LXL04_012505 | RubberDandelionOmics

Gene overview

LXL04_012505

Reference: OH-1004 Chr: Chr03 Coordinates: 13423766-13424812 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1047 bp · LXL04_012505|LXL04_012505|OH1004|cDNA

ATGCGCCACCCATCAGCCGCCGAATTCGTGCGAGCCATCAAAACATTCATCGTATCATTCTCAAACACACCACCCGACCCCGAAAAAGACAGCTCATCCGTCCAACAATTCCTCGCCAACATGGAAGCTTCCTTCCGGGCCCACCCGCTCTGGTCAACCGGGTCCGAAGAAGAACTCGATAGCGCAGGCGAAGGCCTCGAGAAATACATCATGACAAAACTCTTCCCCCGTGTCTTCGCCTCCCACCAACCCGACATCAA...

CDS

Download CDS FASTA

1047 bp · LXL04_012505|LXL04_012505|OH1004|CDS

ATGCGCCACCCATCAGCCGCCGAATTCGTGCGAGCCATCAAAACATTCATCGTATCATTCTCAAACACACCACCCGACCCCGAAAAAGACAGCTCATCCGTCCAACAATTCCTCGCCAACATGGAAGCTTCCTTCCGGGCCCACCCGCTCTGGTCAACCGGGTCCGAAGAAGAACTCGATAGCGCAGGCGAAGGCCTCGAGAAATACATCATGACAAAACTCTTCCCCCGTGTCTTCGCCTCCCACCAACCCGACATCAA...

Protein

Download Protein FASTA

348 aa · LXL04_012505|LXL04_012505|OH1004|PROTEIN

MRHPSAAEFVRAIKTFIVSFSNTPPDPEKDSSSVQQFLANMEASFRAHPLWSTGSEEELDSAGEGLEKYIMTKLFPRVFASHQPDINLDDQLHEKISLIQQFIKPEQLDIQPIYQNETSWLLAQKELQKINIYKAPRDKLVCILSCCKVISNLLLNASVNADESPPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESRLVGEAAYFFTNMLSAEAFVTNMDGKAISMDEMEFQKNMESAQAVIYGLSDYNTGQSIS...

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_012505`
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_012505

Location Chr03:13423766-13424812 (+)

Description Similar to VPS9A: Vacuolar protein sorting-associated protein 9A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19770`	Functions as a guanine nucleotide exchange factor (GEF) for Rab small GTPases.	VPS9a, the common activator for two distinct types of Rab5 GTPases, is essential for the development of Arabidopsis thaliana.2007 · DOI: 10.1105/tpc.107.053876 GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system.2010 · DOI: 10.1074/jbc.m110.152132

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0262900`	Functions as a guanine nucleotide exchange factor (GEF) for Rab small GTPases.	OsVPS9A functions cooperatively with OsRAB5A to regulate post-Golgi dense vesicle-mediated storage protein trafficking to the protein storage vacuole in rice endosperm cells.2013 · DOI: 10.1093/mp/sst081

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012505 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000919 cell plate assembly Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006897 endocytosis Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0042546 cell wall biogenesis Biological Process

GO:0045324 late endosome to vacuole transport Biological Process

GO:0048528 post-embryonic root development Biological Process

GO:0051223 regulation of protein transport Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005768 endosome Cellular Component

KEGG gene cross-reference

ath:AT3G19770

dosa:Os03g0262900

hsa:26130

spo:2540886

xla:100037133

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.

Cytoplasm0.677

Rank 1 · LXL04_012505 · OH-1004

Golgi apparatus0.264

Rank 2 · LXL04_012505 · OH-1004

Nucleus0.168

Rank 3 · LXL04_012505 · OH-1004

Lysosome / Vacuole0.111

Rank 4 · LXL04_012505 · OH-1004

Cell membrane0.087

Rank 5 · LXL04_012505 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF18151.7DUF560111-75 aa

PF02204.24VPS9121-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012505	`PF18151.7`	DUF5601	11	75	3.3e-15	56.6
LXL04_012505	`PF02204.24`	VPS9	121	225	1.6e-31	109.4

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
`Q9LT31`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 9A	61.804%	Swiss-Prot	strong database homology
`Q10NQ3`	Oryza sativa subsp. japonica	Vacuolar protein sorting-associated protein 9A	58.824%	Swiss-Prot	strong database homology

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