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

Rsa1.0_00022.1_g00002.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

M-type_MADS

Protein Properties

Length: 62aa MW: 6826.94 Da PI: 11.1479

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00022.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	68.5	6.3e-22	9	56	1	48
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48 k ienks rqvtfskRr+g++ KA LSvLC+ vav+++s +gkly Rsa1.0_00022.1_g00002.1 9 KLIENKSSRQVTFSKRRTGLIEKARQLSVLCESSVAVLVVSASGKLYN 56 579*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF55455	1.57E-23	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	27.081	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.8E-30	1	60	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-22	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.4E-21	11	55	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-22	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.1E-22	38	59	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 62 aa Download sequence Send to blast
MGRRKVEIKL IENKSSRQVT FSKRRTGLIE KARQLSVLCE SSVAVLVVSA SGKLYNSSSG 60 DK

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	Rsa1.0_00022.1_g00002.1

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	AC166741	8e-80	AC166741.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH080C09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009130486.1	9e-35	PREDICTED: agamous-like MADS-box protein AGL27 isoform X1
Refseq	XP_009130487.1	9e-35	PREDICTED: agamous-like MADS-box protein AGL27 isoform X2
Swissprot	Q9FPN7	2e-30	AGL31_ARATH; Agamous-like MADS-box protein AGL31
TrEMBL	A0A3P6BBE5	4e-34	A0A3P6BBE5_BRACM; Uncharacterized protein
STRING	Bra031888.1-P	3e-34	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM78	28	413

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G65060.2	7e-20	MIKC_MADS family protein

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]