LXL04_037243 | RubberDandelionOmics

Gene overview

LXL04_037243

Reference: OH-1004 Chr: Chr09 Coordinates: 4135659-4136666 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

543 bp · LXL04_037243|LXL04_037243|OH1004|cDNA

ATGCTAACTGCGTTCCTCACTCAGTTTCTTTCTGTTGAATTGAATAGTAAGAAGGAAGCTCAAGGCTGCATATATAATGCTTCTTACGACACCCAATTTGGATTCTGCTGCGACATAGACGAAGAAACTTCCCAAAAACTCGCAGGTTTGCCAGAAGTATTATCGATTAATCCTGATCCAGATTTCAACTCTATACAAAAAGATTATACCAATGAAAAGACTGAATCACATTCGTCTAATAAATTGAAGAACTGGCTTGT...

CDS

Download CDS FASTA

543 bp · LXL04_037243|LXL04_037243|OH1004|CDS

ATGCTAACTGCGTTCCTCACTCAGTTTCTTTCTGTTGAATTGAATAGTAAGAAGGAAGCTCAAGGCTGCATATATAATGCTTCTTACGACACCCAATTTGGATTCTGCTGCGACATAGACGAAGAAACTTCCCAAAAACTCGCAGGTTTGCCAGAAGTATTATCGATTAATCCTGATCCAGATTTCAACTCTATACAAAAAGATTATACCAATGAAAAGACTGAATCACATTCGTCTAATAAATTGAAGAACTGGCTTGT...

Protein

Download Protein FASTA

180 aa · LXL04_037243|LXL04_037243|OH1004|PROTEIN

MLTAFLTQFLSVELNSKKEAQGCIYNASYDTQFGFCCDIDEETSQKLAGLPEVLSINPDPDFNSIQKDYTNEKTESHSSNKLKNWLVRVEMPPLSVITRAQLVDYYTQILTKVLGNEKDAQKCIYHISSQSNYGFCCEVNDEHANELSSVPGVISVRPDESFDSDDKNYGDYNIQDSSIV

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_037243`
TK1151 ID	TkA04G263960
OH-1004 ID	LXL04_037243
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.734 / OH-1004 86.667 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_037243

Location Chr09:4135659-4136666 (+)

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
`At1g32580`	Involved in organellar RNA editing.	No verified direct reference in this release
`At2g35240`	Involved in organellar RNA editing.	No verified direct reference in this release

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_037243 · 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: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:AT3G20930

dosa:Os02g0730800

osa:4330618

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.

Cytoplasm0.506

Rank 1 · LXL04_037243 · OH-1004

Nucleus0.223

Rank 2 · LXL04_037243 · OH-1004

Extracellular0.150

Rank 3 · LXL04_037243 · OH-1004

Lysosome / Vacuole0.104

Rank 4 · LXL04_037243 · OH-1004

Endoplasmic reticulum0.095

Rank 5 · LXL04_037243 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF21864.2MORF_dom8-73 aa

PF21864.2MORF_dom83-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037243	`PF21864.2`	MORF_dom	8	73	2.5e-58	194.6
LXL04_037243	`PF21864.2`	MORF_dom	83	172	2.5e-58	194.6

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8L440`	Arabidopsis thaliana	Organelle RRM domain-containing protein 1, chloroplastic	45.251%	Swiss-Prot	moderate database homology
`Q9C7Y2`	Arabidopsis thaliana	Multiple organellar RNA editing factor 5, chloroplastic/mitochondrial	37.500%	Swiss-Prot	weak database homology
`O82169`	Arabidopsis thaliana	Multiple organellar RNA editing factor 6, mitochondrial	38.636%	Swiss-Prot	weak database homology
`Q6YWP9`	Oryza sativa subsp. japonica	Organelle RRM domain-containing protein 1, chloroplastic	47.283%	Swiss-Prot	moderate database homology

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