQDEGLE VYIDGFTSVE VVDYNLGWVG VAVHFSYTEE 300 EAEHCYEEFY EDVHTEFLKF GELINFKVCR NGSLHLKGNV YVHYRSLESA LLAYQSINGR 360 YFAGKQVNCE FVNISRWKVA ICGEYMKSRL KTCSRGSACN FIHCFRNPGG DYEWADYDKP 420 PPRFWIRKMT ALFGYSDEYL KHTEREYSGS LSDVRSDQPT DSQRQPSRRC RSREHDHVRP 480 SYRSRTNHSD TRESSRGHKL SRHEESCHGG DGSPSSTRDG SVEREMMYKE TSRHESKWSE 540 HSPGHGVTRK RRIHGRYSDD DDDDDSGEPS HKRKRSRRYG RRGSDSEVQG EVDDEEDART 600 HRSSSDIRSR KEGSSADQKE NHGDDRVHAV GDKSQRERSS SRHSQEGDSS ESRHRPHKDR 660 DINKHRRRYK TGDPDSSDRS MKGKQGRESQ QVKRENVGGS SSDEEREERQ KERSGSRHRK 720 RRSCTMTIAT PFSGAANSVT AAKTVLITGV SKGLGRALSL ELAKRGHTVI GCARTQEKLT 780 ALQSELSSPE NHLLLTADVK SDSSVKEMAH TIMEKKGVPD IIVNNAGTIN KNSKIWEVSA 840 EDFDSVMDTN VKGVVNVLRH FIPLMLPRKQ GIIVNMSSGW GRSGAALVAP YCASKWAIEG 900 LSRSVAKEVA EGMAVVALNP GVINTELLTS CFGNTASLYQ APDAWAVKAA TMILNLTAGD 960 NGGSLTAKSI SNKPPHFKWG PPSK

Sequence ? help Back to Top

Protein Sequence Length: 984 aa Download sequence Send to blast

MTEPQSEKPE EGERLEESME ESKDKSAEMS RKEKRKAMKK LKRKQVRKEI AEKEREEAEA  60
KLNDPAEQEK LKAIEEEEER KREKELREFE ESERAWREAM EIKRKKEEEE ERRWKELEES  120
RKLLEASNDE EDDEYEYIEE GPPEIIFKGN EIILRKNKVR VPKKTVAQVD VNEIADRPTS  180
NPLPPGTEAL SKSQNVSSAQ QILDSVAQEV PNFGTEQDKA HCPFHLKTGA CRFGPRCSRV  240
HFYPDKSCTI LMKNMYNGPG IAWEQDEGLE VYIDGFTSVE VVDYNLGWVG VAVHFSYTEE  300
EAEHCYEEFY EDVHTEFLKF GELINFKVCR NGSLHLKGNV YVHYRSLESA LLAYQSINGR  360
YFAGKQVNCE FVNISRWKVA ICGEYMKSRL KTCSRGSACN FIHCFRNPGG DYEWADYDKP  420
PPRFWIRKMT ALFGYSDEYL KHTEREYSGS LSDVRSDQPT DSQRQPSRRC RSREHDHVRP  480
SYRSRTNHSD TRESSRGHKL SRHEESCHGG DGSPSSTRDG SVEREMMYKE TSRHESKWSE  540
HSPGHGVTRK RRIHGRYSDD DDDDDSGEPS HKRKRSRRYG RRGSDSEVQG EVDDEEDART  600
HRSSSDIRSR KEGSSADQKE NHGDDRVHAV GDKSQRERSS SRHSQEGDSS ESRHRPHKDR  660
DINKHRRRYK TGDPDSSDRS MKGKQGRESQ QVKRENVGGS SSDEEREERQ KERSGSRHRK  720
RRSCTMTIAT PFSGAANSVT AAKTVLITGV SKGLGRALSL ELAKRGHTVI GCARTQEKLT  780
ALQSELSSPE NHLLLTADVK SDSSVKEMAH TIMEKKGVPD IIVNNAGTIN KNSKIWEVSA  840
EDFDSVMDTN VKGVVNVLRH FIPLMLPRKQ GIIVNMSSGW GRSGAALVAP YCASKWAIEG  900
LSRSVAKEVA EGMAVVALNP GVINTELLTS CFGNTASLYQ APDAWAVKAA TMILNLTAGD  960
NGGSLTAKSI SNKPPHFKWG PPSK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3osu_A	5e-27	743	927	5	191	3-oxoacyl-[acyl-carrier-protein] reductase
3osu_B	5e-27	743	927	5	191	3-oxoacyl-[acyl-carrier-protein] reductase
3sj7_A	5e-27	740	927	8	197	3-oxoacyl-(Acyl-carrier-protein) reductase
3sj7_B	5e-27	740	927	8	197	3-oxoacyl-(Acyl-carrier-protein) reductase
4yh8_A	4e-27	213	403	9	167	Splicing factor U2AF 23 kDa subunit
Search in ModeBase

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	AK176670	0.0	AK176670.1 Arabidopsis thaliana mRNA, complete cds, clone: RAFL25-20-N20.
GenBank	AY087973	0.0	AY087973.1 Arabidopsis thaliana clone 40058 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018440617.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 5
Swissprot	Q9SY74	0.0	C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBL	A0A3P6CBJ2	0.0	A0A3P6CBJ2_BRACM; Uncharacterized protein (Fragment)
STRING	Bo8g059320.1	0.0	(Brassica oleracea)

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]