TkA03G340640 | RubberDandelionOmics

Gene overview

TkA03G340640

Reference: TK1151 Chr: Chr03 Coordinates: 83845150-83852696 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

802 bp · TkA03G340640|TK1151|cDNA

GGAACTCCGGGGACTTATTTATACTAGTTTTGTATGTTGTTCCTGTCTTAGATATCATAATATCTCTCTTTACTAATGATGTCCAGTTAAGGTGAAGGTACTAACCCTTGATTTTGAAACAGCATGACTAGGATTCTTGACAGCTACCAGAGCTATAAGGAGACAGAGGAGCTTACCCGCAAATACATACATGGGAAGCTTCCTTCAGAATACGGTGACATGTGTCCTGCTGATGAACTGGCAGAAATGATCCAACGCCA...

CDS

Download CDS FASTA

567 bp · TkA03G340640|TK1151|CDS

ATGGGGAGAGGGAAGGTGGAGCTCAAGCGGATCGAAGACAAGAGCAGCCGTCAAGTCTCCTTTTCTAAGCGACGGAATGGATTGATGAAGAAATCTCATGAGCTGACGGTGCTGTGCGACGTTGACGTTGCTCTTTTCATCTTCTCCAGCAAAGGCATACTCTATGAGTTCTCCACTGGTGAAAGCATGACTAGGATTCTTGACAGCTACCAGAGCTATAAGGAGACAGAGGAGCTTACCCGCAAATACATACATGGGAA...

Protein

Download Protein FASTA

188 aa · TkA03G340640|TK1151|PROTEIN

MGRGKVELKRIEDKSSRQVSFSKRRNGLMKKSHELTVLCDVDVALFIFSSKGILYEFSTGESMTRILDSYQSYKETEELTRKYIHGKLPSEYGDMCPADELAEMIQRHVDENNIKKLDTTDLYQLEHNLYDILRLVKIRKTQVMMEVVKDLQNKEMQLKKEKKTMMNEITEAKLDDTNNDGVMDVEIA

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`TkA03G340640`
TK1151 ID	TkA03G340640
OH-1004 ID	LXL04_008732
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	88.300
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G340640

Location Chr03:83845150-83852696 (-)

Description Similar to J2: MADS-box protein J2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65080`	Transcription factor involved in the negative regulation of flowering time in short days, probably through the photoperiodic and vernalization pathways.	Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family: MAF2 prevents vernalization by short periods of cold.2003 · DOI: 10.1105/tpc.009506 The E2 ubiquitin-conjugating enzymes, AtUBC1 and AtUBC2, play redundant roles and are involved in activation of FLC expression and repression of flowering in Arabidopsis thaliana.2009 · DOI: 10.1111/j.1365-313x.2008.03684.x The Plant Homeo Domain finger protein, VIN3-LIKE 2, is necessary for photoperiod-mediated epigenetic regulation of the floral repressor, MAF5.2010 · DOI: 10.1073/pnas.1010834107 Role of VIN3-LIKE 2 in facultative photoperiodic flowering response in Arabidopsis.2010 · DOI: 10.4161/psb.5.12.14035 AGAMOUS-LIKE 6 is a floral promoter that negatively regulates the FLC/MAF clade genes and positively regulates FT in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2010.04402.x HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis.2011 · DOI: 10.1104/pp.111.174417 Arabidopsis trithorax-related3/SET domain GROUP2 is required for the winter-annual habit of Arabidopsis thaliana.2012 · DOI: 10.1093/pcp/pcs021
`At5g65060`	Probable transcription factor involved in the negative regulation of flowering time, probably through the photoperiodic and vernalization pathways; more efficient in cv.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0752800`	Probable transcription factor.	No verified direct reference in this release
`UniProt: P0C5B1`	Probable transcription factor.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008732 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009631 cold acclimation Biological Process

GO:0010048 vernalization response Biological Process

GO:0010220 positive regulation of vernalization response Biological Process

GO:0010221 negative regulation of vernalization response Biological Process

GO:0010582 floral meristem determinacy Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0048440 carpel development Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding Molecular Function

KEGG gene cross-reference

bdi:100842079

sly:101263981

vvi:100232867

vvi:100232952

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.973

Rank 1 · TkA03G340640 · TK1151

Cytoplasm0.089

Rank 2 · TkA03G340640 · TK1151

Cell membrane0.017

Rank 3 · TkA03G340640 · TK1151

Endoplasmic reticulum0.009

Rank 4 · TkA03G340640 · TK1151

Mitochondrion0.008

Rank 5 · TkA03G340640 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00319SRF-TF10-57 aa

PF31085PorX_mid61-84 aa

PF27248MJ1674_2nd98-171 aa

PF01486K-box100-169 aa

PF27045HAUS3_C100-130 aa

PF27045HAUS3_C120-141 aa

PF31085PorX_mid135-179 aa

PF27045HAUS3_C142-165 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G340640	`PF00319`	SRF-TF	10	57	1e-23	83.2
TkA03G340640	`PF31085`	PorX_mid	61	84	1.8	9.6
TkA03G340640	`PF27248`	MJ1674_2nd	98	171	0.19	13.0
TkA03G340640	`PF01486`	K-box	100	169	2.1e-08	34.9
TkA03G340640	`PF27045`	HAUS3_C	100	130	1.4	9.6
TkA03G340640	`PF27045`	HAUS3_C	120	141	1.4	9.6
TkA03G340640	`PF31085`	PorX_mid	135	179	1.8	9.6
TkA03G340640	`PF27045`	HAUS3_C	142	165	1.4	9.6

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q683D7`	Arabidopsis thaliana	sp\|Q683D7\|MAF5_ARATH Protein MADS AFFECTING FLOWERING 5	35.100%	Swiss-Prot	Medium
`Q9LSR7`	Arabidopsis thaliana	sp\|Q9LSR7\|AGL70_ARATH Agamous-like MADS-box protein AGL70	27.100%	Swiss-Prot	Low
`Q10CQ1`	Oryza sativa subsp. japonica	sp\|Q10CQ1\|MAD14_ORYSJ MADS-box transcription factor 14	42.400%	Swiss-Prot	Medium
`P0C5B1`	Oryza sativa subsp. indica	sp\|P0C5B1\|MAD14_ORYSI MADS-box transcription factor 14	41.300%	Swiss-Prot	Medium

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