LXL04_004634 | RubberDandelionOmics

Gene overview

LXL04_004634

Reference: OH-1004 Chr: Chr01 Coordinates: 141966060-141969267 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1249 bp · LXL04_004634|LXL04_004634|OH1004|cDNA

ATGGAGACGCAATCAGGTCGAACGGAGCAATATGCTGGTAACAACACCGGCAACGACAAGATTCTTGAAACTGCCTTCAAGAAGGAAACAGTTGGGCTTGTCACAAGGGAAGGGTTCACATTCGAACCAaaattgaagaagaagaaaaagagaaaCTTCAAAAGCTATAAAAAGAAGGAGCTTCTGTTACAAAAACTAAAAAAGAGGAAAGTCAAAGCAAACCCAAAGCTATCTTTTGCAGAAGAAATTGAAAAcgggga...

CDS

Download CDS FASTA

1032 bp · LXL04_004634|LXL04_004634|OH1004|CDS

ATGGAGACGCAATCAGGTCGAACGGAGCAATATGCTGGTAACAACACCGGCAACGACAAGATTCTTGAAACTGCCTTCAAGAAGGAAACAGTTGGGCTTGTCACAAGGGAAGGGTTCACATTCGAACCAAAATTGAAGAAGAAGAAAAAGAGAAACTTCAAAAGCTATAAAAAGAAGGAGCTTCTGTTACAAAAACTAAAAAAGAGGAAAGTCAAAGCAAACCCAAAGCTATCTTTTGCAGAAGAAATTGAAAACGGGGA...

Protein

Download Protein FASTA

343 aa · LXL04_004634|LXL04_004634|OH1004|PROTEIN

METQSGRTEQYAGNNTGNDKILETAFKKETVGLVTREGFTFEPKLKKKKKRNFKSYKKKELLLQKLKKRKVKANPKLSFAEEIENGEEEEEEDGEDKNKESNMFGRRGFGKDPTVETSFLPDSEREAEEQAERERLRKQWLREQEQIKNEALEITYSYWDGAGHRRVMQVRKGDTIEEFLRSVQQQLAPEFREIRTTSVDNKNGTDVVYVKEDLIIPHLSEASCEEDNTRSNSSQSGQKQPDPPQLSWKLIKTNMFLHPN...

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_004634`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004634

Location Chr01:141966060-141969267 (-)

Description Similar to XCT: Protein XAP5 CIRCADIAN TIMEKEEPER

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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

View annotation sources

Functional annotation source: OH1004 · LXL04_004634 · 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.

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.

Nucleus0.881

Rank 1 · LXL04_004634 · OH-1004

Cytoplasm0.212

Rank 2 · LXL04_004634 · OH-1004

Mitochondrion0.034

Rank 3 · LXL04_004634 · OH-1004

Cell membrane0.027

Rank 4 · LXL04_004634 · OH-1004

Golgi apparatus0.014

Rank 5 · LXL04_004634 · OH-1004

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.

PF04921.21XAP5151-220 aa

PF17907.8AWS284-316 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004634	`PF04921.21`	XAP5	151	220	5e-14	53.6
LXL04_004634	`PF17907.8`	AWS	284	316	1.8e-12	47.8

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
`Q8H110`	Arabidopsis thaliana	Protein XAP5 CIRCADIAN TIMEKEEPER	60.870%	Swiss-Prot	moderate database homology
`Q2LAE1`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ASHH2	71.579%	Swiss-Prot	weak database homology
`Q69JZ7`	Oryza sativa subsp. japonica	Protein XAP5 CIRCADIAN TIMEKEEPER	61.137%	Swiss-Prot	moderate database homology
`B8BDW1`	Oryza sativa subsp. indica	Protein XAP5 CIRCADIAN TIMEKEEPER	61.137%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card