PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

M-type_MADS

Protein Properties

Length: 98aa MW: 11295.2 Da PI: 10.5885

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc12g088080.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	87	1.1e-27	10	58	2	50
---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS SRF-TF 2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50 ri+n++ rqvtfskRrng+lKKA+EL +LCdaev viifsst kly+y+ Solyc12g088080.1.1 10 RIDNSTSRQVTFSKRRNGLLKKAKELAILCDAEVGVIIFSSTSKLYDYA 58 8***********************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	30.81	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.5E-37	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	5.71E-36	2	62	No hit	No description
SuperFamily	SSF55455	7.19E-28	2	71	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.7E-28	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.3E-25	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.7E-28	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	4.7E-28	38	59	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 98 aa Download sequence Send to blast
MGRGKILIRR IDNSTSRQVT FSKRRNGLLK KAKELAILCD AEVGVIIFSS TSKLYDYANT 60 RFSPPISHTF FACQMLELQF IFNFLEKNFL RVFSFVY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	2e-18	1	60	1	60	MEF2C
5f28_B	2e-18	1	60	1	60	MEF2C
5f28_C	2e-18	1	60	1	60	MEF2C
5f28_D	2e-18	1	60	1	60	MEF2C
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Specifically expressed in roots, mostly in lateral roots (LR) primordia, young emerging LRs, apex and base of LRs, apex of the primary root, and in the stele. Barely detectable in shoots. {ECO:0000269\|PubMed:12837945, ECO:0000269\|PubMed:16021502, ECO:0000269\|PubMed:17148611, ECO:0000269\|PubMed:9430595}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor. Required for root plasticity in response to nitrate, NO(3)(-). Promotes lateral root growth in a NRT1.1-dependent manner. {ECO:0000269\|PubMed:15667327, ECO:0000269\|PubMed:17148611, ECO:0000269\|PubMed:9430595}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc12g088080.1.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by nitrate in root cell culture, (PubMed:9430595, PubMed:17148611). In roots, seems induced by nitrogen (N) deprivation (e.g. nitrate free medium) but rapidly repressed by N re-supply (e.g. nitrate, glutamine and ammonium) (PubMed:16021502). Slight repression in shoots during nitrogen (N) deprivation. {ECO:0000269\|PubMed:16021502, ECO:0000269\|PubMed:17148611, ECO:0000269\|PubMed:9430595}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004252725.1	4e-35	MADS-box transcription factor 23-like isoform X1
Refseq	XP_010314595.1	3e-35	MADS-box transcription factor 23-like isoform X2
Refseq	XP_015060173.1	4e-35	MADS-box transcription factor 23-like
Swissprot	Q9SI38	7e-32	ANR1_ARATH; MADS-box transcription factor ANR1
TrEMBL	A0A2P6PQN2	1e-34	A0A2P6PQN2_ROSCH; Putative transcription factor MADS-type1 family
STRING	Solyc12g088080.1.1	2e-65	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA40	24	625
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G14210.1	3e-34	AGAMOUS-like 44

Link Out ? help Back to Top
Phytozome	Solyc12g088080.1.1

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Yan Y,Wang H,Hamera S,Chen X,Fang R miR444a has multiple functions in the rice nitrate-signaling pathway. Plant J., 2014. 78(1): p. 44-55 [PMID:24460537] Lei L, et al. Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat. Plant Biotechnol. J., 2018. 16(6): p. 1214-1226 [PMID:29193541] Sun CH, et al. Chrysanthemum MADS-box transcription factor CmANR1 modulates lateral root development via homo-/heterodimerization to influence auxin accumulation in Arabidopsis. Plant Sci., 2018. 266: p. 27-36 [PMID:29241564]