LXL04_013588 | RubberDandelionOmics

Gene overview

LXL04_013588

Reference: OH-1004 Chr: Chr03 Coordinates: 32174424-32176937 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1527 bp · LXL04_013588|LXL04_013588|OH1004|cDNA

ATGCCTTCCGACCAACATCAGCCCTTACTCACTTCCGACGAACAGGAAACCGCCTACGATCCCTCCGATAAAGTACATGTCGTAGGAGTAGACGGTGACGGCCAAGACCACTTCGACGAGTACGGAGACAAATCCCCGCCGTTATCATGGCGGAAGCTATGGCTGTTCACGGGACCTGGATTCTTGATGAGCATAGCGTTTCTGGATCCGGGTAACTTGGAGGGTGATCTTCAGGCGGGTGCGATCGCCGGTTATTCACT...

CDS

Download CDS FASTA

1527 bp · LXL04_013588|LXL04_013588|OH1004|CDS

ATGCCTTCCGACCAACATCAGCCCTTACTCACTTCCGACGAACAGGAAACCGCCTACGATCCCTCCGATAAAGTACATGTCGTAGGAGTAGACGGTGACGGCCAAGACCACTTCGACGAGTACGGAGACAAATCCCCGCCGTTATCATGGCGGAAGCTATGGCTGTTCACGGGACCTGGATTCTTGATGAGCATAGCGTTTCTGGATCCGGGTAACTTGGAGGGTGATCTTCAGGCGGGTGCGATCGCCGGTTATTCACT...

Protein

Download Protein FASTA

508 aa · LXL04_013588|LXL04_013588|OH1004|PROTEIN

MPSDQHQPLLTSDEQETAYDPSDKVHVVGVDGDGQDHFDEYGDKSPPLSWRKLWLFTGPGFLMSIAFLDPGNLEGDLQAGAIAGYSLLWLLLWATAIGLLIQLLSARLGVVTGRHLAELCREEYPNWAGKLLWIMTELALIGADIQEVIGSAIALKILTIGFLPLWAGVLITAFDCFIFLFLENYGVRKLEALFAILIAVMAVSFAWMFGETKPNMKELLVGIVVPKLNSKTIQQAVGVVGCIIMPHNVFLHSALVQSRE...

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_013588`
TK1151 ID	TkA02G486730
OH-1004 ID	LXL04_013588
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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

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Basic Information and Functional Annotation

Gene ID LXL04_013588

Location Chr03:32174424-32176937 (+)

Description Similar to NRAMP4: Metal transporter Nramp4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67330`	Vacuolar metal transporter involved in intracellular metal homeostasis.	Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes.2000 · DOI: 10.1073/pnas.97.9.4991 Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron.2005 · DOI: 10.1038/sj.emboj.7600864 Export of vacuolar manganese by AtNRAMP3 and AtNRAMP4 is required for optimal photosynthesis and growth under manganese deficiency.2010 · DOI: 10.1104/pp.109.150946
`At2g23150`	Vacuolar metal transporter involved in intracellular metal homeostasis.	Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes.2000 · DOI: 10.1073/pnas.97.9.4991 AtNRAMP3, a multispecific vacuolar metal transporter involved in plant responses to iron deficiency.2003 · DOI: 10.1046/j.1365-313x.2003.01760.x Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron.2005 · DOI: 10.1038/sj.emboj.7600864 NRAMP genes function in Arabidopsis thaliana resistance to Erwinia chrysanthemi infection.2009 · DOI: 10.1111/j.1365-313x.2008.03775.x Export of vacuolar manganese by AtNRAMP3 and AtNRAMP4 is required for optimal photosynthesis and growth under manganese deficiency.2010 · DOI: 10.1104/pp.109.150946
`At1g47240`	Seems to be involved in iron uptake.	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_013588 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006826 iron ion transport Biological Process

GO:0006828 manganese ion transport Biological Process

GO:0006879 intracellular iron ion homeostasis Biological Process

GO:0009617 response to bacterium Biological Process

GO:0009624 response to nematode Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010039 response to iron ion Biological Process

GO:0010043 response to zinc ion Biological Process

GO:0015691 cadmium ion transport Biological Process

GO:0015692 lead ion transport Biological Process

GO:0030001 metal ion transport Biological Process

GO:0030003 intracellular monoatomic cation homeostasis Biological Process

KEGG gene cross-reference

ath:AT1G47240

ath:AT2G23150

ath:AT5G67330

pop:18101156

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.

Lysosome / Vacuole0.425

Rank 1 · LXL04_013588 · OH-1004

Cell membrane0.224

Rank 2 · LXL04_013588 · OH-1004

Cytoplasm0.164

Rank 3 · LXL04_013588 · OH-1004

Endoplasmic reticulum0.154

Rank 4 · LXL04_013588 · OH-1004

Golgi apparatus0.151

Rank 5 · LXL04_013588 · 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.

PF01566.26Nramp60-457 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013588	`PF01566.26`	Nramp	60	457	1.6e-129	433.0

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
`Q9FN18`	Arabidopsis thaliana	Metal transporter Nramp4	73.077%	Swiss-Prot	strong database homology
`Q9SNV9`	Arabidopsis thaliana	Metal transporter Nramp3	73.000%	Swiss-Prot	strong database homology
`Q9C6B2`	Arabidopsis thaliana	Metal transporter Nramp2	73.444%	Swiss-Prot	strong database homology

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