LXL04_005989 | RubberDandelionOmics

Gene overview

LXL04_005989

Reference: OH-1004 Chr: Chr01 Coordinates: 176696355-176698050 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

726 bp · LXL04_005989|LXL04_005989|OH1004|cDNA

ATGAGTACAGGAGAGCTTCTCAACGTCGAGCCTTTAGAGCTCAAATTTCCATTTGAATTGAAGAAACAGATCTCTTGCTCGCTTCTGTTATTGAATAAAACCGATAACCATGTAGCTTTCAAGGTGAAGACAACAAATCCAAAGAAGTATTGCGTTCGGCCTAATACTGGAGTAGTTATGCCTCGATCAACATGTGACGTAATAGTAACAATGCAGGCACAGAAGGAAGCTCCTCCAGACATGGTCTGCAAGGACAAGTT...

CDS

Download CDS FASTA

726 bp · LXL04_005989|LXL04_005989|OH1004|CDS

ATGAGTACAGGAGAGCTTCTCAACGTCGAGCCTTTAGAGCTCAAATTTCCATTTGAATTGAAGAAACAGATCTCTTGCTCGCTTCTGTTATTGAATAAAACCGATAACCATGTAGCTTTCAAGGTGAAGACAACAAATCCAAAGAAGTATTGCGTTCGGCCTAATACTGGAGTAGTTATGCCTCGATCAACATGTGACGTAATAGTAACAATGCAGGCACAGAAGGAAGCTCCTCCAGACATGGTCTGCAAGGACAAGTT...

Protein

Download Protein FASTA

241 aa · LXL04_005989|LXL04_005989|OH1004|PROTEIN

MSTGELLNVEPLELKFPFELKKQISCSLLLLNKTDNHVAFKVKTTNPKKYCVRPNTGVVMPRSTCDVIVTMQAQKEAPPDMVCKDKFLLQSVVATPGAAAKDITPEMFSKQSGRVVEECKLKVIYLPPPQPPSPVLEEPDEGAPSPKVSFTDNRTTNISSTSEVSRQYADSHDNSAQVRSLISKLTDEKNAAVQQSKKIRQEMELLTRGGNNKSQGGGGASIIIVIIIALIGLVTGYLLNN

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_005989`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_005989

Location Chr01:176696355-176698050 (-)

Description Similar to PVA11: Vesicle-associated protein 1-1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g60600`	Part of a membrane-cytoskeletal adapter complex that forms a bridge between the endoplasmic reticulum and the plasma membrane.	No verified direct reference in this release
`At2g45140`	Vesicle-associated protein that binds the oxysterol-binding protein ORP3A and allows its targeting to the ER.	The targeting of the oxysterol-binding protein ORP3a to the endoplasmic reticulum relies on the plant VAP33 homolog PVA12.2009 · DOI: 10.1111/j.1365-313x.2009.03815.x
`At4g00170`	May play a role in vesicle trafficking.	No verified direct reference in this release
`At5g47180`	May play a role in vesicle trafficking.	No verified direct reference in this release
`At2g23830`	May play a role in vesicle trafficking.	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_005989 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006605 protein targeting Biological Process

GO:0061817 endoplasmic reticulum-plasma membrane tethering Biological Process

GO:0090158 endoplasmic reticulum membrane organization Biological Process

GO:0000326 protein storage vacuole Cellular Component

GO:0005776 autophagosome Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009536 plastid Cellular Component

GO:0032586 protein storage vacuole membrane Cellular Component

GO:0043495 protein-membrane adaptor activity Molecular Function

KEGG gene cross-reference

ath:AT2G23830

ath:AT2G45140

ath:AT3G60600

ath:AT4G00170

ath:AT5G47180

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Endoplasmic reticulum0.582

Rank 1 · LXL04_005989 · OH-1004

Golgi apparatus0.276

Rank 2 · LXL04_005989 · OH-1004

Cell membrane0.135

Rank 3 · LXL04_005989 · OH-1004

Cytoplasm0.135

Rank 4 · LXL04_005989 · OH-1004

Nucleus0.120

Rank 5 · LXL04_005989 · 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.

PF00635.33Motile_Sperm7-111 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005989	`PF00635.33`	Motile_Sperm	7	111	2.5e-30	105.3

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
`Q8VZ95`	Arabidopsis thaliana	Vesicle-associated protein 1-1	61.187%	Swiss-Prot	strong database homology
`Q9SHC8`	Arabidopsis thaliana	Vesicle-associated protein 1-2	59.259%	Swiss-Prot	strong database homology
`Q84WW5`	Arabidopsis thaliana	Vesicle-associated protein 1-3	53.942%	Swiss-Prot	strong database homology
`Q9LVU1`	Arabidopsis thaliana	Vesicle-associated protein 2-1	41.102%	Swiss-Prot	moderate database homology
`O82213`	Arabidopsis thaliana	Vesicle-associated protein 3-1	66.667%	Swiss-Prot	moderate database homology

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