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

RrC5597_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: 360aa MW: 39030.8 Da PI: 8.2818

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC5597_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	39.4	1e-12	48	73	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C +++rtG C yG+rC+F+H+p RrC5597_p1 48 DEPDCIYYLRTGVCGYGSRCRFNHPP 73 6899********************97 PP
2	zf-CCCH	39.2	1.1e-12	95	120	2	27
-S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHgp 27 +++ C++f+rtGtCk+G++Ck++H++ RrC5597_p1 95 GQPVCQHFMRTGTCKFGASCKYHHPR 120 5789********************96 PP
3	zf-CCCH	40.1	5.9e-13	145	169	2	26
-S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 2 ktelCrffartGtCkyGdrCkFaHg 26 ++++C++++rtG+Ck+G++C+F+H+ RrC5597_p1 145 GEKECSYYMRTGQCKFGSTCRFHHP 169 7899********************9 PP
4	zf-CCCH	42.4	1.2e-13	278	303	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 ++++ C++f+rtG Ck+G++C+F+H+ RrC5597_p1 278 PGEPDCQYFMRTGDCKFGASCRFHHP 303 5789*********************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	14.371	46	74	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	5.5E-5	46	73	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	4.3E-10	48	73	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	3.14E-6	50	74	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	2.2E-5	52	72	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.5E-6	93	120	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	16.277	93	121	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.9E-10	95	120	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.31E-6	95	121	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.7E-5	98	120	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.3E-6	143	170	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.657	143	171	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	2.5E-10	145	169	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.44E-6	146	171	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	1.2E-4	149	168	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.788	277	305	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.7E-7	277	304	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.5E-11	279	303	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	6.15E-6	282	305	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.9E-5	283	303	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: 360 aa Download sequence Send to blast
MMERYDRAGE ERSRADPPPP GTETGLEGSL WRLGLRGGGG ESFPERPDEP DCIYYLRTGV 60 CGYGSRCRFN HPPNRAPVLG GGLRTEPTEF PERMGQPVCQ HFMRTGTCKF GASCKYHHPR 120 QRGGDSVNNT PPVSLTYMGF PLRPGEKECS YYMRTGQCKF GSTCRFHHPL PPSAQPPPPQ 180 QLSTGSAVYP SLQSQSGVYL ARPQLLPGSY VQSPYGTYSQ MVLPPPGVVP YSGWNPYQVI 240 AMPSPGSQPS IGSSSVPLAS AYQSGPSSNK EQSFPQRPGE PDCQYFMRTG DCKFGASCRF 300 HHPLEAAPPK GVTLSSIGLP LRPKALFRLS TSMTGGVSQS EPPAETKTDD SASVEVETSS

Sequence ? help Back to Top

Protein Sequence Length: 360 aa Download sequence Send to blast

MMERYDRAGE ERSRADPPPP GTETGLEGSL WRLGLRGGGG ESFPERPDEP DCIYYLRTGV  60
CGYGSRCRFN HPPNRAPVLG GGLRTEPTEF PERMGQPVCQ HFMRTGTCKF GASCKYHHPR  120
QRGGDSVNNT PPVSLTYMGF PLRPGEKECS YYMRTGQCKF GSTCRFHHPL PPSAQPPPPQ  180
QLSTGSAVYP SLQSQSGVYL ARPQLLPGSY VQSPYGTYSQ MVLPPPGVVP YSGWNPYQVI  240
AMPSPGSQPS IGSSSVPLAS AYQSGPSSNK EQSFPQRPGE PDCQYFMRTG DCKFGASCRF  300
HHPLEAAPPK GVTLSSIGLP LRPKALFRLS TSMTGGVSQS EPPAETKTDD SASVEVETSS

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_018442996.1	0.0	PREDICTED: zinc finger CCCH domain-containing protein 58-like
Swissprot	Q6NPN3	1e-163	C3H58_ARATH; Zinc finger CCCH domain-containing protein 58
TrEMBL	A0A397XL79	0.0	A0A397XL79_BRACM; Uncharacterized protein
STRING	Bra002167.1-P	0.0	(Brassica rapa)

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-141	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]