LXL04_005576 | RubberDandelionOmics

Gene overview

LXL04_005576

Reference: OH-1004 Chr: Chr01 Coordinates: 168618493-168621187 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1806 bp · LXL04_005576|LXL04_005576|OH1004|cDNA

ATGCGCAACCGGAGGTACTTAGCCTCCAGCGACGACGAGGAAGACGACGCGCCTCCGCAGCCAACACCGGAAATGAGGTCTAGTCAGCGGAAGAGAAAGAGGATGAAATTTTACGAAGACGATGacgaagaagaaggagaagaagaagcaATTAAACAAGTAGCTAAAATGAAACGGGACAATAAAAAATCCAAGGGCGATGAAGAGGAAGAGAAAGAAGCTTCGCCGCCGCCTGAGgacgaggaagaagaagaagaaga...

CDS

Download CDS FASTA

1806 bp · LXL04_005576|LXL04_005576|OH1004|CDS

ATGCGCAACCGGAGGTACTTAGCCTCCAGCGACGACGAGGAAGACGACGCGCCTCCGCAGCCAACACCGGAAATGAGGTCTAGTCAGCGGAAGAGAAAGAGGATGAAATTTTACGAAGACGATGACGAAGAAGAAGGAGAAGAAGAAGCAATTAAACAAGTAGCTAAAATGAAACGGGACAATAAAAAATCCAAGGGCGATGAAGAGGAAGAGAAAGAAGCTTCGCCGCCGCCTGAGGACGAGGAAGAAGAAGAAGAAGA...

Protein

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601 aa · LXL04_005576|LXL04_005576|OH1004|PROTEIN

MRNRRYLASSDDEEDDAPPQPTPEMRSSQRKRKRMKFYEDDDEEEGEEEAIKQVAKMKRDNKKSKGDEEEEKEASPPPEDEEEEEEEAPVEDAKPIGEVVRVSGKGKTRRNHYKSFEFDGLSYELEDPVLLVPDPEGPNKKPYVAIIKDVTETKDGSVMVTGQWFYRPEEAEKKNGGNWQSSDTRELFYSFHRDEVPAESVMHKCVVHFIPAHKQIPSRKLHPGFIVQKVYDTIFKRLFKLTDKDYEDNMQHEIDLLVQK...

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_005576`
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_005576

Location Chr01:168618493-168621187 (+)

Description Similar to EBS: Chromatin remodeling protein EBS

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g11560`	Transcriptional repressor.	A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis .2017 · DOI: 10.1073/pnas.1710683114 Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis.2020 · DOI: 10.1038/s41467-020-20089-0 A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis.2021 · DOI: 10.1111/jipb.13067
`At4g22140`	Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulating the transcription of target genes.	No verified direct reference in this release
`At4g04260`	Chromatin remodeling factor that binds to methylated histone (e.g. H3K4me2/3) to prevent their acetylation (e.g. H3K9K14Ac), likely by recruiting histone deacetylase (HDAC) complexes, and thus regulate the transcription of target genes.	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_005576 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0009791 post-embryonic development Biological Process

GO:0009845 seed germination Biological Process

GO:0009908 flower development Biological Process

GO:0010220 positive regulation of vernalization response Biological Process

GO:0034244 negative regulation of transcription elongation by RNA polymerase II Biological Process

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

GO:0048579 negative regulation of long-day photoperiodism, flowering Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0001217 DNA-binding transcription repressor activity Molecular Function

KEGG gene cross-reference

ath:AT4G04260

ath:AT4G22140

bdi:100843157

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.

Nucleus0.965

Rank 1 · LXL04_005576 · OH-1004

Cytoplasm0.079

Rank 2 · LXL04_005576 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_005576 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_005576 · OH-1004

Plastid0.012

Rank 5 · LXL04_005576 · 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.

PF01426.25BAH122-241 aa

PF07500.20TFIIS_M345-467 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005576	`PF01426.25`	BAH	122	241	3.2e-19	69.7
LXL04_005576	`PF07500.20`	TFIIS_M	345	467	1.3e-16	61.8

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
`Q8RXT5`	Arabidopsis thaliana	ASI1-immunoprecipitated protein 3	52.991%	Swiss-Prot	strong database homology
`F4JL28`	Arabidopsis thaliana	Chromatin remodeling protein EBS	35.780%	Swiss-Prot	weak database homology
`F4JGB7`	Arabidopsis thaliana	Chromatin remodeling protein At4g04260	36.047%	Swiss-Prot	weak database homology

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