LXL04_009495 | RubberDandelionOmics

Gene overview

LXL04_009495

Reference: OH-1004 Chr: Chr02 Coordinates: 127442574-127445548 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2232 bp · LXL04_009495|LXL04_009495|OH1004|cDNA

ATGGCTTCTTCGTCAATCGTGATCAAGCTAATATCTGTATATATCCCTGATTTTTTACAGGTTAAGTTCGGGGAAACACTCAGACGCTTCACTGCATCCATCAACGACAAGAAACTTGACCTTGACGTTGTTGCTTTAAGGGCAAAGATCCGTAGCTTCTTCAATTTCAACCCTGATGTTGCTTTCACTCTCACATACGTTGATGAAGATGGAGATGCTGTTACTCTTGCTGATGATGACGATCTTCATGATGTTGTCCG...

CDS

Download CDS FASTA

2232 bp · LXL04_009495|LXL04_009495|OH1004|CDS

ATGGCTTCTTCGTCAATCGTGATCAAGCTAATATCTGTATATATCCCTGATTTTTTACAGGTTAAGTTCGGGGAAACACTCAGACGCTTCACTGCATCCATCAACGACAAGAAACTTGACCTTGACGTTGTTGCTTTAAGGGCAAAGATCCGTAGCTTCTTCAATTTCAACCCTGATGTTGCTTTCACTCTCACATACGTTGATGAAGATGGAGATGCTGTTACTCTTGCTGATGATGACGATCTTCATGATGTTGTCCG...

Protein

Download Protein FASTA

743 aa · LXL04_009495|LXL04_009495|OH1004|PROTEIN

MASSSIVIKLISVYIPDFLQVKFGETLRRFTASINDKKLDLDVVALRAKIRSFFNFNPDVAFTLTYVDEDGDAVTLADDDDLHDVVRQSLNPLRLTVTLPKDNNTPTGPSGTSTPMRSVPPPPPPPPHHPSGPLSDFLKSMPEPLSNFLKSMPEPFRDQLTKLPLELASKASQSSTPGISELAEKLTAAYLNQMPNSMAVPRPSTEPESSSSKNKEKSVFVSEDVKSTDIEPPKRVDLKHPYFDYDSFPAPVEGYNGKPS...

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_009495`
TK1151 ID	TkA03G442050
OH-1004 ID	LXL04_009495
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_009495

Location Chr02:127442574-127445548 (-)

Description Similar to NBR1: Protein NBR1 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g24690`	Autophagic substrate degraded in the vacuole by non-selective autophagy.	Plant NBR1 is a selective autophagy substrate and a functional hybrid of the mammalian autophagic adapters NBR1 and p62/SQSTM1.2011 · DOI: 10.4161/auto.7.9.16389 NBR1-mediated selective autophagy targets insoluble ubiquitinated protein aggregates in plant stress responses.2013 · DOI: 10.1371/journal.pgen.1003196 E3 ubiquitin ligase CHIP and NBR1-mediated selective autophagy protect additively against proteotoxicity in plant stress responses.2014 · DOI: 10.1371/journal.pgen.1004116

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009495 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006914 autophagy Biological Process

GO:0015031 protein transport Biological Process

GO:0016236 macroautophagy Biological Process

GO:0032480 negative regulation of type I interferon production Biological Process

GO:0032720 negative regulation of tumor necrosis factor production Biological Process

GO:0045087 innate immune response Biological Process

GO:0050687 negative regulation of defense response to virus Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051258 protein polymerization Biological Process

GO:0071211 protein targeting to vacuole involved in autophagy Biological Process

GO:1900181 negative regulation of protein localization to nucleus Biological Process

GO:0000407 phagophore assembly site Cellular Component

KEGG gene cross-reference

ath:AT4G24690

gga:419902

pon:100174370

sot:102582603

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.

Cytoplasm0.533

Rank 1 · LXL04_009495 · OH-1004

Nucleus0.493

Rank 2 · LXL04_009495 · OH-1004

Cell membrane0.100

Rank 3 · LXL04_009495 · OH-1004

Endoplasmic reticulum0.067

Rank 4 · LXL04_009495 · OH-1004

Golgi apparatus0.036

Rank 5 · LXL04_009495 · 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.

PF00564.31PB141-97 aa

PF00569.24ZZ343-377 aa

PF16158.12N_BRCA1_IG442-543 aa

PF24932.2UBA_NBR1_C659-698 aa

PF24932.2UBA_NBR1_C701-738 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009495	`PF00564.31`	PB1	41	97	3.3e-08	34.1
LXL04_009495	`PF00569.24`	ZZ	343	377	7.5e-09	36.0
LXL04_009495	`PF16158.12`	N_BRCA1_IG	442	543	4.7e-31	108.3
LXL04_009495	`PF24932.2`	UBA_NBR1_C	659	698	5.6e-32	110.1
LXL04_009495	`PF24932.2`	UBA_NBR1_C	701	738	5.6e-32	110.1

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
`Q9SB64`	Arabidopsis thaliana	Protein NBR1 homolog	40.784%	Swiss-Prot	moderate database homology

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