LXL04_003588 | RubberDandelionOmics

Gene overview

LXL04_003588

Reference: OH-1004 Chr: Chr01 Coordinates: 86847925-86853658 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4344 bp · LXL04_003588|LXL04_003588|OH1004|cDNA

ATGGAGTTTGTGGGGAGAACAGTGAGGAAAGAATTTAAAGGATTTGGGGTTTTCTCCGGAGTCGTGAAATCATACGATTCCTCATCTGGTTTCTTCGAGATCGGCTACGAAGATGGCGATTCTGAAGAAATTGATTTCTCCGAGTTGGCTGCTCTTTTGGAACTAGATGGAGTTATTATGGAGCATTCCCCATCTCTGCTGGCTAAGCAATCGTCCAGGGTTGGGAAAAGACCTAAAAAGAGGCGTAGGGTTCTTTGCTC...

CDS

Download CDS FASTA

4344 bp · LXL04_003588|LXL04_003588|OH1004|CDS

ATGGAGTTTGTGGGGAGAACAGTGAGGAAAGAATTTAAAGGATTTGGGGTTTTCTCCGGAGTCGTGAAATCATACGATTCCTCATCTGGTTTCTTCGAGATCGGCTACGAAGATGGCGATTCTGAAGAAATTGATTTCTCCGAGTTGGCTGCTCTTTTGGAACTAGATGGAGTTATTATGGAGCATTCCCCATCTCTGCTGGCTAAGCAATCGTCCAGGGTTGGGAAAAGACCTAAAAAGAGGCGTAGGGTTCTTTGCTC...

Protein

Download Protein FASTA

1447 aa · LXL04_003588|LXL04_003588|OH1004|PROTEIN

MEFVGRTVRKEFKGFGVFSGVVKSYDSSSGFFEIGYEDGDSEEIDFSELAALLELDGVIMEHSPSLLAKQSSRVGKRPKKRRRVLCSSISGNENEFSSSLGNAAVVDDSNLDSVEGELVSEVNIVNNVTKKLGISSNDNNDVGSNCENLTFKDVGLNVNSRVHDLDQNGKGNADEIKLNSDLDDENDPESKLKDLVDDSVKKEQILDLNMDLDYSQNKNQDIDLGGYVKGENSGGNETMNTSSTDVSLDLDPHGNLGSGK...

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_003588`
TK1151 ID	TkA01G332340
OH-1004 ID	LXL04_003588
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_003588

Location Chr01:86847925-86853658 (+)

Description Similar to PTM: DDT domain-containing protein PTM

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g35210`	Membrane-bound transcription factor required for the plastid-to-nucleus retrograde signaling.	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_003588 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006325 chromatin organization 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:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006508 proteolysis Biological Process

GO:0010019 chloroplast-nucleus signaling pathway Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0034728 nucleosome organization Biological Process

GO:0045824 negative regulation of innate immune response Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT5G35210

cel:CELE_F26H11.2

dme:Dmel_CG32346

hsa:2186

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.

Nucleus0.970

Rank 1 · LXL04_003588 · OH-1004

Cytoplasm0.077

Rank 2 · LXL04_003588 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_003588 · OH-1004

Endoplasmic reticulum0.013

Rank 4 · LXL04_003588 · OH-1004

Plastid0.012

Rank 5 · LXL04_003588 · 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.

PF21743.4PTM_DIR17_Tudor5-53 aa

PF02791.23DDT359-413 aa

PF00628.36PHD546-587 aa

PF24294.3Chromo_PTM1033-1116 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003588	`PF21743.4`	PTM_DIR17_Tudor	5	53	5.6e-16	58.8
LXL04_003588	`PF02791.23`	DDT	359	413	7.1e-16	58.8
LXL04_003588	`PF00628.36`	PHD	546	587	2.5e-09	37.7
LXL04_003588	`PF24294.3`	Chromo_PTM	1033	1116	2e-26	92.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4JYC8`	Arabidopsis thaliana	DDT domain-containing protein PTM	27.349%	Swiss-Prot	weak database homology

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