LXL04_032672 | RubberDandelionOmics

Gene overview

LXL04_032672

Reference: OH-1004 Chr: Chr07 Coordinates: 27554195-27559258 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3054 bp · LXL04_032672|LXL04_032672|OH1004|cDNA

ATGTTTTACTGTGTTTTACTGTTCATGATTCTCTCTCAGAACTTCTTTTCGGACGGAAAATACTTCGCAAATGATTTAGTCGCCAATGTTGAAGCAGATAACTGGAGAGCTTCGCATCATCGTTATCAAATTCTTTCATCTTCTGCGGTTGAAGATCTAACTGAGAAAAACAACAAACAGCAGTATAGAATTACAAAGATGAATGCAGATAGCTCAATTTCAGTTACTTCAATGTCAAAGAAAAGAGAGAGGCCTGAAAA...

CDS

Download CDS FASTA

3054 bp · LXL04_032672|LXL04_032672|OH1004|CDS

ATGTTTTACTGTGTTTTACTGTTCATGATTCTCTCTCAGAACTTCTTTTCGGACGGAAAATACTTCGCAAATGATTTAGTCGCCAATGTTGAAGCAGATAACTGGAGAGCTTCGCATCATCGTTATCAAATTCTTTCATCTTCTGCGGTTGAAGATCTAACTGAGAAAAACAACAAACAGCAGTATAGAATTACAAAGATGAATGCAGATAGCTCAATTTCAGTTACTTCAATGTCAAAGAAAAGAGAGAGGCCTGAAAA...

Protein

Download Protein FASTA

1017 aa · LXL04_032672|LXL04_032672|OH1004|PROTEIN

MFYCVLLFMILSQNFFSDGKYFANDLVANVEADNWRASHHRYQILSSSAVEDLTEKNNKQQYRITKMNADSSISVTSMSKKRERPEKGKKLNARAYKKLFQIAGQKMKEASQGGDLITTSVTSTEVNETETLVMKSCSDSKQERHRVTLESEEVFFSNPESANEHPQMDGSECVTMLKTGPTCSAELAESQFEVSIEVQHHVNKLRDYWNRGQNSVFFDGQDRIIKVVQFVLSLLDNVKQPILIITASRSLSLWESEFSK...

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_032672`
TK1151 ID	TkA08G195400
OH-1004 ID	LXL04_032672
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.100
Protein coverage (%)	TK1151 97.211 / OH-1004 94.100 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_032672

Location Chr07:27554195-27559258 (-)

Description Similar to MOM1: Helicase protein MOM1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08060`	Together with PIAL1 and PIAL2, regulates transcriptional gene silencing (TGS) independently of changes in DNA methylation.	Two regulatory levels of transcriptional gene silencing in Arabidopsis.2002 · DOI: 10.1073/pnas.202380499 Two means of transcriptional reactivation within heterochromatin.2003 · DOI: 10.1046/j.1365-313x.2003.01667.x Epigenetic regulation of transcription in intermediate heterochromatin.2006 · DOI: 10.1038/sj.embor.7400835 MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis.2006 · DOI: 10.1038/sj.embor.7400791 Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants.2008 · DOI: 10.1371/journal.pgen.1000165 MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing.2010 · DOI: 10.1038/emboj.2009.328 Locus-specific dependency of endogenous silent loci on MOM1 and non-CG methylation in Arabidopsis thaliana.2010 · DOI: 10.4161/psb.5.6.11663 MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis.2010 · DOI: 10.1104/pp.110.162131 Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing.2010 · DOI: 10.1111/j.1365-313x.2010.04358.x Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1.2012 · DOI: 10.1371/journal.pgen.1002484 The SUMO E3 Ligase-Like Proteins PIAL1 and PIAL2 Interact with MOM1 and Form a Novel Complex Required for Transcriptional Silencing.2016 · DOI: 10.1105/tpc.15.00997
`At5g44800`	Chromatin-remodeling protein that binds DNA through histones and regulates gene transcription.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032672 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0000729 DNA double-strand break processing Biological Process

GO:0001178 regulation of transcriptional start site selection at RNA polymerase II promoter Biological Process

GO:0006335 DNA replication-dependent chromatin assembly Biological Process

GO:0006337 nucleosome disassembly Biological Process

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:0006363 termination of RNA polymerase I transcription Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

KEGG gene cross-reference

ath:AT1G08060

ath:AT5G44800

hsa:1107

sce:YER164W

spo:2542363

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_032672 · OH-1004

Cytoplasm0.189

Rank 2 · LXL04_032672 · OH-1004

Cell membrane0.032

Rank 3 · LXL04_032672 · OH-1004

Mitochondrion0.031

Rank 4 · LXL04_032672 · OH-1004

Golgi apparatus0.016

Rank 5 · LXL04_032672 · 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.

PF00176.30SNF2-rel_dom231-349 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032672	`PF00176.30`	SNF2-rel_dom	231	349	7e-10	39.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9M658`	Arabidopsis thaliana	Helicase protein MOM1	36.436%	Swiss-Prot	weak database homology
`F4KBP5`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 4	27.002%	Swiss-Prot	weak database homology

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