LXL04_016409 | RubberDandelionOmics

Gene overview

LXL04_016409

Reference: OH-1004 Chr: Chr03 Coordinates: 122004170-122005187 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

543 bp · LXL04_016409|LXL04_016409|OH1004|cDNA

ATGGCGATGCGGACTGCGACGTCGGTGGCGGCTGCCGGTCCTCGTGGGCTGAGATCGCTATTCTCAACAGTTTCTACAAACTTCCCCTTTCCTTCACAGCCCGCCAATCAACCGCAGAGGCCGCAGGCTGAACCGTCTACCAACCTCTTCGTATCAGGCAAATCCCCCTTAGCTTCATCTATTTCATTTTTATATGATCTAATCTCTACATATAATTACTCTTGTATGTTTTTATACAGTATAAATCTGTTGTTGGTAAA...

CDS

Download CDS FASTA

543 bp · LXL04_016409|LXL04_016409|OH1004|CDS

ATGGCGATGCGGACTGCGACGTCGGTGGCGGCTGCCGGTCCTCGTGGGCTGAGATCGCTATTCTCAACAGTTTCTACAAACTTCCCCTTTCCTTCACAGCCCGCCAATCAACCGCAGAGGCCGCAGGCTGAACCGTCTACCAACCTCTTCGTATCAGGCAAATCCCCCTTAGCTTCATCTATTTCATTTTTATATGATCTAATCTCTACATATAATTACTCTTGTATGTTTTTATACAGTATAAATCTGTTGTTGGTAAA...

Protein

Download Protein FASTA

180 aa · LXL04_016409|LXL04_016409|OH1004|PROTEIN

MAMRTATSVAAAGPRGLRSLFSTVSTNFPFPSQPANQPQRPQAEPSTNLFVSGKSPLASSISFLYDLISTYNYSCMFLYSINLLLVNAGLSKRTTDEGLRDCFAKFGEVVHARVVKDRASGWSKGFGFVRYSSLEGAAAGIEGMDGKFLDGWVIFAEYARPRDSPPPTPPSSYGNSQYGQ

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_016409`
TK1151 ID	TkA06G023210
OH-1004 ID	LXL04_016409
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	39.200
Protein coverage (%)	TK1151 11.064 / OH-1004 42.778 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016409

Location Chr03:122004170-122005187 (-)

Description Similar to ORRM2: Organelle RRM domain-containing protein 2, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g54580`	Involved in C-to-U editing of mitochondrial RNA.	Two RNA recognition motif-containing proteins are plant mitochondrial editing factors.2015 · DOI: 10.1093/nar/gkv245
`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
`At4g13850`	Promotes the cis-splicing and editing of several mitochondrial RNAs (including NAD5 transcripts).	No verified direct reference in this release
`At5g61030`	Possibly has a role in RNA transcription or processing during stress (By similarity).	Two RNA recognition motif-containing proteins are plant mitochondrial editing factors.2015 · DOI: 10.1093/nar/gkv245
`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

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016409 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0006858 extracellular transport Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009631 cold acclimation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009845 seed germination Biological Process

GO:0016554 cytidine to uridine editing Biological Process

GO:0050658 RNA transport Biological Process

GO:0050688 regulation of defense response to virus Biological Process

GO:0060567 negative regulation of termination of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT1G73530

ath:AT4G13850

ath:AT5G06210

ath:AT5G54580

ath:AT5G61030

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.

Plastid0.502

Rank 1 · LXL04_016409 · OH-1004

Mitochondrion0.283

Rank 2 · LXL04_016409 · OH-1004

Cytoplasm0.151

Rank 3 · LXL04_016409 · OH-1004

Nucleus0.146

Rank 4 · LXL04_016409 · OH-1004

Peroxisome0.041

Rank 5 · LXL04_016409 · 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.

PF00076.29RRM_189-151 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016409	`PF00076.29`	RRM_1	89	151	1.3e-15	57.7

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
`Q9FIU6`	Arabidopsis thaliana	Organelle RRM domain-containing protein 2, mitochondrial	51.176%	Swiss-Prot	strong database homology
`Q9FX45`	Arabidopsis thaliana	Organelle RRM domain-containing protein 6, chloroplastic	46.512%	Swiss-Prot	weak database homology
`Q9SVM8`	Arabidopsis thaliana	Glycine-rich RNA-binding protein 2, mitochondrial	47.191%	Swiss-Prot	weak database homology
`Q9FNR1`	Arabidopsis thaliana	Glycine-rich RNA-binding protein 3, mitochondrial	40.909%	Swiss-Prot	weak database homology
`Q9FFZ6`	Arabidopsis thaliana	Small RNA-binding protein 11, chloroplastic	40.860%	Swiss-Prot	moderate database homology

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