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

Potri.003G119700.4

Organism

Populus trichocarpa

Taxonomic ID

3694

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

MIKC_MADS

Protein Properties

Length: 204aa MW: 23387.1 Da PI: 9.9614

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.003G119700.4	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	96.5	1.1e-30	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fss+gklye+ss Potri.003G119700.4 9 KRIENATSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSSRGKLYEFSS 59 79***********************************************96 PP
2	K-box	71.1	3.4e-24	83	171	10	98
K-box 10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 + + + +++ L k+ie L+ ++R+llGe+Le++s +LqqLe+qL +sl++iR++Kn+l++e ie+l+ ek l een++Lr+k+ Potri.003G119700.4 83 VQDNIQPVKEDTFTLAKKIELLEVSKRKLLGEGLETCSTDDLQQLENQLGRSLTRIRARKNQLFRERIEKLKGEEKILLEENTRLREKV 171 45668889999999************************************************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	32.142	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.6E-41	1	60	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-31	3	23	IPR002100	Transcription factor, MADS-box
CDD	cd00265	6.16E-42	3	71	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.7E-32	3	72	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.3E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-31	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.6E-31	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	5.2E-25	84	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	14.054	87	177	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:0010048	Biological Process	vernalization response
GO:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
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: 204 aa Download sequence Send to blast
MVRGKTQMKR IENATSRQVT FSKRRNGLLK KAFELSVLCD AEVALIVFSS RGKLYEFSSS 60 SINRTIERYQ KRAKDVGISS KMVQDNIQPV KEDTFTLAKK IELLEVSKRK LLGEGLETCS 120 TDDLQQLENQ LGRSLTRIRA RKNQLFRERI EKLKGEEKIL LEENTRLREK VIVLYMLYEL 180 SDPTLSIITS SDFEECITVF GIA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_Q	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_R	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_S	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
5f28_A	1e-18	1	69	1	69	MEF2C
5f28_B	1e-18	1	69	1	69	MEF2C
5f28_C	1e-18	1	69	1	69	MEF2C
5f28_D	1e-18	1	69	1	69	MEF2C
6byy_A	1e-18	1	69	1	69	MEF2 CHIMERA
6byy_B	1e-18	1	69	1	69	MEF2 CHIMERA
6byy_C	1e-18	1	69	1	69	MEF2 CHIMERA
6byy_D	1e-18	1	69	1	69	MEF2 CHIMERA
6bz1_A	1e-18	1	69	1	69	MEF2 CHIMERA
6bz1_B	1e-18	1	69	1	69	MEF2 CHIMERA
6c9l_A	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_B	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_C	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_D	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_E	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_F	1e-18	1	69	1	69	Myocyte-specific enhancer factor 2B
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Mostly expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. Also present in rosette leaves and seedlings and, to a lesser extent, in cauline leaves and flowers. Enriched in apices including the shoot apical meristem and developing leaf primordia. {ECO:0000269\|PubMed:11115127, ECO:0000269\|PubMed:12837945, ECO:0000269\|PubMed:12949148, ECO:0000269\|PubMed:16778081}.

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	Potri.003G119700.4

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	CU224793	0.0	CU224793.1 Populus EST from leave.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024452474.1	1e-116	agamous-like MADS-box protein AGL19 isoform X1
Refseq	XP_024452475.1	1e-116	agamous-like MADS-box protein AGL19 isoform X1
Swissprot	O82743	4e-78	AGL19_ARATH; Agamous-like MADS-box protein AGL19
TrEMBL	B9GW46	1e-115	B9GW46_POPTR; Uncharacterized protein
STRING	XP_006477351.1	2e-87	(Citrus sinensis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G22950.1	6e-71	AGAMOUS-like 19

Link Out ? help Back to Top
Phytozome	Potri.003G119700.4

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]