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

LOC_Os06g23950.1

Common Name

B1077E08.32, OsJ_21264

Organism

Oryza sativa subsp. japonica

Taxonomic ID

39947

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa

Family

M-type_MADS

Protein Properties

Length: 78aa MW: 8595.81 Da PI: 10.2914

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
LOC_Os06g23950.1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	88.3	4.1e-28	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 +rien++ rqvtfskRr g++KKA+EL +LCda+v v++fsstg+ly+ys+ LOC_Os06g23950.1 9 SRIENTTSRQVTFSKRRSGLFKKAKELAILCDAQVGVLVFSSTGRLYDYSN 59 59***********************************************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	1.8E-36	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	28.987	1	61	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	6.67E-27	3	65	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-26	3	23	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.71E-34	3	64	No hit	No description
Pfam	PF00319	1.1E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-26	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-26	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: 78 aa Download sequence Send to blast
MVRGKTVISR IENTTSRQVT FSKRRSGLFK KAKELAILCD AQVGVLVFSS TGRLYDYSNS 60 SNSRNLTYDQ LLGDTVC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
1tqe_Q	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
1tqe_R	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
1tqe_S	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_A	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_B	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_C	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_D	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_E	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
6c9l_F	2e-15	1	66	1	66	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	Q5Z5L9

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	LOC_Os06g23950.1

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	-

Phenotype -- Mutation ? help Back to Top
Source	ID
RiceGE	Os06g23950

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP005646	5e-97	AP005646.2 Oryza sativa Japonica Group genomic DNA, chromosome 6, BAC clone:B1077E08.
GenBank	AP014962	5e-97	AP014962.1 Oryza sativa Japonica Group DNA, chromosome 6, cultivar: Nipponbare, complete sequence.
GenBank	CP012614	5e-97	CP012614.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 6 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015641670.1	5e-36	MADS-box transcription factor 23-like
Swissprot	Q9SI38	7e-28	ANR1_ARATH; MADS-box transcription factor ANR1
TrEMBL	A0A0E0A9B3	3e-48	A0A0E0A9B3_9ORYZ; Uncharacterized protein
TrEMBL	A2YCP0	3e-48	A2YCP0_ORYSI; Uncharacterized protein
TrEMBL	Q5Z5L9	3e-48	Q5Z5L9_ORYSJ; MADS-box protein-like
STRING	OGLUM06G15040.1	6e-49	(Oryza glumipatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP129	38	398
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G57230.2	2e-30	AGAMOUS-like 16

Link Out ? help Back to Top
Phytozome	LOC_Os06g23950.1

Publications ? help Back to Top
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]