LXL04_004702 | RubberDandelionOmics

Gene overview

LXL04_004702

Reference: OH-1004 Chr: Chr01 Coordinates: 143977289-143978936 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

423 bp · LXL04_004702|LXL04_004702|OH1004|cDNA

ATGAAAGCAAATGCATGGTATATCATTGTGCAGATGATGTTTCCTTACTTGCTGCTCTTATAGGGTTGGTAGAAAAATCTCACAATGCTGATCTTCATTGTGTTGATTGGAATCCGATTGATGAAAATTTCATTTTGACTGGAGAATGTGCAGAAAAACTCCAACTTCTGAGTACACTAGATGAACGGGAAAGCAGATTACAAGAAATCCCAGACGTCCATTCAGACCCTAAAATGAATCCACATTACGAATCAGATGAC...

CDS

Download CDS FASTA

258 bp · LXL04_004702|LXL04_004702|OH1004|CDS

ATGGTATATCATTGTGCAGATGATGTTTCCTTACTTGCTGCTCTTATAGGGTTGGTAGAAAAATCTCACAATGCTGATCTTCATTGTGTTGATTGGAATCCGATTGATGAAAATTTCATTTTGACTGGAGAATGTGCAGAAAAACTCCAACTTCTGAGTACACTAGATGAACGGGAAAGCAGATTACAAGAAATCCCAGACGTCCATTCAGACCCTAAAATGAATCCACATTACGAATCAGATGACACCGAGGAGTAG

Protein

Download Protein FASTA

85 aa · LXL04_004702|LXL04_004702|OH1004|PROTEIN

MVYHCADDVSLLAALIGLVEKSHNADLHCVDWNPIDENFILTGECAEKLQLLSTLDERESRLQEIPDVHSDPKMNPHYESDDTEE

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_004702`
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_004702

Location Chr01:143977289-143978936 (+)

Description Similar to NERD: Zinc finger CCCH domain-containing protein 19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q9SIV5`	Plays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences.	No verified direct reference in this release
`At2g19520`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	Regulation of flowering time by FVE, a retinoblastoma-associated protein.2004 · DOI: 10.1038/ng1295 A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana.2004 · DOI: 10.1038/ng1298
`At4g29730`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA (By similarity).	Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time.2018 · DOI: 10.1111/jipb.12630

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004702 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair 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:0009627 systemic acquired resistance Biological Process

GO:0009908 flower development Biological Process

GO:0010224 response to UV-B Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0030154 cell differentiation Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

KEGG gene cross-reference

ath:AT2G16485

ath:AT2G19520

ath:AT4G29730

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.

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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.

Nucleus0.569

Rank 1 · LXL04_004702 · OH-1004

Cytoplasm0.393

Rank 2 · LXL04_004702 · OH-1004

Mitochondrion0.073

Rank 3 · LXL04_004702 · OH-1004

Cell membrane0.055

Rank 4 · LXL04_004702 · OH-1004

Endoplasmic reticulum0.038

Rank 5 · LXL04_004702 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

No result was found for this query.

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
`Q9SIV5`	Arabidopsis thaliana	Zinc finger CCCH domain-containing protein 19	62.162%	Swiss-Prot	weak database homology
`O22607`	Arabidopsis thaliana	WD-40 repeat-containing protein MSI4	61.765%	Swiss-Prot	weak database homology
`Q9SU78`	Arabidopsis thaliana	WD-40 repeat-containing protein MSI5	80.000%	Swiss-Prot	weak database homology

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