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

Lus10006716

Organism

Linum usitatissimum

Taxonomic ID

4006

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum

Family

MIKC_MADS

Protein Properties

Length: 179aa MW: 20383.6 Da PI: 8.7676

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lus10006716	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	97.4	6.2e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+iifs++gklye+ss Lus10006716 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIIFSPRGKLYEFSS 59 79***********************************************96 PP
2	K-box	52.1	2.7e-18	59	107	34	82
K-box 34 eqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqk 82 + R+l+Ge+Le++++ eL++Le qLe+sl++ R++K++l++eqie+l++ Lus10006716 59 SSRRLMGECLETCTIGELRKLECQLERSLSRLRARKTQLFMEQIEKLRE 107 57********************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	1.5E-41	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	31.791	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	7.73E-38	3	60	No hit	No description
PRINTS	PR00404	3.2E-31	3	23	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.57E-29	3	69	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.6E-27	10	57	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	8.807	12	135	IPR002487	Transcription factor, K-box
PRINTS	PR00404	3.2E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	3.2E-31	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	6.7E-15	59	108	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: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: 179 aa Download sequence Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIIFSP RGKLYEFSSS 60 RRLMGECLET CTIGELRKLE CQLERSLSRL RARKTQLFME QIEKLREECG MNTLIQLVPS 120 NKKQLGIAVT EEEEEEEDRE TMEVETELFI GLADPARRRS TAKASTSPPA RIMTPPQN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6byy_A	3e-17	1	60	1	60	MEF2 CHIMERA
6byy_B	3e-17	1	60	1	60	MEF2 CHIMERA
6byy_C	3e-17	1	60	1	60	MEF2 CHIMERA
6byy_D	3e-17	1	60	1	60	MEF2 CHIMERA
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269\|PubMed:15144377, ECO:0000269\|PubMed:17166135}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lus10006716

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_024452478.1	4e-55	agamous-like MADS-box protein AGL19 isoform X3
Swissprot	Q9XJ60	2e-49	MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBL	A0A067H4S1	3e-54	A0A067H4S1_CITSI; Uncharacterized protein
STRING	Lus10006716	1e-125	(Linum usitatissimum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF119	33	360

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G22950.1	3e-48	AGAMOUS-like 19

Link Out ? help Back to Top
Phytozome	Lus10006716

Publications ? help Back to Top
Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics, 2006. 172(4): p. 2501-14 [PMID:16452146] Park SJ, et al. Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod. Plant J., 2008. 56(6): p. 1018-29 [PMID:18774969] Lee S,Jeong DH,An G A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses. Plant Signal Behav, 2008. 3(7): p. 471-4 [PMID:19704489] Maas LF,McClung A,McCouch S Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice. Theor. Appl. Genet., 2010. 120(5): p. 895-908 [PMID:19949767] Sun C, et al. The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice. Plant Cell, 2012. 24(8): p. 3235-47 [PMID:22892321] Choi SC, et al. Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3. Plant Physiol., 2014. 164(3): p. 1326-37 [PMID:24420930] Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor. PeerJ, 2015. 3: p. e817 [PMID:25780769] Jin J, et al. MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice. Plant Physiol., 2015. 168(4): p. 1275-85 [PMID:25855537] Liu X, et al. Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.). Plant Cell Rep., 2016. 35(2): p. 357-68 [PMID:26518431] Hwang YH, et al. Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time. Plant Cell Rep., 2016. 35(4): p. 857-65 [PMID:26754793] Shibaya T, et al. Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice. Plant Cell Physiol., 2016. 57(9): p. 1828-38 [PMID:27318280] Alter P, et al. Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1. Plant Physiol., 2016. 172(1): p. 389-404 [PMID:27457125]