LXL04_024111 | RubberDandelionOmics

Gene overview

LXL04_024111

Reference: OH-1004 Chr: Chr05 Coordinates: 81299585-81300235 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

651 bp · LXL04_024111|LXL04_024111|OH1004|cDNA

ATGAAACAAAAGGGCGTGGACCCCACTTTAGAGCACTATACGTGCATTGTTGGACTTTTAAGTAAGGCGGGACGATTAAATGAAGCTTTAAATTTCATGAAATCAACAAAAATCAAATGGGACACAGTTGCATGGCGTAAGTTACTCAATGCATGTCATGTTCACAGAAATTACACTTTAGGTACCCAAGTTGGAAACTTTATTACGAATTTGGACCCTGAAGATGAAGGAACTTACACCCTTTTGTCGAATATGTATGT...

CDS

Download CDS FASTA

651 bp · LXL04_024111|LXL04_024111|OH1004|CDS

ATGAAACAAAAGGGCGTGGACCCCACTTTAGAGCACTATACGTGCATTGTTGGACTTTTAAGTAAGGCGGGACGATTAAATGAAGCTTTAAATTTCATGAAATCAACAAAAATCAAATGGGACACAGTTGCATGGCGTAAGTTACTCAATGCATGTCATGTTCACAGAAATTACACTTTAGGTACCCAAGTTGGAAACTTTATTACGAATTTGGACCCTGAAGATGAAGGAACTTACACCCTTTTGTCGAATATGTATGT...

Protein

Download Protein FASTA

216 aa · LXL04_024111|LXL04_024111|OH1004|PROTEIN

MKQKGVDPTLEHYTCIVGLLSKAGRLNEALNFMKSTKIKWDTVAWRKLLNACHVHRNYTLGTQVGNFITNLDPEDEGTYTLLSNMYVKGENFSGVTKVRELMKKKKIKKEPGLSWVEIKNQTHVFVSGDDKHAEFVAILDKLKDLFGKIKTIGYVADMGNVLDDVEDEQKEDNIRFHSEKLAVAYGLLKTHEEVPIRIMKNLRICDDCHCVMKFVL

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_024111`
TK1151 ID	TkA06G177730
OH-1004 ID	LXL04_024111
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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_024111

Location Chr05:81299585-81300235 (+)

Description Similar to EMB2744: Pentatricopeptide repeat-containing protein At5g39680

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g39680`	Pentatricopeptide repeat-containing protein At5g39680.	No verified direct reference in this release
`At2g03880`	Pentatricopeptide repeat-containing protein At2g03880, mitochondrial.	No verified direct reference in this release
`At4g37380`	Plays a major role in single RNA editing events in chloroplasts.	No verified direct reference in this release
`At4g13650`	Pentatricopeptide repeat-containing protein At4g13650.	No verified direct reference in this release
`At2g22070`	Pentatricopeptide repeat-containing protein At2g22070.	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_024111 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009451 RNA modification 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:AT2G03880

ath:AT2G22070

ath:AT4G13650

ath:AT4G37380

ath:AT5G39680

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.

Mitochondrion0.608

Rank 1 · LXL04_024111 · OH-1004

Plastid0.160

Rank 2 · LXL04_024111 · OH-1004

Nucleus0.096

Rank 3 · LXL04_024111 · OH-1004

Cytoplasm0.067

Rank 4 · LXL04_024111 · OH-1004

Peroxisome0.013

Rank 5 · LXL04_024111 · 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.

PF20431.5E_motif57-117 aa

PF14432.13DYW_deaminase153-215 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024111	`PF20431.5`	E_motif	57	117	6.4e-15	55.9
LXL04_024111	`PF14432.13`	DYW_deaminase	153	215	4e-21	75.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FK93`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g39680	52.558%	Swiss-Prot	strong database homology
`Q9SI53`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g03880, mitochondrial	46.262%	Swiss-Prot	moderate database homology
`Q9SZT8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein ELI1, chloroplastic	41.121%	Swiss-Prot	moderate database homology
`Q9SVP7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g13650	43.458%	Swiss-Prot	moderate database homology
`Q9SHZ8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g22070	44.231%	Swiss-Prot	moderate database homology

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