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

Thhalv10027162m

Common Name

EUTSA_v10027162mg

Organism

Eutrema salsugineum

Taxonomic ID

72664

Taxonomic Lineage

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

Family

M-type_MADS

Protein Properties

Length: 79aa MW: 9100.72 Da PI: 10.4603

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thhalv10027162m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	93.5	1e-29	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+ii+s++ k+ye+ss Thhalv10027162m 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIILSPRSKIYEFSS 59 79***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	6.1E-38	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	30.74	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.62E-29	3	64	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.1E-30	3	23	IPR002100	Transcription factor, MADS-box
CDD	cd00265	3.19E-35	3	60	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	9.7E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.1E-30	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	7.1E-30	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: 79 aa Download sequence Send to blast
MVRGKTEMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIILSP RSKIYEFSSS 60 RYISFFHPSP FVFLFYLC*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
3mu6_A	4e-16	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_B	4e-16	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_C	4e-16	3	60	2	59	Myocyte-specific enhancer factor 2A
3mu6_D	4e-16	3	60	2	59	Myocyte-specific enhancer factor 2A
5f28_A	5e-16	1	68	1	75	MEF2C
5f28_B	5e-16	1	68	1	75	MEF2C
5f28_C	5e-16	1	68	1	75	MEF2C
5f28_D	5e-16	1	68	1	75	MEF2C
6byy_A	6e-16	1	60	1	60	MEF2 CHIMERA
6byy_B	6e-16	1	60	1	60	MEF2 CHIMERA
6byy_C	6e-16	1	60	1	60	MEF2 CHIMERA
6byy_D	6e-16	1	60	1	60	MEF2 CHIMERA
6bz1_A	6e-16	1	60	1	60	MEF2 CHIMERA
6bz1_B	6e-16	1	60	1	60	MEF2 CHIMERA
6bz1_C	6e-16	1	60	1	60	MEF2 CHIMERA
6bz1_D	6e-16	1	60	1	60	MEF2 CHIMERA
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. {ECO:0000269\|PubMed:16778081}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Thhalv10027162m

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Maintained at very low levels by the polycomb-group (PcG) proteins MSI1, CLF, and EMF2 via histone methylation (H3K27me3). Derepressed upon cold treatment (vernalization). {ECO:0000269\|PubMed:16778081}.

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	AL031018	5e-63	AL031018.1 Arabidopsis thaliana DNA chromosome 4, BAC clone F7H19 (ESSA project).
GenBank	AL161558	5e-63	AL161558.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 58.
GenBank	CP002687	5e-63	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006413597.2	1e-34	agamous-like MADS-box protein AGL19
Refseq	XP_007134936.1	8e-35	hypothetical protein PHAVU_010G088100g
Refseq	XP_007134937.1	8e-35	hypothetical protein PHAVU_010G088100g
Swissprot	O82743	5e-34	AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBL	V4MF18	2e-49	V4MF18_EUTSA; Uncharacterized protein
STRING	XP_006413596.1	3e-50	(Eutrema salsugineum)

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
AT4G22950.1	2e-36	AGAMOUS-like 19

Link Out ? help Back to Top
Phytozome	Thhalv10027162m
Entrez Gene	18028589

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] 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]