LXL04_032505 | RubberDandelionOmics

Gene overview

LXL04_032505

Reference: OH-1004 Chr: Chr07 Coordinates: 24194775-24196431 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1287 bp · LXL04_032505|LXL04_032505|OH1004|cDNA

ATGTCCGGACACCCTCGTAATCGATCTGCTGGTGGTAAACCAGACGGTAGAAGGAAACAAACAAATGCTGGTTCTCCAACTCAGTTGAAACCGAAGATAAAGGTTGCATCAGATGAATCTTCTGGTAGTGCTTCCGTTGATCACAAGGATGATTCTTCACTTACTGGCGAATGTATCTCAAATAAAATGTCAAGTTTAACTCCTAAACCAGATTTAAATCCCCATCCACAAGAGAAATCTCCATTGCCCCCTGTAAAACA...

CDS

Download CDS FASTA

1287 bp · LXL04_032505|LXL04_032505|OH1004|CDS

ATGTCCGGACACCCTCGTAATCGATCTGCTGGTGGTAAACCAGACGGTAGAAGGAAACAAACAAATGCTGGTTCTCCAACTCAGTTGAAACCGAAGATAAAGGTTGCATCAGATGAATCTTCTGGTAGTGCTTCCGTTGATCACAAGGATGATTCTTCACTTACTGGCGAATGTATCTCAAATAAAATGTCAAGTTTAACTCCTAAACCAGATTTAAATCCCCATCCACAAGAGAAATCTCCATTGCCCCCTGTAAAACA...

Protein

Download Protein FASTA

428 aa · LXL04_032505|LXL04_032505|OH1004|PROTEIN

MSGHPRNRSAGGKPDGRRKQTNAGSPTQLKPKIKVASDESSGSASVDHKDDSSLTGECISNKMSSLTPKPDLNPHPQEKSPLPPVKHASPGRWNFQPTPVSSHSTDNVSEQPKSVSTSNSDSKDSNHLHPVLSKSQQGIESQDGIAEKGKQIGDNGGKPEDGDHSSMSRFDICPKKANTGGVKLKPSLHAKNKEKRNQKKLAAEGPIIDILRPGMVIIKGYISSDDQVKMVKTCRELGIGDGGFYQPGYSDGAKLHLKMM...

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_032505`
TK1151 ID	TkA08G182140
OH-1004 ID	LXL04_032505
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
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_032505

Location Chr07:24194775-24196431 (-)

Description Similar to abh1: Alpha-ketoglutarate-dependent dioxygenase abh1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14160`	Dioxygenase that catalyzes DNA N(6)-methyladenine (6 mA) demethylation with a low efficiency.	Identification of AtALKBH1A and AtALKBH1D as DNA N 6 -adenine demethylases in Arabidopsis thaliana.2024 · DOI: 10.1016/j.plantsci.2024.112055
`At5g01780`	Dioxygenase that catalyzes DNA N(6)-methyladenine (6 mA) demethylation to modulate gene expression and regulate seed germination.	Identification of AtALKBH1A and AtALKBH1D as DNA N 6 -adenine demethylases in Arabidopsis thaliana.2024 · DOI: 10.1016/j.plantsci.2024.112055
`At3g14140`	Dioxygenase that may catalyze DNA N(6)-methyladenine (6 mA) demethylation (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_032505 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006307 DNA alkylation repair Biological Process

GO:0009845 seed germination Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0035513 oxidative RNA demethylation Biological Process

GO:0042245 RNA repair Biological Process

GO:0070989 oxidative demethylation Biological Process

GO:0072702 response to methyl methanesulfonate Biological Process

GO:1990983 regulation of translational initiation by tRNA modification Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT3G14140

ath:AT3G14160

ath:AT5G01780

ecj:JW2200

eco:b2212

ecoc:C3026_12360

spo:2539935

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.

Nucleus0.674

Rank 1 · LXL04_032505 · OH-1004

Cytoplasm0.276

Rank 2 · LXL04_032505 · OH-1004

Cell membrane0.063

Rank 3 · LXL04_032505 · OH-1004

Endoplasmic reticulum0.044

Rank 4 · LXL04_032505 · OH-1004

Mitochondrion0.038

Rank 5 · LXL04_032505 · 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.

PF13532.132OG-FeII_Oxy_2214-426 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032505	`PF13532.13`	2OG-FeII_Oxy_2	214	426	1.5e-45	156.5

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
`Q9LJH2`	Arabidopsis thaliana	DNA N(6)-methyladenine demethylase ALKBH1C	57.040%	Swiss-Prot	moderate database homology
`F4KAV2`	Arabidopsis thaliana	DNA N(6)-methyladenine demethylase ALKBH1D	54.167%	Swiss-Prot	moderate database homology
`F4JFR7`	Arabidopsis thaliana	Probable DNA N(6)-methyladenine demethylase ALKBH1B	51.163%	Swiss-Prot	moderate database homology

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