LXL04_030203 | RubberDandelionOmics

Gene overview

LXL04_030203

Reference: OH-1004 Chr: Chr06 Coordinates: 110654303-110668908 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

9717 bp · LXL04_030203|LXL04_030203|OH1004|cDNA

ATGAACATTGTAAGAGGTGTTGCGGGTCTTATTCGAAGGACATCTGGCTTTGGTGGTGAGTATGATGTAGGATCAGCATCTCATAAGTTCCCTGTCCCATCTCCACACGTTAAATTCAGTGACATTGGTGATGAGGCGATATTGTCTGCACTATGGGAGAGATATGAAAGTGTCTCTGAAAAGGCAGAAAGACATACGGCTTTTCATATATTTCTTAAACAGTTTTTAGTAATATACAAGGATTGGGAGCCATTAGATTT...

CDS

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9717 bp · LXL04_030203|LXL04_030203|OH1004|CDS

ATGAACATTGTAAGAGGTGTTGCGGGTCTTATTCGAAGGACATCTGGCTTTGGTGGTGAGTATGATGTAGGATCAGCATCTCATAAGTTCCCTGTCCCATCTCCACACGTTAAATTCAGTGACATTGGTGATGAGGCGATATTGTCTGCACTATGGGAGAGATATGAAAGTGTCTCTGAAAAGGCAGAAAGACATACGGCTTTTCATATATTTCTTAAACAGTTTTTAGTAATATACAAGGATTGGGAGCCATTAGATTT...

Protein

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3238 aa · LXL04_030203|LXL04_030203|OH1004|PROTEIN

MNIVRGVAGLIRRTSGFGGEYDVGSASHKFPVPSPHVKFSDIGDEAILSALWERYESVSEKAERHTAFHIFLKQFLVIYKDWEPLDLDNSLEAASGDESQNPDDEVIIGCSTAHPADIIVILIEEVSNITAIVTESISGSSNSLVITPESFRVLKTLTIITRSRHNCKVLGYYGGIQKLTALMKAVVVQLKTIAGALSSDETLSSSNVQKAGVLQKILVHVVAIVCGFINLQLDIYGKAQIDVENLEGSIEKMATTPEPF...

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_030203`
TK1151 ID	TkA07G386760
OH-1004 ID	LXL04_030203
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 88.481 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_030203

Location Chr06:110654303-110668908 (+)

Description Similar to BCHB: BEACH domain-containing protein B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g58230`	May be involved in the suppression of BCHC1 activity.	BEACH-domain proteins act together in a cascade to mediate vacuolar protein trafficking and disease resistance in Arabidopsis.2015 · DOI: 10.1016/j.molp.2014.11.015

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_030203 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000423 mitophagy Biological Process

GO:0034497 protein localization to phagophore assembly site Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005765 lysosomal membrane Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0019901 protein kinase binding Molecular Function

KEGG gene cross-reference

ath:AT1G58230

ddi:DDB_G0280971

hsa:987

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.

Cytoplasm0.493

Rank 1 · LXL04_030203 · OH-1004

Nucleus0.284

Rank 2 · LXL04_030203 · OH-1004

Golgi apparatus0.170

Rank 3 · LXL04_030203 · OH-1004

Cell membrane0.116

Rank 4 · LXL04_030203 · OH-1004

Lysosome / Vacuole0.110

Rank 5 · LXL04_030203 · 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.

PF28615.1DDB_G0281251537-634 aa

PF20425.5Neurobeachin639-1053 aa

PF13385.14Laminin_G_31068-1186 aa

PF15787.12DUF47041304-1828 aa

PF16057.11DUF48002193-2281 aa

PF14844.13PH_BEACH2486-2545 aa

PF02138.24Beach2584-2860 aa

PF20426.5NBCH_WD402882-3225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030203	`PF28615.1`	DDB_G0281251	537	634	3.2e-31	108.4
LXL04_030203	`PF20425.5`	Neurobeachin	639	1053	1.3e-206	687.3
LXL04_030203	`PF13385.14`	Laminin_G_3	1068	1186	2.8e-06	28.3
LXL04_030203	`PF15787.12`	DUF4704	1304	1828	1.4e-154	516.3
LXL04_030203	`PF16057.11`	DUF4800	2193	2281	2.7e-06	27.5
LXL04_030203	`PF14844.13`	PH_BEACH	2486	2545	2.3e-13	50.8
LXL04_030203	`PF02138.24`	Beach	2584	2860	1.3e-122	409.2
LXL04_030203	`PF20426.5`	NBCH_WD40	2882	3225	1.3e-186	620.2
LXL04_030203	`PF23414.2`	Beta-prop_EML_2	2958	3101	5.7e-13	49.6
LXL04_030203	`PF24814.2`	WD40_Prp19	2969	3139	8.4e-15	55.3
LXL04_030203	`PF23381.2`	Beta-prop_IFT122_1st	2970	3034	3.6e-24	86.3
LXL04_030203	`PF25175.2`	Beta-prop_WDR5	2970	3222	1.5e-19	71.1
LXL04_030203	`PF25174.2`	Beta-prop_THOC3	2970	3037	5.7e-17	62.3
LXL04_030203	`PF25173.2`	Beta-prop_WDR3_1st	2971	3136	3.2e-15	57.0
LXL04_030203	`PF25172.2`	Beta-prop_WDR3_2nd	2972	3079	3.8e-10	40.2
LXL04_030203	`PF24807.2`	WD40_CDC20-Fz	2975	3103	3.1e-08	34.0

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
`F4I9T0`	Arabidopsis thaliana	BEACH domain-containing protein B	62.581%	Swiss-Prot	strong database homology

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