TkA08G133240 | RubberDandelionOmics

Gene overview

TkA08G133240

Reference: TK1151 Chr: Chr08 Coordinates: 34622505-34622852 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

348 bp · TkA08G133240|TK1151|cDNA

TTAGGTTACCCGGTCAACAACCGGTTGTCAATAGTAACCGGTAAGCAAATCCCCAAATCGCTAACACAGCAGCAGGGTAGCTCGTCGAAGAAGATAAACGGCGAGGAAGAAGGAGACGATCGGGATTTCGGATATTACGTGAAGGTGATACGGTATTTGGAATGTGAAGGGCATATAGATACGGGATTTCGGAAGAAGTTTCTTACGTGGTATAGTTTGAAAGCGAGTGAACAGGAGGTTAAAATCGTGAAAGTGTTTGT...

CDS

Download CDS FASTA

348 bp · TkA08G133240|TK1151|CDS

TTAGGTTACCCGGTCAACAACCGGTTGTCAATAGTAACCGGTAAGCAAATCCCCAAATCGCTAACACAGCAGCAGGGTAGCTCGTCGAAGAAGATAAACGGCGAGGAAGAAGGAGACGATCGGGATTTCGGATATTACGTGAAGGTGATACGGTATTTGGAATGTGAAGGGCATATAGATACGGGATTTCGGAAGAAGTTTCTTACGTGGTATAGTTTGAAAGCGAGTGAACAGGAGGTTAAAATCGTGAAAGTGTTTGT...

Protein

Download Protein FASTA

115 aa · TkA08G133240|TK1151|PROTEIN

LGYPVNNRLSIVTGKQIPKSLTQQQGSSSKKINGEEEGDDRDFGYYVKVIRYLECEGHIDTGFRKKFLTWYSLKASEQEVKIVKVFVDALMEDPALLAGQPNGYFFRCDYREEEV

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	`TkA08G133240`
TK1151 ID	TkA08G133240
OH-1004 ID	LXL04_031866
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 38.462 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 TkA08G133240

Location Chr08:34622505-34622852 (-)

Description Similar to VIL2: VIN3-like protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g30200`	Maybe involved in both the vernalization and photoperiod pathways by regulating gene expression.	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
`At5g57380`	Plays a central role in vernalization by mediating the initial transcriptional repression of the homeotic gene FLC, a floral repressor, after a cold treatment.	Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3.2004 · DOI: 10.1038/nature02195 A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.2006 · DOI: 10.1101/gad.1493306 The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC.2007 · DOI: 10.1016/j.cub.2006.11.052
`At3g24440`	Involved in both the vernalization and photoperiod pathways by regulating expression of the related floral repressors FLOWERING LOCUS C (FLC) and FLOWERING LOCUS M (FLM).	A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.2006 · DOI: 10.1101/gad.1493306 The PHD finger protein VRN5 functions in the epigenetic silencing of Arabidopsis FLC.2007 · DOI: 10.1016/j.cub.2006.11.052 A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization.2008 · DOI: 10.1073/pnas.0808687105
`At2g18880`	Involved in both the vernalization and photoperiod pathways by regulating gene expression.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031866 · 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:0001666 response to hypoxia Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009409 response to cold Biological Process

GO:0009908 flower development Biological Process

GO:0010048 vernalization response Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0032922 circadian regulation of gene expression Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

GO:0048572 short-day photoperiodism Biological Process

GO:0048575 short-day photoperiodism, flowering Biological Process

GO:0048587 regulation of short-day photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT2G18880

ath:AT3G24440

ath:AT4G30200

ath:AT5G57380

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.

Nucleus0.532

Rank 1 · TkA08G133240 · TK1151

Cytoplasm0.389

Rank 2 · TkA08G133240 · TK1151

Cell membrane0.090

Rank 3 · TkA08G133240 · TK1151

Mitochondrion0.074

Rank 4 · TkA08G133240 · TK1151

Endoplasmic reticulum0.065

Rank 5 · TkA08G133240 · 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.

PF23380VIN3_C40-100 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G133240	`PF23380`	VIN3_C	40	100	4.4e-29	100.8

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
`Q9SUM4`	Arabidopsis thaliana	sp\|Q9SUM4\|VIL2_ARATH VIN3-like protein 2	61.100%	Swiss-Prot	Low
`Q9FIE3`	Arabidopsis thaliana	sp\|Q9FIE3\|VIN3_ARATH Protein VERNALIZATION INSENSITIVE 3	57.400%	Swiss-Prot	Medium
`Q9LHF5`	Arabidopsis thaliana	sp\|Q9LHF5\|VIL1_ARATH VIN3-like protein 1	57.400%	Swiss-Prot	Low
`Q5BPT4`	Arabidopsis thaliana	sp\|Q5BPT4\|VIL3_ARATH VIN3-like protein 3	40.900%	Swiss-Prot	Medium

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