LXL04_025617 | RubberDandelionOmics

Gene overview

LXL04_025617

Reference: OH-1004 Chr: Chr05 Coordinates: 114354020-114356018 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

894 bp · LXL04_025617|LXL04_025617|OH1004|cDNA

ATGAGTTGGTCCTGTAGTAACTATCTTTGTCTGTCGAGCTCAAGCTCAAGCTCGAGCTCTCTCATCAGTTCCCATGAACTTACGCGGGTTAACAGCTGCAATTTGTCTTGTGAGTATAAAGAACAAAGAAGGAAAGATCCAATAAACATTGTTGCTTATAACGGCTTGAAACCTCCATCTTATAAACTCGACAAACCCCAAAAGAGGAAAAACCATGCCTTAAAGAAGCCAAATAACATCTCTGCTTACTACAGCTTAAA...

CDS

Download CDS FASTA

894 bp · LXL04_025617|LXL04_025617|OH1004|CDS

ATGAGTTGGTCCTGTAGTAACTATCTTTGTCTGTCGAGCTCAAGCTCAAGCTCGAGCTCTCTCATCAGTTCCCATGAACTTACGCGGGTTAACAGCTGCAATTTGTCTTGTGAGTATAAAGAACAAAGAAGGAAAGATCCAATAAACATTGTTGCTTATAACGGCTTGAAACCTCCATCTTATAAACTCGACAAACCCCAAAAGAGGAAAAACCATGCCTTAAAGAAGCCAAATAACATCTCTGCTTACTACAGCTTAAA...

Protein

Download Protein FASTA

297 aa · LXL04_025617|LXL04_025617|OH1004|PROTEIN

MSWSCSNYLCLSSSSSSSSSLISSHELTRVNSCNLSCEYKEQRRKDPINIVAYNGLKPPSYKLDKPQKRKNHALKKPNNISAYYSLKPPSYKFDALEPYMSKRTLEVHWGEHHRAYVDTLNKYLSKNDVLYGYTMDELLKVTYNNGNPLPEFNVAAQVWNHDFFWESMQPGGGNLPILGLMEQIEKDFGSFANFRQDFIESAMSLFGSGWVWLVLKRNEKRLAIATTTNAVTPLVWDDIPLLSLDMWEHAYYRDYKNDRV...

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_025617`
TK1151 ID	TkA06G048680
OH-1004 ID	LXL04_025617
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

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Basic Information and Functional Annotation

Gene ID LXL04_025617

Location Chr05:114354020-114356018 (-)

Description Similar to FSD3: Superoxide dismutase [Fe] 3, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g23310`	Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems (By similarity).	A heterocomplex of iron superoxide dismutases defends chloroplast nucleoids against oxidative stress and is essential for chloroplast development in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061341
`At5g51100`	Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems (By similarity).	A heterocomplex of iron superoxide dismutases defends chloroplast nucleoids against oxidative stress and is essential for chloroplast development in Arabidopsis.2008 · DOI: 10.1105/tpc.108.061341
`At4g25100`	Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0143000`	Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025617 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007623 circadian rhythm Biological Process

GO:0009411 response to UV Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009642 response to light intensity Biological Process

GO:0010193 response to ozone Biological Process

GO:0019430 removal of superoxide radicals Biological Process

GO:0046686 response to cadmium ion Biological Process

GO:0046688 response to copper ion Biological Process

GO:0000427 plastid-encoded plastid RNA polymerase complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT4G25100

ath:AT5G23310

ath:AT5G51100

dosa:Os06g0143000

osa:4340091

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.

Plastid0.981

Rank 1 · LXL04_025617 · OH-1004

Mitochondrion0.031

Rank 2 · LXL04_025617 · OH-1004

Cytoplasm0.018

Rank 3 · LXL04_025617 · OH-1004

Nucleus0.014

Rank 4 · LXL04_025617 · OH-1004

Peroxisome0.014

Rank 5 · LXL04_025617 · 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.

PF00081.28Sod_Fe_N84-168 aa

PF02777.24Sod_Fe_C180-276 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025617	`PF00081.28`	Sod_Fe_N	84	168	3.8e-17	63.2
LXL04_025617	`PF02777.24`	Sod_Fe_C	180	276	1.8e-33	115.4

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
`Q9FMX0`	Arabidopsis thaliana	Superoxide dismutase [Fe] 3, chloroplastic	71.101%	Swiss-Prot	strong database homology
`Q9LU64`	Arabidopsis thaliana	Superoxide dismutase [Fe] 2, chloroplastic	50.679%	Swiss-Prot	moderate database homology
`P21276`	Arabidopsis thaliana	Superoxide dismutase [Fe] 1, chloroplastic	51.942%	Swiss-Prot	moderate database homology
`Q5VSB7`	Oryza sativa subsp. japonica	Superoxide dismutase [Fe] 2, chloroplastic	61.017%	Swiss-Prot	strong database homology

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