LXL04_030719 | RubberDandelionOmics

Gene overview

LXL04_030719

Reference: OH-1004 Chr: Chr06 Coordinates: 121354474-121357666 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2826 bp · LXL04_030719|LXL04_030719|OH1004|cDNA

ATGTATGCAGTTTTCAGCTGTGAAGTCGATGCAGAAAACTGTGACACGAATTTGTTGAATGTTATGTACATGGAAACCCCAAACCCCGAAGAAACCCTAATTGAGGGTTTAGCGACATCTAAACAAGGTGGAAATGCGAATCTATTGGAAGAAAAAGCTAATTCGTTTGATTTGGGGGAAGATAACTCCGCTAAACCTCACTCACCACCAGTTTCGGAAAATGTTGATTTGAGCAGCCATGCAGATGTTCATATGAAAGG...

CDS

Download CDS FASTA

2826 bp · LXL04_030719|LXL04_030719|OH1004|CDS

ATGTATGCAGTTTTCAGCTGTGAAGTCGATGCAGAAAACTGTGACACGAATTTGTTGAATGTTATGTACATGGAAACCCCAAACCCCGAAGAAACCCTAATTGAGGGTTTAGCGACATCTAAACAAGGTGGAAATGCGAATCTATTGGAAGAAAAAGCTAATTCGTTTGATTTGGGGGAAGATAACTCCGCTAAACCTCACTCACCACCAGTTTCGGAAAATGTTGATTTGAGCAGCCATGCAGATGTTCATATGAAAGG...

Protein

Download Protein FASTA

941 aa · LXL04_030719|LXL04_030719|OH1004|PROTEIN

MYAVFSCEVDAENCDTNLLNVMYMETPNPEETLIEGLATSKQGGNANLLEEKANSFDLGEDNSAKPHSPPVSENVDLSSHADVHMKGISLFVELTGDLEHGSSKGNNQSEIVDAYKHCGVNVGDLVWAMIRKQTWWPGIVCEASSVQIRENGILVRCFGNGNYIWCHPDELKTFIQHFEQLLSLSSNQRRSKMFFSAIDEALSEVGNRVKKEFTCSCFSKVVEKRVDNHDISLTRFDPATFFDYVKDLARDVSSVNKIDY...

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_030719`
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_030719

Location Chr06:121354474-121357666 (-)

Description Similar to ATM: Serine/threonine-protein kinase ATM

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48190`	Serine/threonine protein kinase which activates checkpoint signaling upon genotoxic stresses such as ionizing radiation (IR) or DNA replication stalling.	No verified direct reference in this release
`At3g09670`	Together with PDP1, PDP3 and PDP6, interacts with MSI4/FVE and MSI5 to suppress FLC, MAF4 and MAF5 expression by regulating the function of the PRC2 complex and modulating H3K27me3 level, thereby promoting flowering.	No verified direct reference in this release
`At5g40340`	Together with PDP1, PDP2 and PDP6, interacts with MSI4/FVE and MSI5 to suppress FLC, MAF4 and MAF5 expression by regulating the function of the PRC2 complex and modulating H3K27me3 level, thereby promoting flowering.	Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time.2018 · DOI: 10.1111/jipb.12630
`At5g02950`	May influence gene expression by regulating the function of the PRC2 complex and modulating H3K27me3 level.	No verified direct reference in this release
`At3g27860`	May influence gene expression by regulating the function of the PRC2 complex and modulating H3K27me3 level.	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_030719 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006303 double-strand break repair via nonhomologous end joining Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007129 homologous chromosome pairing at meiosis Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009908 flower development Biological Process

GO:0010212 response to ionizing radiation Biological Process

GO:0010332 response to gamma radiation Biological Process

GO:0032204 regulation of telomere maintenance Biological Process

GO:0033044 regulation of chromosome organization Biological Process

KEGG gene cross-reference

ath:AT3G09670

ath:AT5G40340

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.

Nucleus0.972

Rank 1 · LXL04_030719 · OH-1004

Cytoplasm0.075

Rank 2 · LXL04_030719 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_030719 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_030719 · OH-1004

Plastid0.011

Rank 5 · LXL04_030719 · 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.

PF00855.24PWWP123-204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030719	`PF00855.24`	PWWP	123	204	2.8e-13	50.9

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
`Q9M3G7`	Arabidopsis thaliana	Serine/threonine-protein kinase ATM	38.265%	Swiss-Prot	weak database homology
`Q9SF36`	Arabidopsis thaliana	PWWP domain-containing protein 2	29.798%	Swiss-Prot	weak database homology
`Q9FNE4`	Arabidopsis thaliana	PWWP domain-containing protein 3	30.000%	Swiss-Prot	weak database homology
`Q9LYZ0`	Arabidopsis thaliana	PWWP domain-containing protein 5	30.508%	Swiss-Prot	weak database homology
`Q9LK91`	Arabidopsis thaliana	PWWP domain-containing protein 6	29.583%	Swiss-Prot	weak database homology

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