LXL04_022138 | RubberDandelionOmics

Gene overview

LXL04_022138

Reference: OH-1004 Chr: Chr04 Coordinates: 145198850-145200906 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1212 bp · LXL04_022138|LXL04_022138|OH1004|cDNA

ATGGCATCATCCATGGTGCCCGCTCTATCTTCATCCCTCTGCACAACTCCTCAGAAGCCATCAATAATATTCATCCCTTTCTTACCCTCATTTCAGAAGTCCATTTCCCTCCAATTTAACTTCAAATTCCGCAAACCCATATTCAAATTCAATCAGAAGAACACCGTCACCCTAACGGCAATCACCTGTTTGAAATCACGAAGTACATATGAAGCACCAGCAACGAATTCAAGTTACGCTGTCACTGCTCCATCATTGTC...

CDS

Download CDS FASTA

1212 bp · LXL04_022138|LXL04_022138|OH1004|CDS

ATGGCATCATCCATGGTGCCCGCTCTATCTTCATCCCTCTGCACAACTCCTCAGAAGCCATCAATAATATTCATCCCTTTCTTACCCTCATTTCAGAAGTCCATTTCCCTCCAATTTAACTTCAAATTCCGCAAACCCATATTCAAATTCAATCAGAAGAACACCGTCACCCTAACGGCAATCACCTGTTTGAAATCACGAAGTACATATGAAGCACCAGCAACGAATTCAAGTTACGCTGTCACTGCTCCATCATTGTC...

Protein

Download Protein FASTA

403 aa · LXL04_022138|LXL04_022138|OH1004|PROTEIN

MASSMVPALSSSLCTTPQKPSIIFIPFLPSFQKSISLQFNFKFRKPIFKFNQKNTVTLTAITCLKSRSTYEAPATNSSYAVTAPSLSESNGHRNWIVVVKAPPPQHAVSKPDIIDYYVKILERVLGRWLIQFLSLESNSEKEAQGCIYNASYDTHFGFCCDIDEETSQKLAGLPEVLSINPDPDFNSIQKDYTNEKTESLLSNKLKNWLVRVEMPPLAVITRAQLVDYYTQILTKVLGNEKDAQKCIYHISSQSNYGFCC...

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_022138`
TK1151 ID	TkA05G447270
OH-1004 ID	LXL04_022138
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.800
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_022138

Location Chr04:145198850-145200906 (+)

Description Similar to ORRM1: Organelle RRM domain-containing protein 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g20930`	Involved in C-to-U editing of chloroplastic RNA.	An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize.2013 · DOI: 10.1073/pnas.1220162110
`At1g73530`	Involved in C-to-U editing of chloroplastic RNA.	An Organelle RNA Recognition Motif Protein Is Required for Photosystem II Subunit psbF Transcript Editing.2017 · DOI: 10.1104/pp.16.01623
`At5g06210`	Probable RNA-binding protein that may be involved in salt and oxidative stress tolerance.	The Arabidopsis chloroplast protein S-RBP11 is involved in oxidative and salt stress responses.2014 · DOI: 10.1007/s00299-013-1560-9

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0730800`	Involved in C-to-U editing of chloroplastic RNA.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022138 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009409 response to cold Biological Process

GO:0016554 cytidine to uridine editing Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:1900871 chloroplast mRNA modification Biological Process

GO:1901002 positive regulation of response to salt stress Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G73530

ath:AT3G20930

ath:AT5G06210

dosa:Os02g0730800

osa:4330618

zma:100304402

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.

Plastid0.944

Rank 1 · LXL04_022138 · OH-1004

Mitochondrion0.063

Rank 2 · LXL04_022138 · OH-1004

Cytoplasm0.048

Rank 3 · LXL04_022138 · OH-1004

Nucleus0.039

Rank 4 · LXL04_022138 · OH-1004

Peroxisome0.024

Rank 5 · LXL04_022138 · 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.

PF21864.2MORF_dom93-196 aa

PF21864.2MORF_dom206-294 aa

PF00076.29RRM_1314-380 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022138	`PF21864.2`	MORF_dom	93	196	2.2e-64	214.0
LXL04_022138	`PF21864.2`	MORF_dom	206	294	2.2e-64	214.0
LXL04_022138	`PF00076.29`	RRM_1	314	380	6.1e-20	71.6

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
`Q8L440`	Arabidopsis thaliana	Organelle RRM domain-containing protein 1, chloroplastic	57.051%	Swiss-Prot	strong database homology
`Q9FX45`	Arabidopsis thaliana	Organelle RRM domain-containing protein 6, chloroplastic	50.562%	Swiss-Prot	weak database homology
`Q9FFZ6`	Arabidopsis thaliana	Small RNA-binding protein 11, chloroplastic	44.898%	Swiss-Prot	weak database homology
`Q6YWP9`	Oryza sativa subsp. japonica	Organelle RRM domain-containing protein 1, chloroplastic	53.049%	Swiss-Prot	strong database homology

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