LXL04_013943 | RubberDandelionOmics

Gene overview

LXL04_013943

Reference: OH-1004 Chr: Chr03 Coordinates: 38823349-38824973 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

564 bp · LXL04_013943|LXL04_013943|OH1004|cDNA

ATGCTcgtcaagTTCGCTGATTGTTTGCTTCGACATTGTTATACTCTCCGTTCTTTTACGAGTTCCTATAGTTTTTCTGTTGTTGATATTCAGAAAAAAACATCATCGTCATCGAGAACGATGGCGTTTCAAAGAGGTGACCGAGTCGAAATTTCAAGCAAAGACCAGGGTTTCGAGGGTTCATACTACCTAGCAAACATCATTGCTTGCCTTTCCAAGAAAGAGTACATTATCCAGTATAGAACTCTGTTAAACGACGA...

CDS

Download CDS FASTA

564 bp · LXL04_013943|LXL04_013943|OH1004|CDS

ATGCTCGTCAAGTTCGCTGATTGTTTGCTTCGACATTGTTATACTCTCCGTTCTTTTACGAGTTCCTATAGTTTTTCTGTTGTTGATATTCAGAAAAAAACATCATCGTCATCGAGAACGATGGCGTTTCAAAGAGGTGACCGAGTCGAAATTTCAAGCAAAGACCAGGGTTTCGAGGGTTCATACTACCTAGCAAACATCATTGCTTGCCTTTCCAAGAAAGAGTACATTATCCAGTATAGAACTCTGTTAAACGACGA...

Protein

Download Protein FASTA

187 aa · LXL04_013943|LXL04_013943|OH1004|PROTEIN

MLVKFADCLLRHCYTLRSFTSSYSFSVVDIQKKTSSSSRTMAFQRGDRVEISSKDQGFEGSYYLANIIACLSKKEYIIQYRTLLNDDGFGPVREIVPADQIQPVPPEVPASGYSRGDVVDAYEKDGWWIGKISGKIGSNYVVYFKNTNEEIAYPSGLLRIHQDWINGAWVNVKREGKCSSAKGKERA

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_013943`
TK1151 ID	TkA02G461510
OH-1004 ID	LXL04_013943
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.100
Protein coverage (%)	TK1151 98.305 / OH-1004 61.497 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013943

Location Chr03:38823349-38824973 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At1g26540`	May be involved in the polar growth of plant cells via transportation of RNAs.	Characterization of DUF724 gene family in Arabidopsis thaliana.2010 · DOI: 10.1007/s11103-009-9551-5
`At2g47230`	May be involved in the polar growth of plant cells via transportation of RNAs.	No verified direct reference in this release
`At1g11420`	May be involved in the polar growth of plant cells via transportation of RNAs.	No verified direct reference in this release
`At1g03300`	May be involved in the polar growth of plant cells via transportation of RNAs.	Characterization of DUF724 gene family in Arabidopsis thaliana.2010 · DOI: 10.1007/s11103-009-9551-5

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013943 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0000325 plant-type vacuole Cellular Component

GO:0000775 chromosome, centromeric region Cellular Component

GO:0000792 heterochromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0042393 histone binding Molecular Function

GO:0042803 protein homodimerization activity Molecular Function

GO:0140566 histone reader activity Molecular Function

KEGG gene cross-reference

ath:AT1G09320

ath:AT1G26540

ath:AT2G47230

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.

Nucleus0.803

Rank 1 · LXL04_013943 · OH-1004

Cytoplasm0.233

Rank 2 · LXL04_013943 · OH-1004

Cell membrane0.054

Rank 3 · LXL04_013943 · OH-1004

Endoplasmic reticulum0.048

Rank 4 · LXL04_013943 · OH-1004

Plastid0.018

Rank 5 · LXL04_013943 · 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.

PF05641.19Agenet46-106 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013943	`PF05641.19`	Agenet	46	106	6.4e-22	78.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q500V5`	Arabidopsis thaliana	Protein AGENET DOMAIN (AGD)-CONTAINING P1	37.589%	Swiss-Prot	moderate database homology
`Q9FZD9`	Arabidopsis thaliana	DUF724 domain-containing protein 3	34.722%	Swiss-Prot	moderate database homology
`O22897`	Arabidopsis thaliana	DUF724 domain-containing protein 6	34.074%	Swiss-Prot	moderate database homology
`F4I8W1`	Arabidopsis thaliana	DUF724 domain-containing protein 2	33.083%	Swiss-Prot	moderate database homology
`Q9ZVT1`	Arabidopsis thaliana	DUF724 domain-containing protein 1	29.286%	Swiss-Prot	weak database homology

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