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

Carubv10016861m

Common Name

CARUB_v10016861mg

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

C2H2

Protein Properties

Length: 611aa MW: 65404.5 Da PI: 9.3328

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10016861m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	16.1	3.2e-05	81	103	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C+ C+k F r nL+ H r H Carubv10016861m 81 FICEVCNKGFQREQNLQLHRRGH 103 89*******************88 PP
2	zf-C2H2	12.4	0.00047	157	179	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC +C+k++ +s+ k H +t+ Carubv10016861m 157 WKCDKCSKRYAVQSDWKAHSKTC 179 58*****************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.30.160.60	6.9E-6	80	103	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.85E-7	80	103	No hit	No description
Pfam	PF12171	3.0E-5	81	103	IPR022755	Zinc finger, double-stranded RNA binding
SMART	SM00355	0.0052	81	103	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	81	103	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	83	103	IPR007087	Zinc finger, C2H2
SMART	SM00355	110	122	152	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.1E-5	145	178	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	2.85E-7	152	177	No hit	No description
SMART	SM00355	140	157	177	IPR015880	Zinc finger, C2H2-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 611 aa Download sequence Send to blast
MAASSSSAAS FFGVRQDDQS HLLPPTSSAA APPPPPHHQQ QPPPPLEAPP QKKKRNQPRT 60 PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK 120 VYLCPEPSCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCD KCSKRYAVQS DWKAHSKTCG 180 TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNNSNNNT 240 SSMILGLSHM GAQQNLDHQS GDVLRLGSGG GGGGAASRSS SDLIAANASG YFMQEQNPSF 300 HDQQDHHHHH QQGFLAANNN IKPSPMSFQQ NLMQFSHDNH NSASSNLFNL SFLSGNNGVT 360 SATSNPNAGA ASAVSSGNLM ISNHYDGESA VGGGGGGGGE GSTGLFPNNL MSSADRISSG 420 SVPSLFSSSI QNPNSTPHMS ATALLQKAAQ MGSTSSNNNN NGSNNNNNNN ASSILRSFGS 480 GMYGENESNL QDLMNSFSNP GATGNVNGVD SPFGSYGGVN KGLSADKQSM TRDFLGVGQI 540 VRSMSGTGGF QQQQQQQQQQ QQQQQQQQHG NSRERVGSSS DSADRSSMNV NTSGGPASTS 600 PPYGIHHASF *

Sequence ? help Back to Top

Protein Sequence Length: 611 aa Download sequence Send to blast

MAASSSSAAS FFGVRQDDQS HLLPPTSSAA APPPPPHHQQ QPPPPLEAPP QKKKRNQPRT  60
PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK  120
VYLCPEPSCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCD KCSKRYAVQS DWKAHSKTCG  180
TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNNSNNNT  240
SSMILGLSHM GAQQNLDHQS GDVLRLGSGG GGGGAASRSS SDLIAANASG YFMQEQNPSF  300
HDQQDHHHHH QQGFLAANNN IKPSPMSFQQ NLMQFSHDNH NSASSNLFNL SFLSGNNGVT  360
SATSNPNAGA ASAVSSGNLM ISNHYDGESA VGGGGGGGGE GSTGLFPNNL MSSADRISSG  420
SVPSLFSSSI QNPNSTPHMS ATALLQKAAQ MGSTSSNNNN NGSNNNNNNN ASSILRSFGS  480
GMYGENESNL QDLMNSFSNP GATGNVNGVD SPFGSYGGVN KGLSADKQSM TRDFLGVGQI  540
VRSMSGTGGF QQQQQQQQQQ QQQQQQQQHG NSRERVGSSS DSADRSSMNV NTSGGPASTS  600
PPYGIHHASF *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_C	4e-33	153	214	3	64	Zinc finger protein JACKDAW
5b3h_F	4e-33	153	214	3	64	Zinc finger protein JACKDAW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269\|PubMed:22898356, ECO:0000269\|PubMed:24821766}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00255	DAP	Transfer from AT2G02070	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10016861m

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ621495	0.0	AJ621495.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 2 (idz2 gene).
GenBank	AY056174	0.0	AY056174.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBank	BT001215	0.0	BT001215.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006290331.1	0.0	protein indeterminate-domain 5, chloroplastic
Swissprot	Q9ZUL3	0.0	IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBL	R0H1U3	0.0	R0H1U3_9BRAS; Uncharacterized protein
STRING	XP_006290331.1	0.0	(Capsella rubella)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G02070.1	0.0	indeterminate(ID)-domain 5

Link Out ? help Back to Top
Phytozome	Carubv10016861m
Entrez Gene	17886304

Publications ? help Back to Top
Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755]