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

Carubv10001057m

Common Name

CARUB_v10001057mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

C3H

Protein Properties

Length: 419aa MW: 46046.3 Da PI: 7.5904

Description

C3H family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10001057m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	33.7	6.2e-11	46	71	1	26
--S---SGGGGTS--TTTTT-SS-SS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHg 26 ++++ C+++ rtG C++G++C+F+H+ Carubv10001057m 46 PGEPDCSYYIRTGLCRFGSTCRFNHP 71 5789*********************9 PP
2	zf-CCCH	34.8	2.8e-11	93	117	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 +++C f+ +tGtCk+G +CkF+H++ Carubv10001057m 93 QPECEFYIKTGTCKFGVTCKFHHPR 117 799********************96 PP
3	zf-CCCH	37.9	3e-12	139	163	3	27
S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 3 telCrffartGtCkyGdrCkFaHgp 27 + C++f+rtG+Ck+G++CkF+H++ Carubv10001057m 139 EDDCSYFLRTGHCKFGGSCKFNHPQ 163 578********************97 PP
4	zf-CCCH	34.6	3.2e-11	289	312	4	27
---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 4 elCrffartGtCkyGdrCkFaHgp 27 +C f+++tG Ck+G CkF+H++ Carubv10001057m 289 LECEFYMKTGDCKFGTVCKFHHPR 312 58********************96 PP
5	zf-CCCH	38.2	2.5e-12	332	358	1	27
--S---SGGGGTS--TTTTT-SS-SSS CS zf-CCCH 1 yktelCrffartGtCkyGdrCkFaHgp 27 ++++lC f++r+G+Ck+G++CkF H++ Carubv10001057m 332 PGEPLCVFYSRYGICKFGPSCKFDHPM 358 589**********************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50103	14.624	45	73	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	5.9E-5	45	72	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.6E-7	47	71	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	9.29E-6	50	73	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	3.4E-4	90	117	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	13.742	90	118	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	5.3E-8	93	117	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	6.41E-6	94	119	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	7.3E-4	96	117	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	14.662	136	164	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	2.0E-5	136	163	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	4.06E-6	137	164	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.4E-10	139	163	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.3E-4	142	162	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	12.549	285	313	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	4.1E-4	285	312	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.31E-5	289	314	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	8.7E-8	290	312	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	7.7E-4	291	312	IPR000571	Zinc finger, CCCH-type
SMART	SM00356	1.4E-7	331	358	IPR000571	Zinc finger, CCCH-type
PROSITE profile	PS50103	15.234	331	359	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	4.5E-9	333	358	IPR000571	Zinc finger, CCCH-type
SuperFamily	SSF90229	1.7E-5	334	358	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	6.4E-4	336	356	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: 419 aa Download sequence Send to blast
MDFDSRVPIS RESISLSPLL HQNAMWQTNL GSDETMGGDG LYPERPGEPD CSYYIRTGLC 60 RFGSTCRFNH PYDRKLVIAT ARTKGEYPER IGQPECEFYI KTGTCKFGVT CKFHHPRNKA 120 GIDERVSVNV LGYPLRPNED DCSYFLRTGH CKFGGSCKFN HPQTQSTKLM VSLRSPVYSA 180 LQSLTGQQSY SWPRTSYVAN PPRFQDPSYA SLGGLVSVQG WNAYGGQLGS LSPSGSDQDY 240 RNQQQNDAEE SSGSQGGVFS SGFHSGNSVP LGQYALPSEN VFPERPGQLE CEFYMKTGDC 300 KFGTVCKFHH PRNRQTPAPD CVLSTVGLPL RPGEPLCVFY SRYGICKFGP SCKFDHPMRV 360 FTYNSNAAAP SSSSSLHQET AITTQLRNLL VSSSVEATPP SSVSETTSAK DTTVDAQH*

Sequence ? help Back to Top

Protein Sequence Length: 419 aa Download sequence Send to blast

MDFDSRVPIS RESISLSPLL HQNAMWQTNL GSDETMGGDG LYPERPGEPD CSYYIRTGLC  60
RFGSTCRFNH PYDRKLVIAT ARTKGEYPER IGQPECEFYI KTGTCKFGVT CKFHHPRNKA  120
GIDERVSVNV LGYPLRPNED DCSYFLRTGH CKFGGSCKFN HPQTQSTKLM VSLRSPVYSA  180
LQSLTGQQSY SWPRTSYVAN PPRFQDPSYA SLGGLVSVQG WNAYGGQLGS LSPSGSDQDY  240
RNQQQNDAEE SSGSQGGVFS SGFHSGNSVP LGQYALPSEN VFPERPGQLE CEFYMKTGDC  300
KFGTVCKFHH PRNRQTPAPD CVLSTVGLPL RPGEPLCVFY SRYGICKFGP SCKFDHPMRV  360
FTYNSNAAAP SSSSSLHQET AITTQLRNLL VSSSVEATPP SSVSETTSAK DTTVDAQH*

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10001057m

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	AF138872	0.0	AF138872.1 Arabidopsis thaliana zinc finger protein 3 (ZFN3) mRNA, complete cds.
GenBank	AY084634	0.0	AY084634.1 Arabidopsis thaliana clone 113763 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006287837.1	0.0	zinc finger CCCH domain-containing protein 57 isoform X1
Swissprot	Q8L7N8	0.0	C3H57_ARATH; Zinc finger CCCH domain-containing protein 57
TrEMBL	R0H793	0.0	R0H793_9BRAS; Uncharacterized protein
STRING	XP_006287837.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3389	28	64

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G16540.1	0.0	zinc finger nuclease 3

Link Out ? help Back to Top
Phytozome	Carubv10001057m
Entrez Gene	17882863

Publications ? help Back to Top
Haas BJ, et al. Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol., 2002. 3(6): p. RESEARCH0029 [PMID:12093376] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Xie W, et al. Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach. Front Plant Sci, 2015. 6: p. 829 [PMID:26528302]