LXL04_039589 | RubberDandelionOmics

Gene overview

LXL04_039589

Reference: OH-1004 Chr: JAJTUU010000015.1 Coordinates: 541553-557618 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3848 bp · LXL04_039589|LXL04_039589|OH1004|cDNA

ATGGACAAGTCTTGGATGGGATCACAAAGAAATAGACAACCTTATATGAGGGGAGTTGAAGAATTTTTGGAATATGCGGTTTCAAATTTCAAGCTTTCTAACAACATCGATCCTCTAGAAATTCCATGTCCATGTATCAAGTGTGTGAACCACTTACCTCATTCGGTGCAATTGGTACGTGATCACTTAATCACACATGGAATTAATGAAACCTACACGAACTGGACATATCATGGAGAACAATACGATCCACCATTACC...

CDS

Download CDS FASTA

3624 bp · LXL04_039589|LXL04_039589|OH1004|CDS

ATGGACAAGTCTTGGATGGGATCACAAAGAAATAGACAACCTTATATGAGGGGAGTTGAAGAATTTTTGGAATATGCGGTTTCAAATTTCAAGCTTTCTAACAACATCGATCCTCTAGAAATTCCATGTCCATGTATCAAGTGTGTGAACCACTTACCTCATTCGGTGCAATTGGTACGTGATCACTTAATCACACATGGAATTAATGAAACCTACACGAACTGGACATATCATGGAGAACAATACGATCCACCATTACC...

Protein

Download Protein FASTA

1207 aa · LXL04_039589|LXL04_039589|OH1004|PROTEIN

MDKSWMGSQRNRQPYMRGVEEFLEYAVSNFKLSNNIDPLEIPCPCIKCVNHLPHSVQLVRDHLITHGINETYTNWTYHGEQYDPPLPYIVDDDFDMDTSYVVDSMDDTTEKPTDAAENEELVQAAEELFMDDPTKFREMLEDAEKPLYEGCPNFTKLSAIIQLLNLKKGNEMYSGTYEAKKAFKQLGSGYEKIHACVNRCILYRNEYENLTECPNCGKSRWKVDEQKNKIYENVPANVMWYFPIIPRMKRLKVEPGVMRH...

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_039589`
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_039589

Location JAJTUU010000015.1:541553-557618 (-)

Description Similar to AGDP1: Protein AGENET DOMAIN (AGD)-CONTAINING P1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g09320`	Heterochromatin-binding protein that preferentially occupies long transposons and specifically recognizes the histone H3 'Lys-9' methylation (H3K9me) marks, with a stronger affinity for dimethylated H3K9 (H3K9me2).	Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.2018 · DOI: 10.1038/s41467-018-06965-w Plant HP1 protein ADCP1 links multivalent H3K9 methylation readout to heterochromatin formation.2019 · DOI: 10.1038/s41422-018-0104-9

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039589 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0000775 chromosome, centromeric region Cellular Component

GO:0000792 heterochromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0042393 histone binding Molecular Function

GO:0140566 histone reader activity Molecular Function

KEGG gene cross-reference

ath:AT1G09320

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.

Nucleus0.787

Rank 1 · LXL04_039589 · OH-1004

Cytoplasm0.263

Rank 2 · LXL04_039589 · OH-1004

Extracellular0.032

Rank 3 · LXL04_039589 · OH-1004

Cell membrane0.030

Rank 4 · LXL04_039589 · OH-1004

Endoplasmic reticulum0.030

Rank 5 · LXL04_039589 · 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.

PF13963.12Transpos_assoc3-80 aa

PF02992.21Transposase_21256-460 aa

PF13952.12DUF4216759-821 aa

PF05641.19Agenet965-1026 aa

PF05641.19Agenet1108-1165 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039589	`PF13963.12`	Transpos_assoc	3	80	2.2e-18	66.9
LXL04_039589	`PF02992.21`	Transposase_21	256	460	8.7e-78	261.1
LXL04_039589	`PF13952.12`	DUF4216	759	821	3.8e-20	72.9
LXL04_039589	`PF05641.19`	Agenet	965	1026	7.3e-17	62.3
LXL04_039589	`PF05641.19`	Agenet	1108	1165	7.3e-17	62.3

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
`Q500V5`	Arabidopsis thaliana	Protein AGENET DOMAIN (AGD)-CONTAINING P1	25.185%	Swiss-Prot	weak database homology

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