LXL04_016131 | RubberDandelionOmics

Gene overview

LXL04_016131

Reference: OH-1004 Chr: Chr03 Coordinates: 111742819-111746228 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1104 bp · LXL04_016131|LXL04_016131|OH1004|cDNA

ATGATGCGGAGTATTGCAGGATTTAGAGTAATTCACGAAACACAAAAGGCGAAAGGCAAAATTACTGTCACAATCGCCTGTTTCAAAGAAGGCAATTTACTTTTTAAACGATATGTATACGGATATTGCAACAAGATTCATAGCTTGAAAGTTAGACACTTGCCAGTTGTAGAGAATGGGGAGGTTATTGCTTTACTTGATATAGCAAAATGTTTATATGATGCTATTGCCTGTACGGAAAGGGCTGCTGAAAAGGGGAA...

CDS

Download CDS FASTA

1104 bp · LXL04_016131|LXL04_016131|OH1004|CDS

ATGATGCGGAGTATTGCAGGATTTAGAGTAATTCACGAAACACAAAAGGCGAAAGGCAAAATTACTGTCACAATCGCCTGTTTCAAAGAAGGCAATTTACTTTTTAAACGATATGTATACGGATATTGCAACAAGATTCATAGCTTGAAAGTTAGACACTTGCCAGTTGTAGAGAATGGGGAGGTTATTGCTTTACTTGATATAGCAAAATGTTTATATGATGCTATTGCCTGTACGGAAAGGGCTGCTGAAAAGGGGAA...

Protein

Download Protein FASTA

367 aa · LXL04_016131|LXL04_016131|OH1004|PROTEIN

MMRSIAGFRVIHETQKAKGKITVTIACFKEGNLLFKRYVYGYCNKIHSLKVRHLPVVENGEVIALLDIAKCLYDAIACTERAAEKGKAIVATVEGWGLFELIKGLIKDLDGDDNYEMGEDDFKEAQNSVARLIQMLYNDDPREVLKIIHMVKKHIMSGGAKRLPFTIPSLIYNALKTIEVLSMVPAPDLALRLYLECAEAANDCDLEPLGYVVNETLRILIFLRFNEEVTFFLQCCPAWDELKHTREANGSDKEAKVVYD...

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_016131`
TK1151 ID	TkA02G186330
OH-1004 ID	LXL04_016131
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.900
Protein coverage (%)	TK1151 94.152 / OH-1004 43.869 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_016131

Location Chr03:111742819-111746228 (-)

Description Similar to VPS35B: Vacuolar protein sorting-associated protein 35B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75850`	Plays a role in vesicular protein sorting.	Arabidopsis VPS35, a retromer component, is required for vacuolar protein sorting and involved in plant growth and leaf senescence.2008 · DOI: 10.1093/pcp/pcn006
`At2g17790`	Plays a role in vesicular protein sorting.	Loss-of-function mutations of retromer large subunit genes suppress the phenotype of an Arabidopsis zig mutant that lacks Qb-SNARE VTI11.2010 · DOI: 10.1105/tpc.109.069294
`At3g51310`	Plays a role in vesicular protein sorting.	No verified direct reference in this release
`At5g63490`	CBS domain-containing protein CBSCBSPB1.	No verified direct reference in this release
`At5g50640`	CBS domain-containing protein CBSCBSPB5.	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_016131 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009536 plastid Cellular Component

GO:0010008 endosome membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0030904 retromer complex Cellular Component

KEGG gene cross-reference

ath:AT1G75850

ath:AT2G17790

ath:AT3G51310

ath:AT5G50530

ath:AT5G50640

ath:AT5G63490

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.

Nucleus0.419

Rank 1 · LXL04_016131 · OH-1004

Cytoplasm0.403

Rank 2 · LXL04_016131 · OH-1004

Mitochondrion0.112

Rank 3 · LXL04_016131 · OH-1004

Cell membrane0.106

Rank 4 · LXL04_016131 · OH-1004

Endoplasmic reticulum0.076

Rank 5 · LXL04_016131 · 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.

PF03635.24Vps3585-181 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016131	`PF03635.24`	Vps35	85	181	4.5e-15	56.0

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4I0P8`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35B	52.448%	Swiss-Prot	weak database homology
`Q7X659`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35A	41.150%	Swiss-Prot	moderate database homology
`A8R7K9`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35C	42.500%	Swiss-Prot	weak database homology
`Q9FMV3`	Arabidopsis thaliana	CBS domain-containing protein CBSCBSPB1	82.692%	Swiss-Prot	weak database homology
`P0DH79`	Arabidopsis thaliana	CBS domain-containing protein CBSCBSPB5	78.846%	Swiss-Prot	weak database homology

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