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_18284.1_g00001.1

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: 61aa MW: 6913.13 Da PI: 11.5883

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_18284.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	94.7	4.3e-30	10	58	2	50
---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS SRF-TF 2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50 rienk++rqvtfskRr+g+ KKA+E+SvLCda+va+i+fs++gkl+eys Rsa1.0_18284.1_g00001.1 10 RIENKIRRQVTFSKRRTGLVKKAQEISVLCDADVALIVFSTKGKLFEYS 58 8***********************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	30.684	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	1.1E-35	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.57E-27	2	59	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-29	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	4.9E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-29	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.5E-29	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: 61 aa Download sequence Send to blast
MGRGRVQLRR IENKIRRQVT FSKRRTGLVK KAQEISVLCD ADVALIVFST KGKLFEYSAG 60 S

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	6e-19	1	59	1	59	MEF2C
5f28_B	6e-19	1	59	1	59	MEF2C
5f28_C	6e-19	1	59	1	59	MEF2C
5f28_D	6e-19	1	59	1	59	MEF2C
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that promotes early floral meristem identity in synergy with APETALA1 and CAULIFLOWER. Is required subsequently for the transition of an inflorescence meristem into a floral meristem (PubMed:28586421). Seems to be partially redundant to the function of APETALA1 and CAULIFLOWER in the up-regulation of LEAFY. Is also required for normal pattern of cell division, expansion and differentiation during morphogenesis of the silique (PubMed:28586421). Probably not required for fruit elongation but instead is required to prevent ectopic activity of IND. Represses SAUR10 expression in stems and inflorescence branches (PubMed:28586421). {ECO:0000269\|PubMed:10648231, ECO:0000269\|PubMed:15035986, ECO:0000269\|PubMed:28586421, ECO:0000269\|PubMed:9502732}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_18284.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Dramatically up-regulated upon the transition from vegetative to reproductive development.

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	AP001314	1e-72	AP001314.1 Arabidopsis thaliana genomic DNA, chromosome 3, BAC clone:T6J22.
GenBank	AY141238	1e-72	AY141238.1 Arabidopsis thaliana MADS-box protein AGL79 mRNA, complete cds.
GenBank	CP002686	1e-72	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010425772.1	4e-35	PREDICTED: truncated transcription factor CAULIFLOWER A-like
Refseq	XP_010502999.1	4e-35	PREDICTED: truncated transcription factor CAULIFLOWER A-like isoform X1
Refseq	XP_010503000.1	3e-35	PREDICTED: truncated transcription factor CAULIFLOWER A-like isoform X2
Refseq	XP_010514674.1	3e-35	PREDICTED: truncated transcription factor CAULIFLOWER A-like isoform X1
Refseq	XP_010514677.1	3e-35	PREDICTED: truncated transcription factor CAULIFLOWER D-like isoform X2
Swissprot	Q38876	1e-30	AGL8_ARATH; Agamous-like MADS-box protein AGL8
TrEMBL	A0A078HDI9	2e-34	A0A078HDI9_BRANA; BnaC02g38130D protein
STRING	Bostr.0556s0620.1.p	1e-34	(Boechera stricta)
STRING	XP_010425772.1	1e-34	(Camelina sativa)
STRING	XP_010502999.1	1e-34	(Camelina sativa)
STRING	XP_010514674.1	1e-34	(Camelina sativa)

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
AT3G30260.1	3e-37	AGAMOUS-like 79

Publications ? help Back to Top
Yu Y, et al. MlWRKY12, a novel Miscanthus transcription factor, participates in pith secondary cell wall formation and promotes flowering. Plant Sci., 2013. 212: p. 1-9 [PMID:24094048] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] Jaradat MR,Ruegger M,Bowling A,Butler H,Cutler AJ A comprehensive transcriptome analysis of silique development and dehiscence in Arabidopsis and Brassica integrating genotypic, interspecies and developmental comparisons. GM Crops Food, 2014. 5(4): p. 302-20 [PMID:25523176] Wang C,Dehesh K From retrograde signaling to flowering time. Plant Signal Behav, 2015. 10(6): p. e1022012 [PMID:26098376] Borghi M,Xie DY Tissue-specific production of limonene in Camelina sativa with the Arabidopsis promoters of genes BANYULS and FRUITFULL. Planta, 2016. 243(2): p. 549-61 [PMID:26530959] Yu Y, et al. WRKY71 accelerates flowering via the direct activation of FLOWERING LOCUS T and LEAFY in Arabidopsis thaliana. Plant J., 2016. 85(1): p. 96-106 [PMID:26643131] McCarthy EW,Mohamed A,Litt A Functional Divergence of APETALA1 and FRUITFULL is due to Changes in both Regulation and Coding Sequence. Front Plant Sci, 2015. 6: p. 1076 [PMID:26697035] Davin N, et al. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. Plant J., 2016. 86(5): p. 376-90 [PMID:26952251] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] José Ripoll J, et al. microRNA regulation of fruit growth. Nat Plants, 2015. 1(4): p. 15036 [PMID:27247036] Li W,Wang H,Yu D Arabidopsis WRKY Transcription Factors WRKY12 and WRKY13 Oppositely Regulate Flowering under Short-Day Conditions. Mol Plant, 2016. 9(11): p. 1492-1503 [PMID:27592586] Eldridge T, et al. Fruit shape diversity in the Brassicaceae is generated by varying patterns of anisotropy. Development, 2016. 143(18): p. 3394-406 [PMID:27624834] Bemer M, et al. FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture. J. Exp. Bot., 2017. 68(13): p. 3391-3403 [PMID:28586421] Sehra B,Franks RG Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development. Front Plant Sci, 2017. 8: p. 1712 [PMID:29085379] Balanzà V, et al. Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nat Commun, 2018. 9(1): p. 565 [PMID:29422669]