LXL04_002580 | RubberDandelionOmics

Gene overview

LXL04_002580

Reference: OH-1004 Chr: Chr01 Coordinates: 52343811-52345474 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

405 bp · LXL04_002580|LXL04_002580|OH1004|cDNA

ATGGGGAAGAAGATTATGAGTTTTGGCAGGTTTTTGGACAGTTTGTGTCTCTCAAATGGTGGTGCAAGTTCTTGTCTTTGTTGCATTAACAATTTTGAAATACAAGATGATTATGAGTTTGAGGCAGAACCACTTGTAGATCAGTCCAAAGATGCATCGGATAAACCTCAAACTCTTGCCTTCTTTCTAAAACCAAAGATGGTGGTGCTAAGGGTGTCCATGCATTGCAATGGTTGTGCAAGGAAAGTCCAAAGACACAT...

CDS

Download CDS FASTA

405 bp · LXL04_002580|LXL04_002580|OH1004|CDS

ATGGGGAAGAAGATTATGAGTTTTGGCAGGTTTTTGGACAGTTTGTGTCTCTCAAATGGTGGTGCAAGTTCTTGTCTTTGTTGCATTAACAATTTTGAAATACAAGATGATTATGAGTTTGAGGCAGAACCACTTGTAGATCAGTCCAAAGATGCATCGGATAAACCTCAAACTCTTGCCTTCTTTCTAAAACCAAAGATGGTGGTGCTAAGGGTGTCCATGCATTGCAATGGTTGTGCAAGGAAAGTCCAAAGACACAT...

Protein

Download Protein FASTA

134 aa · LXL04_002580|LXL04_002580|OH1004|PROTEIN

MGKKIMSFGRFLDSLCLSNGGASSCLCCINNFEIQDDYEFEAEPLVDQSKDASDKPQTLAFFLKPKMVVLRVSMHCNGCARKVQRHISKMDGVTSYQVDLETKMVIVMGDIVPFEVLESVSKVKNAQLWTEPIS

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_002580`
TK1151 ID	TkA01G438140
OH-1004 ID	LXL04_002580
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_002580

Location Chr01:52343811-52345474 (+)

Description Similar to NAKR2: Protein SODIUM POTASSIUM ROOT DEFECTIVE 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g37390`	Protein SODIUM POTASSIUM ROOT DEFECTIVE 2.	No verified direct reference in this release
`At5g02600`	Required for root meristem maintenance after germination.	Arabidopsis NPCC6/NaKR1 is a phloem mobile metal binding protein necessary for phloem function and root meristem maintenance.2010 · DOI: 10.1105/tpc.110.080010 NaKR1 regulates long-distance movement of FLOWERING LOCUS T in Arabidopsis.2016 · DOI: 10.1038/nplants.2016.75
`At3g53530`	Heavy metal-associated protein involved in salt tolerance.	Overexpression of NaKR3 enhances salt tolerance in Arabidopsis.2016 · DOI: 10.4238/gmr.15016378
`At5g27690`	Heavy-metal-binding protein.	No verified direct reference in this release
`At1g66240`	Plays an important role in copper homeostasis by conferring tolerance to excess of copper and subclinical copper deficiency during vegetative stage.	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_002580 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006825 copper ion transport Biological Process

GO:0009908 flower development Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010233 phloem transport Biological Process

GO:0055078 sodium ion homeostasis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005773 vacuole Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT1G66240

ath:AT2G37390

ath:AT3G53530

ath:AT5G02600

ath:AT5G27690

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.

Cytoplasm0.332

Rank 1 · LXL04_002580 · OH-1004

Nucleus0.319

Rank 2 · LXL04_002580 · OH-1004

Cell membrane0.273

Rank 3 · LXL04_002580 · OH-1004

Endoplasmic reticulum0.118

Rank 4 · LXL04_002580 · OH-1004

Plastid0.092

Rank 5 · LXL04_002580 · 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.

PF00403.33HMA70-122 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002580	`PF00403.33`	HMA	70	122	2.9e-14	53.9

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
`Q58FZ0`	Arabidopsis thaliana	Protein SODIUM POTASSIUM ROOT DEFECTIVE 2	47.826%	Swiss-Prot	moderate database homology
`Q8LDS4`	Arabidopsis thaliana	Protein SODIUM POTASSIUM ROOT DEFECTIVE 1	60.606%	Swiss-Prot	weak database homology
`Q8RXH8`	Arabidopsis thaliana	Protein SODIUM POTASSIUM ROOT DEFECTIVE 3	59.420%	Swiss-Prot	moderate database homology
`Q84J88`	Arabidopsis thaliana	Heavy metal-associated isoprenylated plant protein 36	36.364%	Swiss-Prot	moderate database homology
`Q94BT9`	Arabidopsis thaliana	Copper transport protein ATX1	43.077%	Swiss-Prot	weak database homology

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