LXL04_012188 | RubberDandelionOmics

Gene overview

LXL04_012188

Reference: OH-1004 Chr: Chr03 Coordinates: 8057031-8059100 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1698 bp · LXL04_012188|LXL04_012188|OH1004|cDNA

ATGATGGGATCCGAGAGCCAGGGCTTCGAAGAAGCCCAGCTCTATGCATCTCGTGAAGAAATGGAGTCTCTTGTTCTTGACGATGATGATATTAAAAATAACAATAACGATAACAGTTCGTCATCCAGATTCAACGGCGGTGCAAATGGAGATGGTGGTCAACATCACCATCCtctctcttcatctttgccGTTTGCGGAAATACCGACCACCGACGATGATGATCCCTTGTTATCATCGCCGTCCCCTCACAAAAGCCC...

CDS

Download CDS FASTA

1698 bp · LXL04_012188|LXL04_012188|OH1004|CDS

ATGATGGGATCCGAGAGCCAGGGCTTCGAAGAAGCCCAGCTCTATGCATCTCGTGAAGAAATGGAGTCTCTTGTTCTTGACGATGATGATATTAAAAATAACAATAACGATAACAGTTCGTCATCCAGATTCAACGGCGGTGCAAATGGAGATGGTGGTCAACATCACCATCCTCTCTCTTCATCTTTGCCGTTTGCGGAAATACCGACCACCGACGATGATGATCCCTTGTTATCATCGCCGTCCCCTCACAAAAGCCC...

Protein

Download Protein FASTA

565 aa · LXL04_012188|LXL04_012188|OH1004|PROTEIN

MMGSESQGFEEAQLYASREEMESLVLDDDDIKNNNNDNSSSSRFNGGANGDGGQHHHPLSSSLPFAEIPTTDDDDPLLSSPSPHKSPNAFNSFLEPPSYADAVFRSFDGDHGKQINGHGAVSTSSPSSSSDYLKISVTDPQKDQDLKNSLVPGGNTFVTYLITTWTNLPEFNGTEFSVRRRFKDVVTLSDRLSDSYRGFFIPLRPDKSVVEGQVMQKQEFVEQRRMALEKYLRKLAAHPVIRRSEELRVFLQVQGKLPLV...

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_012188`
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_012188

Location Chr03:8057031-8059100 (-)

Description Similar to SNX2A: Sorting nexin 2A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g58440`	Plays a role in vesicular protein sorting (By similarity).	No verified direct reference in this release
`At5g07120`	Plays a role in vesicular protein sorting.	Overexpression of Arabidopsis sorting nexin AtSNX2b inhibits endocytic trafficking to the vacuole.2008 · DOI: 10.1093/mp/ssn057
`At5g06140`	Plays a role in vesicular protein sorting.	AtSNX1 defines an endosome for auxin-carrier trafficking in Arabidopsis.2006 · DOI: 10.1038/nature05046 Evidence for a sorting endosome in Arabidopsis root cells.2008 · DOI: 10.1111/j.1365-313x.2007.03338.x Differential degradation of PIN2 auxin efflux carrier by retromer-dependent vacuolar targeting.2008 · DOI: 10.1073/pnas.0808073105 BLOS1, a putative BLOC-1 subunit, interacts with SNX1 and modulates root growth in Arabidopsis.2010 · DOI: 10.1242/jcs.069732 Analyses of sorting nexins reveal distinct retromer-subcomplex functions in development and protein sorting in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078451

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012188 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006623 protein targeting to vacuole Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0031623 receptor internalization Biological Process

GO:0032502 developmental process Biological Process

GO:0034498 early endosome to Golgi transport Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0045324 late endosome to vacuole transport Biological Process

KEGG gene cross-reference

ath:AT5G06140

ath:AT5G07120

ath:AT5G58440

hsa:6642

mmu:56440

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.

Cytoplasm0.427

Rank 1 · LXL04_012188 · OH-1004

Golgi apparatus0.343

Rank 2 · LXL04_012188 · OH-1004

Cell membrane0.193

Rank 3 · LXL04_012188 · OH-1004

Lysosome / Vacuole0.138

Rank 4 · LXL04_012188 · OH-1004

Nucleus0.124

Rank 5 · LXL04_012188 · 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.

PF00787.30PX170-253 aa

PF09325.16Vps5320-556 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012188	`PF00787.30`	PX	170	253	2.4e-19	70.4
LXL04_012188	`PF09325.16`	Vps5	320	556	6.8e-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
`Q8L5Z7`	Arabidopsis thaliana	Sorting nexin 2A	63.776%	Swiss-Prot	strong database homology
`B9DFS6`	Arabidopsis thaliana	Sorting nexin 2B	61.724%	Swiss-Prot	strong database homology
`Q9FG38`	Arabidopsis thaliana	Sorting nexin 1	27.991%	Swiss-Prot	weak database homology

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