LXL04_001744 | RubberDandelionOmics

Gene overview

LXL04_001744

Reference: OH-1004 Chr: Chr01 Coordinates: 32280071-32281166 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

651 bp · LXL04_001744|LXL04_001744|OH1004|cDNA

ATGGCAAAAACCCGCACCACAAGAAAAACCCTAGATTCTTACACCGTCAAAGGCTCAAATAAATCCATCAAACCCGGCGATTGCGTGTTGATGCGTCCGGCCGATTCATCGAAGCCATCGTATGTAGCGAAAGTGGAGAAGCTGGAATCGGACGCCAAAGGAAGTAACGTGAAAGTTCATATACAGTGGTACTACCGCCCGGAGGAATCGATCGGTGGCCGGAGACAGTTTCACGGCATTAAAGAGGTTTTCCTCTCCGA...

CDS

Download CDS FASTA

651 bp · LXL04_001744|LXL04_001744|OH1004|CDS

ATGGCAAAAACCCGCACCACAAGAAAAACCCTAGATTCTTACACCGTCAAAGGCTCAAATAAATCCATCAAACCCGGCGATTGCGTGTTGATGCGTCCGGCCGATTCATCGAAGCCATCGTATGTAGCGAAAGTGGAGAAGCTGGAATCGGACGCCAAAGGAAGTAACGTGAAAGTTCATATACAGTGGTACTACCGCCCGGAGGAATCGATCGGTGGCCGGAGACAGTTTCACGGCATTAAAGAGGTTTTCCTCTCCGA...

Protein

Download Protein FASTA

216 aa · LXL04_001744|LXL04_001744|OH1004|PROTEIN

MAKTRTTRKTLDSYTVKGSNKSIKPGDCVLMRPADSSKPSYVAKVEKLESDAKGSNVKVHIQWYYRPEESIGGRRQFHGIKEVFLSDHHDVQSADTIEGKCTVHTFKSYTKLDAVGNEDYFCRFEYNSSTGAFNPDRVAVYCKCEMPYNPDDLMVQCDACTDWFHPACIDMTPEDAKKIEHFFCLNCSSEEQKLLQNSHATSRHTDVKVTTKRRRR

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_001744`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_001744

Location Chr01:32280071-32281166 (+)

Description Similar to EBS: Chromatin remodeling protein EBS

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_001744 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006482 protein demethylation 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:0010628 positive regulation of gene expression Biological Process

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

GO:0045815 transcription initiation-coupled chromatin remodeling Biological Process

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

KEGG gene cross-reference

ath:AT4G04260

ath:AT4G22140

ath:AT4G39100

dre:503778

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.

Nucleus0.917

Rank 1 · LXL04_001744 · OH-1004

Cytoplasm0.176

Rank 2 · LXL04_001744 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_001744 · OH-1004

Mitochondrion0.021

Rank 4 · LXL04_001744 · OH-1004

Endoplasmic reticulum0.018

Rank 5 · LXL04_001744 · 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.

PF01426.25BAH23-135 aa

PF30811.1PHD_UBR7-like140-193 aa

PF00628.36PHD142-187 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001744	`PF01426.25`	BAH	23	135	2.6e-25	89.4
LXL04_001744	`PF30811.1`	PHD_UBR7-like	140	193	6.3e-10	39.6
LXL04_001744	`PF00628.36`	PHD	142	187	4.1e-08	33.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4JL28`	Arabidopsis thaliana	Chromatin remodeling protein EBS	68.900%	Swiss-Prot	strong database homology
`Q9FEN9`	Arabidopsis thaliana	Chromatin remodeling protein SHL	66.667%	Swiss-Prot	strong database homology
`F4JGB7`	Arabidopsis thaliana	Chromatin remodeling protein At4g04260	61.579%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card