LXL04_038842 | RubberDandelionOmics

Gene overview

LXL04_038842

Reference: OH-1004 Chr: Chr09 Coordinates: 51729748-51736872 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4719 bp · LXL04_038842|LXL04_038842|OH1004|cDNA

ATGGGAACGGCGAAGTTGTTAGATTCGGAAGAAGGTGGTGCGGTGAAACCAGCAGAAATGAAGAAAAAAGGAAAACAAGCCAAACCAACCACAGAGACATCTGATGTTACAATGGAAGATAAACCAAATGTCCCCaccaaaaccaaaccaaaaaGAGAAAGATCATCAAACACCACAGACCCCCCTCAAGTTTCCAGAAAGATGCCAAAACGAGCTGCTTCTTGCACCGACTTCAAAACCAAACCAGTCCGCCTTTCCGA...

CDS

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4719 bp · LXL04_038842|LXL04_038842|OH1004|CDS

ATGGGAACGGCGAAGTTGTTAGATTCGGAAGAAGGTGGTGCGGTGAAACCAGCAGAAATGAAGAAAAAAGGAAAACAAGCCAAACCAACCACAGAGACATCTGATGTTACAATGGAAGATAAACCAAATGTCCCCACCAAAACCAAACCAAAAAGAGAAAGATCATCAAACACCACAGACCCCCCTCAAGTTTCCAGAAAGATGCCAAAACGAGCTGCTTCTTGCACCGACTTCAAAACCAAACCAGTCCGCCTTTCCGA...

Protein

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1572 aa · LXL04_038842|LXL04_038842|OH1004|PROTEIN

MGTAKLLDSEEGGAVKPAEMKKKGKQAKPTTETSDVTMEDKPNVPTKTKPKRERSSNTTDPPQVSRKMPKRAASCTDFKTKPVRLSEKSSTIENKKVKIVEEEIAALSIVPGPDDPRPNRRLTDFILHDENGNPQPVEMLEVNDLYISGQILPLEKTSEKEKEKEIGVRCEGFGRIEDWSISGYEDGSPVIWVSTELADYDCVKPSGTYRKLFGLFQEKANACIQVYKRLSKSSGGNPDLSLDELLASLVRSMSGSKNFP...

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_038842`
TK1151 ID	TkA04G470340
OH-1004 ID	LXL04_038842
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_038842

Location Chr09:51729748-51736872 (+)

Description Similar to MET1B: DNA (cytosine-5)-methyltransferase 1B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g49160`	Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability.	No verified direct reference in this release
`At4g14140`	Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability.	No verified direct reference in this release
`At4g08990`	Maintains chromatin CpG methylation that plays a role in genomic imprinting, regulation of embryogenesis and seed viability.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0182900`	Major CG methylase that methylates chromatin CpG residues and maintains DNA methylation.	The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice.2014 · DOI: 10.1007/s11103-014-0178-9 Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.2014 · DOI: 10.1073/pnas.1410761111
`Os03g0798300`	Probably methylates CpG residues and maintains DNA methylation.	Characterization of two rice DNA methyltransferase genes and RNAi-mediated reactivation of a silenced transgene in rice callus.2004 · DOI: 10.1007/s00425-003-1112-6 The MET1b gene encoding a maintenance DNA methyltransferase is indispensable for normal development in rice.2014 · DOI: 10.1007/s11103-014-0178-9

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038842 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010069 zygote asymmetric cytokinesis in embryo sac Biological Process

GO:0010229 inflorescence development Biological Process

GO:0032259 methylation Biological Process

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

GO:0071514 genomic imprinting Biological Process

GO:0141044 epigenetic programming in the endosperm Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT4G08990

ath:AT4G14140

ath:AT5G49160

dosa:Os03g0798300

dosa:Os07g0182900

osa:4334435

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.

Nucleus0.927

Rank 1 · LXL04_038842 · OH-1004

Cytoplasm0.110

Rank 2 · LXL04_038842 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_038842 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_038842 · OH-1004

Mitochondrion0.017

Rank 5 · LXL04_038842 · 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.

PF12047.14DNMT1-RFD115-251 aa

PF12047.14DNMT1-RFD420-571 aa

PF01426.25BAH774-904 aa

PF01426.25BAH946-1085 aa

PF00145.24DNA_methylase1133-1176 aa

PF00145.24DNA_methylase1214-1561 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038842	`PF12047.14`	DNMT1-RFD	115	251	1.3e-78	262.7
LXL04_038842	`PF12047.14`	DNMT1-RFD	420	571	1.3e-78	262.7
LXL04_038842	`PF01426.25`	BAH	774	904	1.3e-37	129.1
LXL04_038842	`PF01426.25`	BAH	946	1085	1.3e-37	129.1
LXL04_038842	`PF00145.24`	DNA_methylase	1133	1176	4.2e-48	165.2
LXL04_038842	`PF00145.24`	DNA_methylase	1214	1561	4.2e-48	165.2

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
`P34881`	Arabidopsis thaliana	DNA (cytosine-5)-methyltransferase 1	58.726%	Swiss-Prot	strong database homology
`O23273`	Arabidopsis thaliana	DNA (cytosine-5)-methyltransferase 4	56.389%	Swiss-Prot	strong database homology
`Q9M0S8`	Arabidopsis thaliana	DNA (cytosine-5)-methyltransferase 2	55.440%	Swiss-Prot	strong database homology
`B1Q3J6`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase 1B	58.168%	Swiss-Prot	strong database homology
`Q7Y1I7`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase 1A	57.087%	Swiss-Prot	strong database homology

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