LXL04_028047 | RubberDandelionOmics

Gene overview

LXL04_028047

Reference: OH-1004 Chr: Chr06 Coordinates: 29671104-29672699 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1596 bp · LXL04_028047|LXL04_028047|OH1004|cDNA

ATGATCAGGAAAACTGTTGATCCCTCTTTTAATGCCACCGTGAAAACCTTTTCAGAAAAATGCAAAACCGTAAATCAATTCAAAGAAATCCACGCCCGCCTCATCAAATGTCACCTGCCGGAAAATCCCGTTGCCATCGGACCTCTGCTCTCAGTCCTAGCGACCTCTAAGACTGCTTCTTTCTTCTCCTATGCTCGTTTAATCTTCCAACACCTGCGATTCCGGAACACTTTCATGTACAATACCATGATTCGAGGTTA...

CDS

Download CDS FASTA

1596 bp · LXL04_028047|LXL04_028047|OH1004|CDS

ATGATCAGGAAAACTGTTGATCCCTCTTTTAATGCCACCGTGAAAACCTTTTCAGAAAAATGCAAAACCGTAAATCAATTCAAAGAAATCCACGCCCGCCTCATCAAATGTCACCTGCCGGAAAATCCCGTTGCCATCGGACCTCTGCTCTCAGTCCTAGCGACCTCTAAGACTGCTTCTTTCTTCTCCTATGCTCGTTTAATCTTCCAACACCTGCGATTCCGGAACACTTTCATGTACAATACCATGATTCGAGGTTA...

Protein

Download Protein FASTA

531 aa · LXL04_028047|LXL04_028047|OH1004|PROTEIN

MIRKTVDPSFNATVKTFSEKCKTVNQFKEIHARLIKCHLPENPVAIGPLLSVLATSKTASFFSYARLIFQHLRFRNTFMYNTMIRGYLQNGDQASAFFCYIDMLRFGLVPNNYTFPPLIKACSSITNSKFIGYSVHGHVLKLGFEDDQFVGSALVDFYFANSEIGNARTVFDEIPIKDVVLWTNLIDGYGKNEDILNARKLFDEMPERTVISWSAIMAAYSRVNDFHEVIHLFTKMQKLNIKPNDSILVTVLTACANLGA...

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_028047`
TK1151 ID	TkA07G115650
OH-1004 ID	LXL04_028047
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 98.694 / OH-1004 99.623 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_028047

Location Chr06:29671104-29672699 (-)

Description Similar to PCMP-E78: Pentatricopeptide repeat-containing protein At2g20540

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g20540`	Pentatricopeptide repeat-containing protein At2g20540.	No verified direct reference in this release
`At5g66520`	Pentatricopeptide repeat-containing protein At5g66520.	No verified direct reference in this release
`At5g48910`	Pentatricopeptide repeat-containing protein At5g48910.	No verified direct reference in this release
`At5g06540`	Pentatricopeptide repeat-containing protein At5g06540.	No verified direct reference in this release
`At5g08305`	Pentatricopeptide repeat-containing protein At5g08305.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028047 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0016554 cytidine to uridine editing Biological Process

GO:0031425 chloroplast RNA processing Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:1900865 chloroplast RNA 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

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G20540

ath:AT5G06540

ath:AT5G08305

ath:AT5G48910

ath:AT5G66520

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Mitochondrion0.668

Rank 1 · LXL04_028047 · OH-1004

Plastid0.150

Rank 2 · LXL04_028047 · OH-1004

Nucleus0.053

Rank 3 · LXL04_028047 · OH-1004

Cytoplasm0.035

Rank 4 · LXL04_028047 · OH-1004

Cell membrane0.005

Rank 5 · LXL04_028047 · 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.

PF13041.13PPR_276-123 aa

PF13041.13PPR_2177-209 aa

PF12854.14PPR_1178-205 aa

PF01535.27PPR180-208 aa

PF13041.13PPR_2209-255 aa

PF13041.13PPR_2310-357 aa

PF20431.5E_motif431-492 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028047	`PF13041.13`	PPR_2	76	123	4.3e-40	136.3
LXL04_028047	`PF13041.13`	PPR_2	177	209	4.3e-40	136.3
LXL04_028047	`PF12854.14`	PPR_1	178	205	3e-21	75.6
LXL04_028047	`PF01535.27`	PPR	180	208	1e-36	123.3
LXL04_028047	`PF13041.13`	PPR_2	209	255	4.3e-40	136.3
LXL04_028047	`PF13041.13`	PPR_2	310	357	4.3e-40	136.3
LXL04_028047	`PF20431.5`	E_motif	431	492	8.8e-07	29.8

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
`Q9SIL5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g20540	34.059%	Swiss-Prot	moderate database homology
`Q9FJY7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g66520	34.200%	Swiss-Prot	moderate database homology
`Q9FI80`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g48910	35.728%	Swiss-Prot	moderate database homology
`Q9FG16`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g06540	34.286%	Swiss-Prot	moderate database homology
`P0C8Q7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g08305	34.653%	Swiss-Prot	moderate database homology

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