LXL04_024817 | RubberDandelionOmics

Gene overview

LXL04_024817

Reference: OH-1004 Chr: Chr05 Coordinates: 99486550-99489176 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1035 bp · LXL04_024817|LXL04_024817|OH1004|cDNA

TTGGTGATCGCCGACGAATCAAGGAAAGCGATAACTGAGATGCAAGGAGGAGAAAAAGAAGCTCAACGATACGTGTGGGACGGTGCAATTCCGCTGCAAGTTCATCTTCACGACTCCGAAGTCACCACTCTACCGCCGCCTCCGCCTGCTCTGATCCTAGCTCCACGAATAGGATACCTACCTCTGTTATCTTCACAACTCAAGCCGTTCTTTAGTGGTGCACTTCCTCCTGGAGTAGACACTGTCTGGTTTGAGTACAA...

CDS

Download CDS FASTA

1035 bp · LXL04_024817|LXL04_024817|OH1004|CDS

TTGGTGATCGCCGACGAATCAAGGAAAGCGATAACTGAGATGCAAGGAGGAGAAAAAGAAGCTCAACGATACGTGTGGGACGGTGCAATTCCGCTGCAAGTTCATCTTCACGACTCCGAAGTCACCACTCTACCGCCGCCTCCGCCTGCTCTGATCCTAGCTCCACGAATAGGATACCTACCTCTGTTATCTTCACAACTCAAGCCGTTCTTTAGTGGTGCACTTCCTCCTGGAGTAGACACTGTCTGGTTTGAGTACAA...

Protein

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344 aa · LXL04_024817|LXL04_024817|OH1004|PROTEIN

MVIADESRKAITEMQGGEKEAQRYVWDGAIPLQVHLHDSEVTTLPPPPPALILAPRIGYLPLLSSQLKPFFSGALPPGVDTVWFEYKGLPLKWYIPTGVLFDLLCAEPERPWNLTVHFRGYPGNILIPCDGEDSVKWSYINSLKEAAYIIHGSSKNVMNMSQPDQVELWRSVINGKLETYNRISSKLKLGVMTDDFSEKINPSLKPQHTGNETEPTAPLKASRIPVRLYVWSVDQDFEDLEAVPHFESWDQISYINRPVE...

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_024817`
TK1151 ID	TkA06G105850
OH-1004 ID	LXL04_024817
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 96.221 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_024817

Location Chr05:99486550-99489176 (-)

Description Similar to ATG5: Autophagy protein 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g17290`	Required for autophagy.	Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways.2005 · DOI: 10.1104/pp.105.060673 Stromal protein degradation is incomplete in Arabidopsis thaliana autophagy mutants undergoing natural senescence.2013 · DOI: 10.1186/1756-0500-6-17 Organ-specific quality control of plant peroxisomes is mediated by autophagy.2014 · DOI: 10.1242/jcs.139709

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2X052`	Required for autophagy.	No verified direct reference in this release
`Os02g0117800`	Required for autophagy.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_024817 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000045 autophagosome assembly Biological Process

GO:0000422 autophagy of mitochondrion Biological Process

GO:0000423 mitophagy Biological Process

GO:0001974 blood vessel remodeling Biological Process

GO:0002376 immune system process Biological Process

GO:0002718 regulation of cytokine production involved in immune response Biological Process

GO:0006914 autophagy Biological Process

GO:0006995 cellular response to nitrogen starvation Biological Process

GO:0009267 cellular response to starvation Biological Process

GO:0009410 response to xenobiotic stimulus Biological Process

GO:0009620 response to fungus Biological Process

GO:0010040 response to iron(II) ion Biological Process

KEGG gene cross-reference

ath:AT5G17290

dosa:Os02g0117800

hsa:9474

mmu:11793

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.

Cytoplasm0.625

Rank 1 · LXL04_024817 · OH-1004

Nucleus0.254

Rank 2 · LXL04_024817 · OH-1004

Golgi apparatus0.163

Rank 3 · LXL04_024817 · OH-1004

Lysosome / Vacuole0.118

Rank 4 · LXL04_024817 · OH-1004

Endoplasmic reticulum0.106

Rank 5 · LXL04_024817 · 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.

PF20638.4ATG5_UblA25-118 aa

PF20637.3ATG5_HBR132-188 aa

PF04106.19ATG5_UblB223-331 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024817	`PF20638.4`	ATG5_UblA	25	118	8.4e-29	100.8
LXL04_024817	`PF20637.3`	ATG5_HBR	132	188	5.6e-24	84.4
LXL04_024817	`PF04106.19`	ATG5_UblB	223	331	1.6e-21	77.4

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
`Q9FFI2`	Arabidopsis thaliana	Autophagy protein 5	61.446%	Swiss-Prot	strong database homology
`A2X052`	Oryza sativa subsp. indica	Autophagy protein 5	54.270%	Swiss-Prot	strong database homology
`Q6ZGL4`	Oryza sativa subsp. japonica	Autophagy protein 5	53.994%	Swiss-Prot	strong database homology

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