LXL04_027697 | RubberDandelionOmics

Gene overview

LXL04_027697

Reference: OH-1004 Chr: Chr06 Coordinates: 21992192-21995072 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1500 bp · LXL04_027697|LXL04_027697|OH1004|cDNA

ATGAAAGGCGGCGCTAAGAGGAAGAGCGTCAGCTCCGACACACCACCACCTCGGGTCCACAACGATCTCGCTTCTCCCGGGAACGATAAGGCAGAGTACCACAATCAAGACGGTGAACAACAGCAGCTGCTGCCGCTGAATGACAAGTATGAAGACGAAGAAGAGGATGAATATGACGAGGAGTATGACGATCAGTTCGGCGACCAAGAAAACGACGGAGAAGGCGGTGAAGCCGAGGATGGTGACGAGCGTCCTAAGCT...

CDS

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1500 bp · LXL04_027697|LXL04_027697|OH1004|CDS

ATGAAAGGCGGCGCTAAGAGGAAGAGCGTCAGCTCCGACACACCACCACCTCGGGTCCACAACGATCTCGCTTCTCCCGGGAACGATAAGGCAGAGTACCACAATCAAGACGGTGAACAACAGCAGCTGCTGCCGCTGAATGACAAGTATGAAGACGAAGAAGAGGATGAATATGACGAGGAGTATGACGATCAGTTCGGCGACCAAGAAAACGACGGAGAAGGCGGTGAAGCCGAGGATGGTGACGAGCGTCCTAAGCT...

Protein

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499 aa · LXL04_027697|LXL04_027697|OH1004|PROTEIN

MKGGAKRKSVSSDTPPPRVHNDLASPGNDKAEYHNQDGEQQQLLPLNDKYEDEEEDEYDEEYDDQFGDQENDGEGGEAEDGDERPKLAEGFYEIESVRKKRSRKGKVQYLIKWRGWPEAANTWEPFENLLSCSDVIDAFEERIRSGKQKPGRKQKQKSVAPIQPQPKKKKKKQQQQQEEQQNSPSATYEIPSTKVKIVQESLSHPSESDPTCAQSNVNTATHSNDNQSLSDFHEIGEKNETIELNVKLSELKTPSSTVKE...

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	`LXL04_027697`
TK1151 ID	TkA07G086590
OH-1004 ID	LXL04_027697
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	95.300
Protein coverage (%)	TK1151 76.230 / OH-1004 55.912 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_027697

Location Chr06:21992192-21995072 (+)

Description Similar to LHP1: Chromo domain protein LHP1

Arabidopsis / Rice Reference Genes and Papers

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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_027697 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0003006 developmental process involved in reproduction Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009410 response to xenobiotic stimulus 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

mmu:52609

rno:362962

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.

Nucleus0.974

Rank 1 · LXL04_027697 · OH-1004

Cytoplasm0.085

Rank 2 · LXL04_027697 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_027697 · OH-1004

Endoplasmic reticulum0.012

Rank 4 · LXL04_027697 · OH-1004

Plastid0.008

Rank 5 · LXL04_027697 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF00385.31Chromo92-142 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027697	`PF00385.31`	Chromo	92	142	5.8e-17	62.1

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	Chromo domain-containing protein LHP1	39.886%	Swiss-Prot	moderate database homology
`Q339W7`	Oryza sativa subsp. japonica	Probable chromo domain-containing protein LHP1	35.088%	Swiss-Prot	moderate database homology

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