LXL04_032669 | RubberDandelionOmics

Gene overview

LXL04_032669

Reference: OH-1004 Chr: Chr07 Coordinates: 27533610-27536159 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2244 bp · LXL04_032669|LXL04_032669|OH1004|cDNA

ATGAACGTAGACAAATCTTTTTCGAATCTTACAATGTCAGAGAAAAGAAAAAGGCTTATGGCTTTGGTGGATATGAGGAAAAGTATGAAGAGAAAAAGGTATGAAATACACTCCATGATTCAAACAGGAGAGTCTGTAATTATCAAAAAGCCCAAGGTGAAGAAGAAGCCCATCAATGAAAGCActaaaatgaacaaatttaacgCACACACATTCAAAAAATTATTCCAAAATAAAGGGCCAAAGGTGAAGAAGCTATC...

CDS

Download CDS FASTA

2244 bp · LXL04_032669|LXL04_032669|OH1004|CDS

ATGAACGTAGACAAATCTTTTTCGAATCTTACAATGTCAGAGAAAAGAAAAAGGCTTATGGCTTTGGTGGATATGAGGAAAAGTATGAAGAGAAAAAGGTATGAAATACACTCCATGATTCAAACAGGAGAGTCTGTAATTATCAAAAAGCCCAAGGTGAAGAAGAAGCCCATCAATGAAAGCACTAAAATGAACAAATTTAACGCACACACATTCAAAAAATTATTCCAAAATAAAGGGCCAAAGGTGAAGAAGCTATC...

Protein

Download Protein FASTA

747 aa · LXL04_032669|LXL04_032669|OH1004|PROTEIN

MNVDKSFSNLTMSEKRKRLMALVDMRKSMKRKRYEIHSMIQTGESVIIKKPKVKKKPINESTKMNKFNAHTFKKLFQNKGPKVKKLSHIDTASDPSNDSSEIEEYWVPVHLSHMQIETYCSLLNSNLEALSSSLRDDSSLSDILTQTQKCCDHPYLVDPTLRESLKTDVGDDRLDAEISVSGKLQLLDKLLLEIKKCGLRVLVLFQSPVTWKTISLGDILDDLVDKRFGHDSYIRIHGKIISNQDRENRKRNLKMFNNLE...

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_032669`
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_032669

Location Chr07:27533610-27536159 (+)

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_032669 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II 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:0007051 spindle organization Biological Process

GO:0007098 centrosome cycle Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0042659 regulation of cell fate specification Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

KEGG gene cross-reference

ath:AT1G08060

ath:AT5G44800

hsa:1107

hsa:6594

mmu:93761

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.

Nucleus0.928

Rank 1 · LXL04_032669 · OH-1004

Cytoplasm0.144

Rank 2 · LXL04_032669 · OH-1004

Cell membrane0.025

Rank 3 · LXL04_032669 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_032669 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_032669 · 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.

PF11496.15HDA2-3103-333 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032669	`PF11496.15`	HDA2-3	103	333	6.7e-07	29.5

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
`Q9M658`	Arabidopsis thaliana	Helicase protein MOM1	36.790%	Swiss-Prot	moderate database homology
`F4KBP5`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 4	30.743%	Swiss-Prot	weak database homology

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