LXL04_038124 | RubberDandelionOmics

Gene overview

LXL04_038124

Reference: OH-1004 Chr: Chr09 Coordinates: 31865391-31866575 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

642 bp · LXL04_038124|LXL04_038124|OH1004|cDNA

ATGGCGAAGACAAAGCCTGGAAAGAAAGATTTAGATACTTACACTATCAAAGGAACCAACAAACTCGTTAGACCTGGAGACTGTGTGTTGATGAGGCCTGCTGATTCCGATAAGCCACCGTACGTAGCGCGTGTGGAGAAGCTGGAGGCTGATCACCGGAACAATGTGAAGGTGAGAGTTAGGTGGTATTACCGGCCAGAGGAGTCACTCGGAGGAAGACGCCAGTTTCACGGCGTTAAGGAGCTGTTTTTATCCGATCA...

CDS

Download CDS FASTA

642 bp · LXL04_038124|LXL04_038124|OH1004|CDS

ATGGCGAAGACAAAGCCTGGAAAGAAAGATTTAGATACTTACACTATCAAAGGAACCAACAAACTCGTTAGACCTGGAGACTGTGTGTTGATGAGGCCTGCTGATTCCGATAAGCCACCGTACGTAGCGCGTGTGGAGAAGCTGGAGGCTGATCACCGGAACAATGTGAAGGTGAGAGTTAGGTGGTATTACCGGCCAGAGGAGTCACTCGGAGGAAGACGCCAGTTTCACGGCGTTAAGGAGCTGTTTTTATCCGATCA...

Protein

Download Protein FASTA

213 aa · LXL04_038124|LXL04_038124|OH1004|PROTEIN

MAKTKPGKKDLDTYTIKGTNKLVRPGDCVLMRPADSDKPPYVARVEKLEADHRNNVKVRVRWYYRPEESLGGRRQFHGVKELFLSDHYDMQSAHTIEGKCIVHSFKNYTKLDNVGTEDYFCRFEYKAATGGFTPDRVAVYCKCEMPYNPDDLMVQCEGCKDWFHPSCMGMTIEEAKKLEQFLCSDCSSDDDTKGFPISQSTEAKMEVKRRKQR

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_038124`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_038124

Location Chr09:31865391-31866575 (+)

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
`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
`At4g39100`	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
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_038124 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

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:0010228 vegetative to reproductive phase transition of meristem 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:0003682 chromatin binding Molecular Function

KEGG gene cross-reference

ath:AT4G04260

ath:AT4G22140

ath:AT4G39100

hsa:57597

mmu:268515

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.919

Rank 1 · LXL04_038124 · OH-1004

Cytoplasm0.184

Rank 2 · LXL04_038124 · OH-1004

Cell membrane0.032

Rank 3 · LXL04_038124 · OH-1004

Endoplasmic reticulum0.023

Rank 4 · LXL04_038124 · OH-1004

Mitochondrion0.023

Rank 5 · LXL04_038124 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF01426.25BAH23-134 aa

PF30811.1PHD_UBR7-like139-188 aa

PF20826.3PHD_5139-186 aa

PF00628.36PHD141-186 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038124	`PF01426.25`	BAH	23	134	2.4e-25	89.5
LXL04_038124	`PF30811.1`	PHD_UBR7-like	139	188	3.2e-10	40.5
LXL04_038124	`PF20826.3`	PHD_5	139	186	9.8e-07	29.5
LXL04_038124	`PF00628.36`	PHD	141	186	2e-09	38.0

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
`F4JL28`	Arabidopsis thaliana	Chromatin remodeling protein EBS	75.799%	Swiss-Prot	strong database homology
`Q9FEN9`	Arabidopsis thaliana	Chromatin remodeling protein SHL	61.792%	Swiss-Prot	strong database homology
`F4JGB7`	Arabidopsis thaliana	Chromatin remodeling protein At4g04260	63.256%	Swiss-Prot	strong database homology

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