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

RrC38_p5

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: 387aa MW: 40812.3 Da PI: 7.6756

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC38_p5	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	36.1	1.1e-11	46	71	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C +++rtG C yG++C+F+H+p RrC38_p5 46 DEPDCVYYLRTGVCGYGSKCQFNHPP 71 6899********************97 PP
2	zf-CCCH	38	2.8e-12	92	117	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C++f+rtG Ck+G++Ck++H++ RrC38_p5 92 GQPVCQHFMRTGDCKFGASCKYHHPR 117 5789********************96 PP
3	zf-CCCH	40.9	3.3e-13	142	166	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C++++rtG+Ck+G++CkF+H+ RrC38_p5 142 GEKECPYYMRTGQCKFGSTCKFHHP 166 7899********************9 PP
4	zf-CCCH	36.7	7.2e-12	265	290	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 +++++C +f+rtG CkyG +C+++H+ RrC38_p5 265 PGQPECTYFLRTGDCKYGTSCRYHHP 290 5789*********************9 PP
5	zf-CCCH	31.9	2.2e-10	310	335	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 ++t+ C++fa+ G+Ck G+ CkF H+ RrC38_p5 310 PGTAQCSHFAQHGICKLGPACKFDHS 335 689**********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00356	1.3E-5	44	71	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.22	44	72	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.9E-8	46	71	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	5.36E-6	49	72	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.7E-6	50	70	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.2E-5	90	117	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.76	90	118	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.19E-6	92	118	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.0E-9	92	117	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.3E-5	95	117	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	9.7E-7	140	167	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.854	140	168	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	6.0E-11	142	166	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.7E-6	143	168	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.2E-5	146	165	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	3.0E-6	264	291	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.591	264	292	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	6.0E-9	266	290	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	5.1E-6	268	292	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.1E-4	270	290	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.9E-4	309	336	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.366	309	337	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	2.22E-5	310	336	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	7.5E-8	310	335	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: 387 aa Download sequence Send to blast
MEQHGGGGTG DEGSLSDPVT DTGLEASMSR LGLGGGGSES YPKRPDEPDC VYYLRTGVCG 60 YGSKCQFNHP PNRPPVSGDL RTEAGEVPER MGQPVCQHFM RTGDCKFGAS CKYHHPRQGS 120 GGGDSVTSPI SFNHMGFPLR PGEKECPYYM RTGQCKFGST CKFHHPVPPG DHQAPSHHPL 180 PTSPPAIYPS QQFGVVVPRP YPTYSQMVLS PGMVGWNPYQ ASVSAIPSPG TPSSVYGTKP 240 LSPSAPAYQS GSASSNKEQS FPQRPGQPEC TYFLRTGDCK YGTSCRYHHP LEAASPKGIS 300 LSHIGLPLRP GTAQCSHFAQ HGICKLGPAC KFDHSSSLST LAPSLSSSSD QGTEVHSSSS 360 IKPKTTASGE SETVAAGVSS SSSMTGD

Sequence ? help Back to Top

Protein Sequence Length: 387 aa Download sequence Send to blast

MEQHGGGGTG DEGSLSDPVT DTGLEASMSR LGLGGGGSES YPKRPDEPDC VYYLRTGVCG  60
YGSKCQFNHP PNRPPVSGDL RTEAGEVPER MGQPVCQHFM RTGDCKFGAS CKYHHPRQGS  120
GGGDSVTSPI SFNHMGFPLR PGEKECPYYM RTGQCKFGST CKFHHPVPPG DHQAPSHHPL  180
PTSPPAIYPS QQFGVVVPRP YPTYSQMVLS PGMVGWNPYQ ASVSAIPSPG TPSSVYGTKP  240
LSPSAPAYQS GSASSNKEQS FPQRPGQPEC TYFLRTGDCK YGTSCRYHHP LEAASPKGIS  300
LSHIGLPLRP GTAQCSHFAQ HGICKLGPAC KFDHSSSLST LAPSLSSSSD QGTEVHSSSS  360
IKPKTTASGE SETVAAGVSS SSSMTGD

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_018463879.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 58-like
Refseq	XP_018463880.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 58-like
Swissprot	Q6NPN3	1e-176	C3H58_ARATH; Zinc finger CCCH domain-containing protein 58
TrEMBL	A0A3P6A222	0.0	A0A3P6A222_BRACM; Uncharacterized protein
STRING	Bo3g013210.1	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-169	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]