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

RrC53_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: 396aa MW: 41648.2 Da PI: 7.8445

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC53_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	38.4	2.1e-12	48	73	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C +++rtG C yG+rC+F+H++ RrC53_p3 48 DEADCIYYLRTGACGYGSRCRFNHPR 73 6799********************96 PP
2	zf-CCCH	30.5	6.4e-10	99	118	8	27
GGGGTS--TTTTT-SS-SSS CS zf-CCCH 8 ffartGtCkyGdrCkFaHgp 27 +f+rtGtCk+G++Ck++H++ RrC53_p3 99 HFMRTGTCKFGATCKYHHPR 118 8*****************96 PP
3	zf-CCCH	40.2	5.8e-13	240	264	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C++f+rtG Ck+G++C+++H+ RrC53_p3 240 DQPECQYFMRTGDCKFGSSCRYHHP 264 689*********************9 PP
4	zf-CCCH	32.9	1.1e-10	286	311	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 + + C +fa+ G+Ck+G+ CkF H++ RrC53_p3 286 GVAQCTHFAQHGICKFGPACKFDHSM 311 6788********************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	7.5E-5	46	73	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.986	46	74	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.5E-10	48	73	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.75E-6	49	74	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.9E-5	52	73	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	0.38	95	118	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	10.69	98	119	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.6E-7	99	118	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.155	238	266	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.8E-6	238	265	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	3.0E-10	240	264	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.22E-6	241	267	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	5.9E-5	244	264	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.723	284	312	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.4E-4	284	311	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.8E-8	286	310	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.02E-5	287	312	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.6E-4	290	311	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 396 aa Download sequence Send to blast
MERYGRSGEE GSRSDPSLEW TTTTHGGQTG VQASMWRGGG ESYPERPDEA DCIYYLRTGA 60 CGYGSRCRFN HPRDRGAVIG GGVRGGGDGA LPERMGQPHF MRTGTCKFGA TCKYHHPRQG 120 GGGSVAPVTL SYLGYPLRPG EKECSYYLRT GQYSTIQFLS SSSLNLSYTL FIQRLNLSPL 180 NNMASLTAMP SPGTQPSIGP SSVYGMAPLS PSGTAYTGTY QPGGTSLTTS KEESFPQRPD 240 QPECQYFMRT GDCKFGSSCR YHHPLDAVQP KTGVLFSSIG LPLRPGVAQC THFAQHGICK 300 FGPACKFDHS MSSSLSYSPS ASSLTDMPVA PYPIGSSSLS GASAPVSSSD VPTTTQAVTA 360 AASAPMVSGL SSQEPAETSG DSASVSGSIE AKTSSS

Sequence ? help Back to Top

Protein Sequence Length: 396 aa Download sequence Send to blast

MERYGRSGEE GSRSDPSLEW TTTTHGGQTG VQASMWRGGG ESYPERPDEA DCIYYLRTGA  60
CGYGSRCRFN HPRDRGAVIG GGVRGGGDGA LPERMGQPHF MRTGTCKFGA TCKYHHPRQG  120
GGGSVAPVTL SYLGYPLRPG EKECSYYLRT GQYSTIQFLS SSSLNLSYTL FIQRLNLSPL  180
NNMASLTAMP SPGTQPSIGP SSVYGMAPLS PSGTAYTGTY QPGGTSLTTS KEESFPQRPD  240
QPECQYFMRT GDCKFGSSCR YHHPLDAVQP KTGVLFSSIG LPLRPGVAQC THFAQHGICK  300
FGPACKFDHS MSSSLSYSPS ASSLTDMPVA PYPIGSSSLS GASAPVSSSD VPTTTQAVTA  360
AASAPMVSGL SSQEPAETSG DSASVSGSIE AKTSSS

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_006407949.1	0.0	zinc finger CCCH domain-containing protein 34
Swissprot	Q9SQU4	1e-145	C3H34_ARATH; Zinc finger CCCH domain-containing protein 34
TrEMBL	V4M3D6	0.0	V4M3D6_EUTSA; Uncharacterized protein
STRING	XP_006407949.1	0.0	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1779	27	86

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18550.1	1e-92	C3H family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546]