TkA08G298890 | RubberDandelionOmics

Gene overview

TkA08G298890

Reference: TK1151 Chr: Chr08 Coordinates: 77490129-77493695 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1737 bp · TkA08G298890|TK1151|cDNA

TGAATTACCATTCGTGAAACACGCCGTCGAGTACTGCAGAAGAAAAAACTGCAAAATCCGATCCAATTTATCGTAATCGATTCCTCTCCAATCAACTCTCTCAATCTCATTCTCGCTTGCGTCCTGTCATTGTATAAGCCTGTCACTCTGTCAGACTCAAGTGAAAAGGTAAAGGACTGCCAGAAGAACTGAAGAAATACTCAACCCTTCGGCAAAGACCAAAGTGATTCATACGACTCCGATGACGGGCGGAGCTAGAA...

CDS

Download CDS FASTA

1140 bp · TkA08G298890|TK1151|CDS

ATGACGGGCGGAGCTAGAAGGAGAGCTCTCAGCTCTGATCTTCGATCACCACCATCGCACCCGGTCCAATCCGAGATCAGTGATTTAGGGAACGAAGAGGTCGACAACGAGAAGCAGAAGCTGGAACAAGAGCAGCAGCAGTCCATGAATGGCGGCGACGAGGGTGGAAATGAGTACGATGAAGAAGAGGACGAAGAATACCAGGCTGAAGATCAATCTGTCGACGTAAATTTCCAAGGAGAAGAACAAGCTGATGGAGA...

Protein

Download Protein FASTA

379 aa · TkA08G298890|TK1151|PROTEIN

MTGGARRRALSSDLRSPPSHPVQSEISDLGNEEVDNEKQKLEQEQQQSMNGGDEGGNEYDEEEDEEYQAEDQSVDVNFQGEEQADGDESKGDNERPKLAEGYYEIEAVRRKRKRKGETQYLVKWRDWPESSNTWEPVKNLKSCVDFIEAFEERWRSRSNRKRKRKNSAVPTPQPKKKQNQPPHQRSPDATYDVPSVKIKIIEDPSPIPSVNNSNFSTSNDSGSLIGSPQIQEPKIKNESENMTQFAIHIQEDPVGNGNGT...

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	`TkA08G298890`
TK1151 ID	TkA08G298890
OH-1004 ID	LXL04_033679
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.900
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA08G298890

Location Chr08:77490129-77493695 (+)

Description Similar to LHP1: Chromo domain protein LHP1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g17690`	Structural component of heterochromatin involved in gene repression, including several floral homeotic genes and FLT that regulates flowering time.	Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis.2001 · DOI: 10.1242/dev.128.23.4847 Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes.2003 · DOI: 10.1093/pcp/pcg091 Characterization of the Arabidopsis TU8 glucosinolate mutation, an allele of TERMINAL FLOWER2.2004 · DOI: 10.1023/b:plan.0000040897.49151.98 LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC.2006 · DOI: 10.1073/pnas.0507427103 Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1.2006 · DOI: 10.1038/ng1795 Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.11.019 The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes.2016 · DOI: 10.1105/tpc.16.00244 The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana.1998 · DOI: 10.1093/genetics/149.2.597

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0324900`	Structural component of heterochromatin involved in gene repression.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033679 · 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:0000278 mitotic cell cycle Biological Process

GO:0000723 telomere maintenance Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009648 photoperiodism Biological Process

GO:0009744 response to sucrose Biological Process

GO:0009825 multidimensional cell growth Biological Process

GO:0009908 flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010016 shoot system morphogenesis Biological Process

GO:0010048 vernalization response Biological Process

KEGG gene cross-reference

ath:AT5G17690

dme:Dmel_CG8409

gga:426314

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

Open Annotation Module

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.

Nucleus0.976

Rank 1 · TkA08G298890 · TK1151

Cytoplasm0.094

Rank 2 · TkA08G298890 · TK1151

Cell membrane0.018

Rank 3 · TkA08G298890 · TK1151

Mitochondrion0.008

Rank 4 · TkA08G298890 · TK1151

Endoplasmic reticulum0.008

Rank 5 · TkA08G298890 · 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.

PF09531Ndc1_Nup9-48 aa

PF00385Chromo103-153 aa

PF01393Chromo_shadow103-126 aa

PF14061Mtf2_C103-125 aa

PF09531Ndc1_Nup140-224 aa

PF01393Chromo_shadow339-376 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G298890	`PF09531`	Ndc1_Nup	9	48	7.1	5.9
TkA08G298890	`PF00385`	Chromo	103	153	3.3e-16	59.7
TkA08G298890	`PF01393`	Chromo_shadow	103	126	3.7e-08	33.7
TkA08G298890	`PF14061`	Mtf2_C	103	125	0.12	13.3
TkA08G298890	`PF09531`	Ndc1_Nup	140	224	7.1	5.9
TkA08G298890	`PF01393`	Chromo_shadow	339	376	3.7e-08	33.7

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
`Q946J8`	Arabidopsis thaliana	sp\|Q946J8\|LHP1_ARATH Chromo domain-containing protein LHP1	34.800%	Swiss-Prot	Medium
`Q339W7`	Oryza sativa subsp. japonica	sp\|Q339W7\|LHP1_ORYSJ Probable chromo domain-containing protein LHP1	35.500%	Swiss-Prot	Medium

JBrowse

View in Genome Browser

Gene Card