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

Carubv10020979m

Common Name

CARUB_v10020979mg

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

MIKC_MADS

Protein Properties

Length: 198aa MW: 22263.3 Da PI: 5.4668

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10020979m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	69.9	2.3e-22	9	56	1	48
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48 krienks rqvtfskRrng++ KA LS+LCd vav+++s +gkly Carubv10020979m 9 KRIENKSSRQVTFSKRRNGLIDKARQLSILCDSSVAVVVVSASGKLYN 56 79********************************************96 PP
2	K-box	36.1	2.8e-13	95	164	29	98
K-box 29 enLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 e L+ q +l ++++Ls+ L +Le+qLe++l+ R++K+el++e+++ lq e+ l+een+ L +++ Carubv10020979m 95 ELLEIVQSNLEETNINNLSVDFLISLEEQLENALSVSRARKTELMMESLKSLQGEENLLREENQVLASQM 164 66777888899999***************************************************99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	28.231	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	6.4E-34	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	9.29E-27	1	72	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.1E-24	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.0E-22	10	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.1E-24	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.1E-24	38	59	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	11.173	80	170	IPR002487	Transcription factor, K-box
Pfam	PF01486	2.4E-9	96	164	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009910	Biological Process	negative regulation of flower development
GO:0010221	Biological Process	negative regulation of vernalization response
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 198 aa Download sequence Send to blast
MGRRKIEIKR IENKSSRQVT FSKRRNGLID KARQLSILCD SSVAVVVVSA SGKLYNSCSG 60 DDMSKIIERY EIQHADELKA LDLAEKTRNY LPHKELLEIV QSNLEETNIN NLSVDFLISL 120 EEQLENALSV SRARKTELMM ESLKSLQGEE NLLREENQVL ASQMGKKNTF LATEDERGIS 180 PENSSGNQIP ETLPLLK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	2e-16	1	70	1	69	MEF2 CHIMERA
6byy_B	2e-16	1	70	1	69	MEF2 CHIMERA
6byy_C	2e-16	1	70	1	69	MEF2 CHIMERA
6byy_D	2e-16	1	70	1	69	MEF2 CHIMERA
6bz1_A	2e-16	1	70	1	69	MEF2 CHIMERA
6bz1_B	2e-16	1	70	1	69	MEF2 CHIMERA
6bz1_C	2e-16	1	70	1	69	MEF2 CHIMERA
6bz1_D	2e-16	1	70	1	69	MEF2 CHIMERA
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that prevents vernalization by short periods of cold. Acts as a floral repressor. {ECO:0000269\|PubMed:12724541, ECO:0000269\|PubMed:19139056, ECO:0000269\|PubMed:20551443}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10020979m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Requires EARLY FLOWERING 7 (ELF7) and ELF8 to be expressed. Up-regulated by HUA2. {ECO:0000269\|PubMed:15520273, ECO:0000269\|PubMed:15659097}.

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	AF342808	0.0	AF342808.1 Arabidopsis thaliana MADS affecting flowering 1 (MAF1) mRNA, complete cds.
GenBank	AK117577	0.0	AK117577.1 Arabidopsis thaliana mRNA for (NM_148660) MADS affecting flowering 1(MAF1); protein id: At1g77080.4, supported by cDNA: 92459., supported by cDNA: gi_13649968, supported by cDNA: gi_16580104 [Arabidopsis thaliana] gb\|AAK37527.1\|AF342808_1 (AF342808) MADS affecting flowering 1 [Arabidopsis thaliana] gb\|AAK54440.1\| (AY034083) MADS box FLC1-like nuclear protein [Arabidopsis thaliana] gb\|AAM67028.1\| (AY088709) MADS affecting flowering 1 [Arabidopsis thaliana], complete cds, clone: RAFL17-22-J12.
GenBank	AK175247	0.0	AK175247.1 Arabidopsis thaliana mRNA, complete cds, clone: RAFL21-67-N06.
GenBank	AK176270	0.0	AK176270.1 Arabidopsis thaliana mRNA, complete cds, clone: RAFL23-17-J21.
GenBank	AK227948	0.0	AK227948.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL14-50-E05.
GenBank	AY034083	0.0	AY034083.1 Arabidopsis thaliana MADS box FLC1-like nuclear protein (FK1) mRNA, complete cds.
GenBank	AY088709	0.0	AY088709.1 Arabidopsis thaliana clone 92459 mRNA, complete sequence.
GenBank	BT004598	0.0	BT004598.1 Arabidopsis thaliana At1g77080 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006302848.1	1e-140	agamous-like MADS-box protein AGL27
Swissprot	Q9FPN7	1e-108	AGL31_ARATH; Agamous-like MADS-box protein AGL31
TrEMBL	R0GJ27	1e-139	R0GJ27_9BRAS; Uncharacterized protein
STRING	XP_006302848.1	1e-139	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM986	19	87

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G77080.4	1e-104	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Carubv10020979m
Entrez Gene	17895692

Publications ? help Back to Top
Suter L,Rüegg M,Zemp N,Hennig L,Widmer A Gene regulatory variation mediates flowering responses to vernalization along an altitudinal gradient in Arabidopsis. Plant Physiol., 2014. 166(4): p. 1928-42 [PMID:25339407]