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

RrC4325_p1

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: 347aa MW: 37796.5 Da PI: 8.8572

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4325_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	37	5.6e-12	45	69	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 ++ C +++rtG C yG+rC+F+H++ RrC4325_p1 45 EPDCIYYLRTGVCGYGSRCRFNHPR 69 589********************96 PP
2	zf-CCCH	37.7	3.5e-12	90	115	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C++f+rtGtC++G++Ck++H++ RrC4325_p1 90 GQPVCQHFMRTGTCRFGATCKYHHPR 115 5789********************96 PP
3	zf-CCCH	40.3	5.1e-13	138	162	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C++++rtG+Ck+G++C+F+H+ RrC4325_p1 138 GEKECSYYMRTGQCKFGSTCRFHHP 162 7899********************9 PP
4	zf-CCCH	41.6	2.1e-13	285	310	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 +++++C++f+rtG Ck+G++C+F+H+ RrC4325_p1 285 PGQPECQYFMRTGDCKFGNSCRFHHP 310 5789*********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	7.7E-5	42	69	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.573	42	70	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.1E-9	45	69	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.7E-6	46	71	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.9E-5	48	69	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	5.3E-6	88	115	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.948	88	116	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.22E-6	90	116	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	7.8E-10	90	115	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	4.2E-5	93	115	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.356	136	164	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.3E-6	136	163	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.7E-10	138	162	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.7E-6	139	163	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	9.3E-5	142	161	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.7E-7	284	311	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.07	284	312	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.5E-10	286	310	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.09E-6	288	312	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	4.0E-5	290	310	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: 347 aa Download sequence Send to blast
MERYGRAGEQ GSRSDPSLET GLEASMWRLG LGGGGGESYP ERLSEPDCIY YLRTGVCGYG 60 SRCRFNHPRN RAPVLGGLRT EAGEFPERMG QPVCQHFMRT GTCRFGATCK YHHPRQGGRD 120 SFTTPVSLSY MGFPLRPGEK ECSYYMRTGQ CKFGSTCRFH HPVPPGVQAP SPQQQQLSTG 180 SAIYPPLQSQ SLPSSQQFGV AIPRPQLLPG SYLQSPYGYN QMLLPPPGMV PYSGWNPYQA 240 SISATPSPGT QPSMGSSSIY GIRPLSPPAP AYPSSNNEQT FPQRPGQPEC QYFMRTGDCK 300 FGNSCRFHHP LEAASPKGVS LSHIGLPLRP SAESKNGDSA SIEVKTS

Sequence ? help Back to Top

Protein Sequence Length: 347 aa Download sequence Send to blast

MERYGRAGEQ GSRSDPSLET GLEASMWRLG LGGGGGESYP ERLSEPDCIY YLRTGVCGYG  60
SRCRFNHPRN RAPVLGGLRT EAGEFPERMG QPVCQHFMRT GTCRFGATCK YHHPRQGGRD  120
SFTTPVSLSY MGFPLRPGEK ECSYYMRTGQ CKFGSTCRFH HPVPPGVQAP SPQQQQLSTG  180
SAIYPPLQSQ SLPSSQQFGV AIPRPQLLPG SYLQSPYGYN QMLLPPPGMV PYSGWNPYQA  240
SISATPSPGT QPSMGSSSIY GIRPLSPPAP AYPSSNNEQT FPQRPGQPEC QYFMRTGDCK  300
FGNSCRFHHP LEAASPKGVS LSHIGLPLRP SAESKNGDSA SIEVKTS

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_018454621.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 58
Swissprot	Q6NPN3	0.0	C3H58_ARATH; Zinc finger CCCH domain-containing protein 58
TrEMBL	A0A078IZT2	0.0	A0A078IZT2_BRANA; BnaA02g35100D protein
STRING	Bo2g016570.1	0.0	(Brassica oleracea)

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-174	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]