LXL04_026258 | RubberDandelionOmics

Gene overview

LXL04_026258

Reference: OH-1004 Chr: Chr05 Coordinates: 123984295-123987140 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2065 bp · LXL04_026258|LXL04_026258|OH1004|cDNA

CAATGGTATCGAATCCATTTCTCAAGACCTAAACAACACGTTCTTGGAGAAAATAAAAAGAGGATCCATGATGAACGTAGAAATGAAGAATGGGGAGATTGAAAGAGACAAAAGAGAGGAAATGGAAATGGAAAGAGACAAGAAGGATGATGATCATGTGAGGTTGCAACCATGGACAAAGCAAATTACTATTCGTGGAATTGTGGCGAGTGCTATTATAGGGTGTATTTACAGTATTATAGCTATGAAACTAAATCTCA...

CDS

Download CDS FASTA

2022 bp · LXL04_026258|LXL04_026258|OH1004|CDS

TTGGAGAAAATAAAAAGAGGATCCATGATGAACGTAGAAATGAAGAATGGGGAGATTGAAAGAGACAAAAGAGAGGAAATGGAAATGGAAAGAGACAAGAAGGATGATGATCATGTGAGGTTGCAACCATGGACAAAGCAAATTACTATTCGTGGAATTGTGGCGAGTGCTATTATAGGGTGTATTTACAGTATTATAGCTATGAAACTAAATCTCACAACTGGAATGACACCTAATATGAACGTGTCGGCCGCACTTCT...

Protein

Download Protein FASTA

673 aa · LXL04_026258|LXL04_026258|OH1004|PROTEIN

MEKIKRGSMMNVEMKNGEIERDKREEMEMERDKKDDDHVRLQPWTKQITIRGIVASAIIGCIYSIIAMKLNLTTGMTPNMNVSAALLAFVFMRTWTKMLQKSGISSVPFTRHENTMIQTCSVACYSIAIGGGYGSYLLGLNKKTWEMAGGVNSPGTYKEPGVGWMMGYSFLVCFIGLFVLIPLRKVLIVDYKLVFPSGMATAVLINGFHTQGDDMAKKQVKGFAKYFSASFLWGFFQWFFTGKEEECGFVQFPTFGLKAW...

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_026258`
TK1151 ID	TkA06G017580
OH-1004 ID	LXL04_026258
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.800
Protein coverage (%)	TK1151 100.000 / OH-1004 98.811 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_026258

Location Chr05:123984295-123987140 (-)

Description Similar to YSL3: Metal-nicotianamine transporter YSL3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g53550`	May be involved in the lateral transport of nicotianamine- chelated metals in the vasculature.	Mutations in Arabidopsis yellow stripe-like1 and yellow stripe-like3 reveal their roles in metal ion homeostasis and loading of metal ions in seeds.2006 · DOI: 10.1104/pp.106.082586
`At4g24120`	Involved in iron loading of the seeds.	A loss-of-function mutation in AtYSL1 reveals its role in iron and nicotianamine seed loading.2005 · DOI: 10.1111/j.1365-313x.2005.02569.x Mutations in Arabidopsis yellow stripe-like1 and yellow stripe-like3 reveal their roles in metal ion homeostasis and loading of metal ions in seeds.2006 · DOI: 10.1104/pp.106.082586
`At5g24380`	May be involved in the lateral transport of nicotianamine- chelated metals in the vasculature.	Arabidopsis Yellow Stripe-Like2 (YSL2): a metal-regulated gene encoding a plasma membrane transporter of nicotianamine-metal complexes.2004 · DOI: 10.1111/j.1365-313x.2004.02128.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0542200`	May be involved in the transport of nicotianamine-chelated metals.	No verified direct reference in this release
`Os02g0650300`	May participate in rhizosphere Fe³⁺ uptake and phloem iron transport.	Rice OsYSL15 is an iron-regulated iron(III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings.2009 · DOI: 10.1074/jbc.m806042200

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026258 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0003006 developmental process involved in reproduction Biological Process

GO:0006811 monoatomic ion transport Biological Process

GO:0006826 iron ion transport Biological Process

GO:0009624 response to nematode Biological Process

GO:0010039 response to iron ion Biological Process

GO:0010043 response to zinc ion Biological Process

GO:0048316 seed development Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0035673 oligopeptide transmembrane transporter activity Molecular Function

KEGG gene cross-reference

ath:AT4G24120

ath:AT5G24380

ath:AT5G53550

dosa:Os04g0542200

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.

Cell membrane0.625

Rank 1 · LXL04_026258 · OH-1004

Lysosome / Vacuole0.150

Rank 2 · LXL04_026258 · OH-1004

Endoplasmic reticulum0.126

Rank 3 · LXL04_026258 · OH-1004

Cytoplasm0.068

Rank 4 · LXL04_026258 · OH-1004

Golgi apparatus0.045

Rank 5 · LXL04_026258 · 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.

PF03169.21OPT47-657 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026258	`PF03169.21`	OPT	47	657	9.9e-154	514.1

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
`Q2EF88`	Arabidopsis thaliana	Metal-nicotianamine transporter YSL3	66.270%	Swiss-Prot	strong database homology
`Q6R3L0`	Arabidopsis thaliana	Metal-nicotianamine transporter YSL1	65.778%	Swiss-Prot	strong database homology
`Q6R3K9`	Arabidopsis thaliana	Metal-nicotianamine transporter YSL2	65.408%	Swiss-Prot	strong database homology
`Q7XUJ2`	Oryza sativa subsp. japonica	Probable metal-nicotianamine transporter YSL9	64.060%	Swiss-Prot	strong database homology
`Q6H3Z3`	Oryza sativa subsp. japonica	Iron-phytosiderophore transporter YSL15	60.876%	Swiss-Prot	strong database homology

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