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

Carubv10017630m

Common Name

CARUB_v10017630mg

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

TCP

Protein Properties

Length: 329aa MW: 34616.1 Da PI: 7.5055

Description

TCP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10017630m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	TCP	125.7	4.8e-39	79	164	3	87
TCP 3 gkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgtssssasec.eaesssssasnsss 87 +k+++++++hTkv+gR+RR+R++a+caar+F+L++eLG+++d++ti+WLlqqa+p+i+++tg+++++as+ +a++s+s++++++ Carubv10017630m 79 PKRSSNKDRHTKVEGRGRRIRMPALCAARIFQLTRELGHKSDGETIQWLLQQAEPSIIAATGSGTIPASALaSAAASVSNHHHQGG 164 6999****************************************************************999666666666665544 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03634	1.3E-31	83	162	IPR005333	Transcription factor, TCP
PROSITE profile	PS51369	28.016	84	138	IPR017887	Transcription factor TCP subgroup

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008361	Biological Process	regulation of cell size
GO:1900056	Biological Process	negative regulation of leaf senescence
GO:0005634	Cellular Component	nucleus
GO:0000987	Molecular Function	core promoter proximal region sequence-specific DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 329 aa Download sequence Send to blast
MDPKNLNRHQ VPNFLNPSSQ PPPRNQGMGL DDDNNINKDE NRKSSSTTEI KDFQIVVSAS 60 SDKEPNNSST KKSQNQLGPK RSSNKDRHTK VEGRGRRIRM PALCAARIFQ LTRELGHKSD 120 GETIQWLLQQ AEPSIIAATG SGTIPASALA SAAASVSNHH HQGGSLTAGL MISHDLVDGG 180 GSSSGRPPNW GIGGGEGASR SNLPTGLWPN VAGFGSGVPT TGLMSEGAGY RIGFPGFDFP 240 GVGPMSFASI LGGGGGNTHQ MPGLELGLSQ EGNVGVLNPQ SFTQLYQQMG QAQAQAQAQG 300 RVLQHIHHNH EDHQQESGEK DDSQGSGR*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that binds to the site II motif (3'-TGGGCC/T-5') in the promoter of PCNA-2 and to 3'-GCCCG/A-5' elements in the promoters of cyclin CYCB1-1 and ribosomal protein genes. {ECO:0000269\|PubMed:12631321, ECO:0000269\|PubMed:16123132}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00005	PBM	Transfer from 484486	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10017630m

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	AB026649	0.0	AB026649.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone: MOJ10.
GenBank	AJ291749	0.0	AJ291749.1 Arabidopsis thaliana mRNA for putative transcription factor (PCF1 gene).
GenBank	AK118178	0.0	AK118178.1 Arabidopsis thaliana At3g27010 mRNA for unknown protein, complete cds, clone: RAFL19-49-P20.
GenBank	BT006043	0.0	BT006043.1 Arabidopsis thaliana clone U50934 unknown protein (At3g27010) mRNA, complete cds.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006290367.1	0.0	transcription factor TCP20
Swissprot	Q9LSD5	1e-162	TCP20_ARATH; Transcription factor TCP20
TrEMBL	R0HDZ9	0.0	R0HDZ9_9BRAS; Uncharacterized protein
STRING	XP_006290367.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4050	27	59

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G27010.1	1e-150	TCP family protein

Link Out ? help Back to Top
Phytozome	Carubv10017630m
Entrez Gene	17885451

Publications ? help Back to Top
Zhu P, et al. Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(42): p. 11967-11972 [PMID:27708161] Wu JF, et al. LWD-TCP complex activates the morning gene CCA1 in Arabidopsis. Nat Commun, 2016. 7: p. 13181 [PMID:27734958] Guan P, et al. Interacting TCP and NLP transcription factors control plant responses to nitrate availability. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(9): p. 2419-2424 [PMID:28202720] Guan P Dancing with Hormones: A Current Perspective of Nitrate Signaling and Regulation in Arabidopsis. Front Plant Sci, 2017. 8: p. 1697 [PMID:29033968] Zhang N, et al. MOS1 functions closely with TCP transcription factors to modulate immunity and cell cycle in Arabidopsis. Plant J., 2018. 93(1): p. 66-78 [PMID:29086441] Bresso EG,Chorostecki U,Rodriguez RE,Palatnik JF,Schommer C Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development. Plant Physiol., 2018. 176(2): p. 1694-1708 [PMID:29133375] Konishi N,Okubo T,Yamaya T,Hayakawa T,Minamisawa K Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis. Microbes Environ., 2017. 32(4): p. 314-323 [PMID:29187692]