LXL04_029180 | RubberDandelionOmics

Gene overview

LXL04_029180

Reference: OH-1004 Chr: Chr06 Coordinates: 82723409-82739881 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4260 bp · LXL04_029180|LXL04_029180|OH1004|cDNA

ATGGCCCCCACAATTGCAGAATCTGAAGCTGATGGCATTGCTAGTAGTGCTAATCAGCTCTCAGAATGTGCATTGTTGATTGACTCCACTCGGAAATCAGAATCTGTCTTCGAATACATTAATAAGTGTGTTATATGGTCGCCGAAGATGATTCTGAATCTGGCGGATGATGATGGCTGTGAATCGGTTAAAGGCTTCAGTGAGCATCCCAGTTCGATGTCGGAGACAGTCTCGAGAGGAACTAAGAGGATGACACCTGA...

CDS

Download CDS FASTA

4260 bp · LXL04_029180|LXL04_029180|OH1004|CDS

ATGGCCCCCACAATTGCAGAATCTGAAGCTGATGGCATTGCTAGTAGTGCTAATCAGCTCTCAGAATGTGCATTGTTGATTGACTCCACTCGGAAATCAGAATCTGTCTTCGAATACATTAATAAGTGTGTTATATGGTCGCCGAAGATGATTCTGAATCTGGCGGATGATGATGGCTGTGAATCGGTTAAAGGCTTCAGTGAGCATCCCAGTTCGATGTCGGAGACAGTCTCGAGAGGAACTAAGAGGATGACACCTGA...

Protein

Download Protein FASTA

1419 aa · LXL04_029180|LXL04_029180|OH1004|PROTEIN

MAPTIAESEADGIASSANQLSECALLIDSTRKSESVFEYINKCVIWSPKMILNLADDDGCESVKGFSEHPSSMSETVSRGTKRMTPDKSCEKSAKCSPKLTPGNSPTSEKCMRSSTGMEVNGTDLDPLPPTLNAHDSNFVYNDDASPVPLTIDQSIITPSVPGECNGTKSDAFPLTSNRHSSDFLYNDNDSPAPLTTDASIITLKCASQNKSVPGEPNGTESDAFPLTSHGLNSDFVYNDDDSPVPLTIDKSIITAKNAY...

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_029180`
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_029180

Location Chr06:82723409-82739881 (+)

Description Similar to CMT2: DNA (cytosine-5)-methyltransferase CMT2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g19020`	May be involved in the CpXpG methylation and in gene silencing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q5KQL9`	Involved in CpXpG DNA methylation.	No verified direct reference in this release
`Os03g0226800`	Involved in CpXpG DNA methylation (By similarity).	No verified direct reference in this release
`Os10g0104900`	Involved in CpXpG DNA methylation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029180 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0032259 methylation Biological Process

GO:0034605 cellular response to heat Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation Biological Process

GO:0141010 transposable element silencing by siRNA-mediated DNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0003886 DNA (cytosine-5-)-methyltransferase activity Molecular Function

GO:0032183 SUMO binding Molecular Function

GO:0051720 DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates Molecular Function

KEGG gene cross-reference

ath:AT4G19020

dosa:Os03g0226800

dosa:Os05g0224800

dosa:Os05g0224900

dosa:Os10g0104900

osa:4338140

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.

Nucleus0.839

Rank 1 · LXL04_029180 · OH-1004

Cytoplasm0.171

Rank 2 · LXL04_029180 · OH-1004

Cell membrane0.050

Rank 3 · LXL04_029180 · OH-1004

Mitochondrion0.029

Rank 4 · LXL04_029180 · OH-1004

Endoplasmic reticulum0.028

Rank 5 · LXL04_029180 · 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.

PF01426.25BAH387-500 aa

PF00385.31Chromo634-689 aa

PF00145.24DNA_methylase698-1056 aa

PF13966.12zf-RVT1183-1268 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029180	`PF01426.25`	BAH	387	500	1.9e-16	60.8
LXL04_029180	`PF00385.31`	Chromo	634	689	9.4e-12	45.4
LXL04_029180	`PF00145.24`	DNA_methylase	698	1056	8e-43	147.8
LXL04_029180	`PF13966.12`	zf-RVT	1183	1268	4.3e-19	69.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q94F87`	Arabidopsis thaliana	DNA (cytosine-5)-methyltransferase CMT2	59.566%	Swiss-Prot	moderate database homology
`Q5KQL9`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT2	53.618%	Swiss-Prot	moderate database homology
`A0A0P0VUY4`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT1	49.631%	Swiss-Prot	moderate database homology
`C0SQ89`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT3	50.775%	Swiss-Prot	moderate database homology

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