LXL04_023880 | RubberDandelionOmics

Gene overview

LXL04_023880

Reference: OH-1004 Chr: Chr05 Coordinates: 72152920-72156844 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1179 bp · LXL04_023880|LXL04_023880|OH1004|cDNA

atgtctaagtcaccatccccggTCAACTTGGCAATTTACCAGGTCAACTCGGACTCGGGTATCGGGTATCCATCCGACATGcgtatCGACGGAATCGGAAGAGAAGGGTTTCTGAGGGTTAAAGCCACCGACGCCGGTGCATCGACTACCAATGCCTTCACCACGTTCCATAGCTACTTACCGCCGGGATTGAACAGAGCTTCTACAATCTCGATTTACATACTAAACTTTGATTTCCTTCCGGCAAACACAGAGCTTCT...

CDS

Download CDS FASTA

1179 bp · LXL04_023880|LXL04_023880|OH1004|CDS

ATGTCTAAGTCACCATCCCCGGTCAACTTGGCAATTTACCAGGTCAACTCGGACTCGGGTATCGGGTATCCATCCGACATGCGTATCGACGGAATCGGAAGAGAAGGGTTTCTGAGGGTTAAAGCCACCGACGCCGGTGCATCGACTACCAATGCCTTCACCACGTTCCATAGCTACTTACCGCCGGGATTGAACAGAGCTTCTACAATCTCGATTTACATACTAAACTTTGATTTCCTTCCGGCAAACACAGAGCTTCT...

Protein

Download Protein FASTA

392 aa · LXL04_023880|LXL04_023880|OH1004|PROTEIN

MSKSPSPVNLAIYQVNSDSGIGYPSDMRIDGIGREGFLRVKATDAGASTTNAFTTFHSYLPPGLNRASTISIYILNFDFLPANTELLQSFQTSVVLPYSLNLSSNRVLWILVLRPILQLRFVVDDYFVMAVEIGDFIEVIGHEPGYEHAYFEGEVIGEYDGILRIQYEHLVVEKDGPNLVEMIHPDHVRPRPPYIDKDVESFQEGDIVDVLWKDGWWQGIMHAVFENMNNEMRYEVFFDYMPKYKKYDVFQPRDVRSHQD...

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_023880`
TK1151 ID	TkA02G153380
OH-1004 ID	LXL04_023880
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
Protein identity (%)	64.000
Protein coverage (%)	TK1151 95.506 / OH-1004 54.592 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_023880

Location Chr05:72152920-72156844 (-)

Description Similar to DUF6: DUF724 domain-containing protein 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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_023880 · 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.

Nucleus0.580

Rank 1 · LXL04_023880 · OH-1004

Cytoplasm0.385

Rank 2 · LXL04_023880 · OH-1004

Endoplasmic reticulum0.078

Rank 3 · LXL04_023880 · OH-1004

Cell membrane0.076

Rank 4 · LXL04_023880 · OH-1004

Mitochondrion0.033

Rank 5 · LXL04_023880 · 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.

PF05641.19Agenet134-193 aa

PF13963.12Transpos_assoc301-364 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023880	`PF05641.19`	Agenet	134	193	1.8e-09	38.6
LXL04_023880	`PF13963.12`	Transpos_assoc	301	364	1.7e-06	28.8

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
`Q9FZD9`	Arabidopsis thaliana	DUF724 domain-containing protein 3	34.091%	Swiss-Prot	weak database homology
`O22897`	Arabidopsis thaliana	DUF724 domain-containing protein 6	30.075%	Swiss-Prot	weak database homology
`Q500V5`	Arabidopsis thaliana	Protein AGENET DOMAIN (AGD)-CONTAINING P1	31.852%	Swiss-Prot	weak database homology

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