LXL04_003523 | RubberDandelionOmics

Gene overview

LXL04_003523

Reference: OH-1004 Chr: Chr01 Coordinates: 82015738-82021474 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3339 bp · LXL04_003523|LXL04_003523|OH1004|cDNA

ATGGCATTTTCTTCTCAATTGTTATCACCAAACGCCGATAACAAACAGAGAGAAAACGACGACGAAGAAGCACCGCTAGAGGAGCAGAAAGTACTGGCTCAATCGGAAGAAGATCATCGTCATAATCATCGTGAGGCGAGGTACGTCGCCCTTGACCTCGTCTACTCAGCAACATCCCCCTGCAGTGGTTACGCGTATGTCATGTCTAAGAAGGTGAAAGCTAGGAAATACGGCGTGCTAGGGGTTCATAAAGACGGCAT...

CDS

Download CDS FASTA

3339 bp · LXL04_003523|LXL04_003523|OH1004|CDS

ATGGCATTTTCTTCTCAATTGTTATCACCAAACGCCGATAACAAACAGAGAGAAAACGACGACGAAGAAGCACCGCTAGAGGAGCAGAAAGTACTGGCTCAATCGGAAGAAGATCATCGTCATAATCATCGTGAGGCGAGGTACGTCGCCCTTGACCTCGTCTACTCAGCAACATCCCCCTGCAGTGGTTACGCGTATGTCATGTCTAAGAAGGTGAAAGCTAGGAAATACGGCGTGCTAGGGGTTCATAAAGACGGCAT...

Protein

Download Protein FASTA

1112 aa · LXL04_003523|LXL04_003523|OH1004|PROTEIN

MAFSSQLLSPNADNKQRENDDEEAPLEEQKVLAQSEEDHRHNHREARYVALDLVYSATSPCSGYAYVMSKKVKARKYGVLGVHKDGISVDPKPTSPKPPVIYFYSRCRRRKRSDRFDNISGYDRFLLNSKAISAVRVKAEDVELNDVDGDVGSIGALVNCSNKKRKTSQELINLGLNSVSLDAPRLRESSRKPNRTDDTSASSGRRRSKNKDNKNVCQKNTGDAIEATEIDDTNKPTTNASRTKRWVRLTFDGVDPQKFL...

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_003523`
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_003523

Location Chr01:82015738-82021474 (-)

Description Similar to ATX2: Histone-lysine N-methyltransferase ATX2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g05830`	Histone methyltransferase.	The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions.2008 · DOI: 10.1105/tpc.107.056614 Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation.2014 · DOI: 10.1111/nph.12493
`At2g31650`	May participate in target-gene transcriptional regulation and associated histone methylation.	Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation.2014 · DOI: 10.1111/nph.12493 Arabidopsis homolog of trithorax1 (ATX1) is required for cell production, patterning, and morphogenesis in root development.2014 · DOI: 10.1093/jxb/eru355
`At5g53430`	Histone methyltransferase.	No verified direct reference in this release
`At4g27910`	Histone methyltransferase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0134500`	Possesses histone H3 methyltransferase activity in vitro.	Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3.2014 · DOI: 10.1104/pp.113.228049

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003523 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010093 specification of floral organ identity Biological Process

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

KEGG gene cross-reference

ath:AT1G05830

ath:AT2G31650

ath:AT4G27910

ath:AT5G53430

dosa:Os09g0134500

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.

Nucleus0.920

Rank 1 · LXL04_003523 · OH-1004

Cytoplasm0.111

Rank 2 · LXL04_003523 · OH-1004

Cell membrane0.040

Rank 3 · LXL04_003523 · OH-1004

Plastid0.019

Rank 4 · LXL04_003523 · OH-1004

Endoplasmic reticulum0.018

Rank 5 · LXL04_003523 · 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.

PF21743.4PTM_DIR17_Tudor273-299 aa

PF00855.24PWWP355-442 aa

PF05964.20FYRN492-549 aa

PF05965.20FYRC556-630 aa

PF13831.13PHD_2666-699 aa

PF13832.13zf-HC5HC2H_2709-831 aa

PF13771.13zf-HC5HC2H730-832 aa

PF00856.34SET961-1067 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003523	`PF21743.4`	PTM_DIR17_Tudor	273	299	9.2e-07	29.3
LXL04_003523	`PF00855.24`	PWWP	355	442	1.4e-16	61.4
LXL04_003523	`PF05964.20`	FYRN	492	549	3.7e-16	59.2
LXL04_003523	`PF05965.20`	FYRC	556	630	6.6e-12	46.1
LXL04_003523	`PF13831.13`	PHD_2	666	699	4.1e-07	30.1
LXL04_003523	`PF13832.13`	zf-HC5HC2H_2	709	831	1.5e-30	106.3
LXL04_003523	`PF13771.13`	zf-HC5HC2H	730	832	3.3e-20	72.8
LXL04_003523	`PF00856.34`	SET	961	1067	3.4e-25	89.2

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
`P0CB22`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX2	57.028%	Swiss-Prot	strong database homology
`Q9C5X4`	Arabidopsis thaliana	Histone H3-lysine(4) N-trimethyltransferase ATX1	56.144%	Swiss-Prot	strong database homology
`Q8GZ42`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX5	34.583%	Swiss-Prot	weak database homology
`Q9SUE7`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX4	35.282%	Swiss-Prot	weak database homology
`Q6K431`	Oryza sativa subsp. japonica	Histone-lysine N-methyltransferase TRX1	57.579%	Swiss-Prot	strong database homology

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