LXL04_008709 | RubberDandelionOmics

Gene overview

LXL04_008709

Reference: OH-1004 Chr: Chr02 Coordinates: 106593800-106596752 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1188 bp · LXL04_008709|LXL04_008709|OH1004|cDNA

ATGGAGACGCAAGCAGGTCGAACGGAGCAATATGCTGGTAACAACACCGGCAACGACAAGATAGACGACGATGTGTTGATTAAGAACGCGAAAGGCCAGTCCGGTCTTCTCCAATTCGGCTCCGGAACCTCCGAAATTCTTGACACTGCCTTCAAGAAGGAAACAGTTGGGCTTGTCACAAGGGAGCAGTATGTTGAAAAAAGGGTTAACATTCGAACCAaaattgaagaagaagaaaaagagaaaCTTCAAAAGCTACA...

CDS

Download CDS FASTA

903 bp · LXL04_008709|LXL04_008709|OH1004|CDS

ATGGAGACGCAAGCAGGTCGAACGGAGCAATATGCTGGTAACAACACCGGCAACGACAAGATAGACGACGATGTGTTGATTAAGAACGCGAAAGGCCAGTCCGGTCTTCTCCAATTCGGCTCCGGAACCTCCGAAATTCTTGACACTGCCTTCAAGAAGGAAACAGTTGGGCTTGTCACAAGGGAGCAGTATGTTGAAAAAAGGGTTAACATTCGAACCAAAATTGAAGAAGAAGAAAAAGAGAAACTTCAAAAGCTACA...

Protein

Download Protein FASTA

300 aa · LXL04_008709|LXL04_008709|OH1004|PROTEIN

METQAGRTEQYAGNNTGNDKIDDDVLIKNAKGQSGLLQFGSGTSEILDTAFKKETVGLVTREQYVEKRVNIRTKIEEEEKEKLQKLQQEEEELQLQKLKKRKVKANPKLSFSEDIENGEEEEEEYGEDTYSFSEREAEEQAERERLRKQWLREQEQIKNEALEITYSYRDGAGHRRVMQVRKGDTIGEFLRSVQQQLAPEFREIRTTSVENLLYVKEDLIIPHILHSSLGSLLRQTLHPNRKNQTIDEIMVCHCKPSYDG...

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_008709`
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_008709

Location Chr02:106593800-106596752 (+)

Description Similar to XCT: Protein XAP5 CIRCADIAN TIMEKEEPER

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21150`	Involved in light regulation of the circadian clock and photomorphogenesis.	No verified direct reference in this release
`At1g77300`	Histone methyltransferase involved in di and tri-methylation of 'Lys-36' of histone H3 (H3K36me2 and H3K36me3).	Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36.2005 · DOI: 10.1038/ncb1329 Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana.2008 · DOI: 10.1128/mcb.01607-07 The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis.2009 · DOI: 10.1371/journal.pone.0007817 Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor.2010 · DOI: 10.1371/journal.ppat.1001137 Histone lysine methyltransferase SDG8 is involved in brassinosteroid-regulated gene expression in Arabidopsis thaliana.2014 · DOI: 10.1093/mp/ssu056

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0535300`	Involved in light regulation of the circadian clock and photomorphogenesis.	No verified direct reference in this release
`UniProt: B8BDW1`	Involved in light regulation of the circadian clock and photomorphogenesis.	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_008709 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009555 pollen development Biological Process

GO:0009637 response to blue light Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010099 regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0010223 secondary shoot formation Biological Process

GO:0010363 regulation of plant-type hypersensitive response Biological Process

GO:0016116 carotenoid metabolic process Biological Process

KEGG gene cross-reference

ath:AT1G77300

ath:AT2G21150

dosa:Os09g0535300

dpo:4801527

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.

Nucleus0.745

Rank 1 · LXL04_008709 · OH-1004

Cytoplasm0.311

Rank 2 · LXL04_008709 · OH-1004

Mitochondrion0.032

Rank 3 · LXL04_008709 · OH-1004

Cell membrane0.027

Rank 4 · LXL04_008709 · OH-1004

Endoplasmic reticulum0.018

Rank 5 · LXL04_008709 · 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.

PF04921.21XAP5161-224 aa

PF17907.8AWS261-296 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008709	`PF04921.21`	XAP5	161	224	6.6e-16	59.7
LXL04_008709	`PF17907.8`	AWS	261	296	1.9e-14	54.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8H110`	Arabidopsis thaliana	Protein XAP5 CIRCADIAN TIMEKEEPER	71.689%	Swiss-Prot	moderate database homology
`Q2LAE1`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ASHH2	79.688%	Swiss-Prot	weak database homology
`Q69JZ7`	Oryza sativa subsp. japonica	Protein XAP5 CIRCADIAN TIMEKEEPER	74.419%	Swiss-Prot	moderate database homology
`B8BDW1`	Oryza sativa subsp. indica	Protein XAP5 CIRCADIAN TIMEKEEPER	74.419%	Swiss-Prot	moderate database homology

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