LXL04_034743 | RubberDandelionOmics

Gene overview

LXL04_034743

Reference: OH-1004 Chr: Chr07 Coordinates: 115439387-115440934 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1548 bp · LXL04_034743|LXL04_034743|OH1004|cDNA

ATGGGACTCATGGCGATGCTCCCTCATTCTCCCGCGAAAACCATCAAGCAAAAAGTCTTGTCCCTAATTCACGACTCAAAAGAACTCCATATCATCTTCCAAATTCATGCATTCCTTCTAAAAACCTCCCTACAATCCAACAATTTCATCGTCACCAAGCTGCTTCGTAATTTCTCTTTGAATTCCTCAAACAATTTGCGTTATGCCAGATCCTTTTTCGACGAAATGCCAAGTCCAGACACATTTCTCTGGAACACCAT...

CDS

Download CDS FASTA

1548 bp · LXL04_034743|LXL04_034743|OH1004|CDS

ATGGGACTCATGGCGATGCTCCCTCATTCTCCCGCGAAAACCATCAAGCAAAAAGTCTTGTCCCTAATTCACGACTCAAAAGAACTCCATATCATCTTCCAAATTCATGCATTCCTTCTAAAAACCTCCCTACAATCCAACAATTTCATCGTCACCAAGCTGCTTCGTAATTTCTCTTTGAATTCCTCAAACAATTTGCGTTATGCCAGATCCTTTTTCGACGAAATGCCAAGTCCAGACACATTTCTCTGGAACACCAT...

Protein

Download Protein FASTA

515 aa · LXL04_034743|LXL04_034743|OH1004|PROTEIN

MGLMAMLPHSPAKTIKQKVLSLIHDSKELHIIFQIHAFLLKTSLQSNNFIVTKLLRNFSLNSSNNLRYARSFFDEMPSPDTFLWNTMIRAYLNSQNHDECLSLFLQLRRQDRLFIDSFSLSLVVQACGRSGFLQNGQTIHAQVFKLGFTNDLFVQTGLTEMYVKFGWIELARKVFSEMKDPDLVSYNVMLAEYMRIGEIGLARQLFDNMPQRDLVSWNTMIHGYASPPHGDKDLVSCNTQSQEALNLFHKMQLSKFLPDK...

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_034743`
TK1151 ID	TkA08G431920
OH-1004 ID	LXL04_034743
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	76.000
Protein coverage (%)	TK1151 98.990 / OH-1004 97.864 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_034743

Location Chr07:115439387-115440934 (+)

Description Similar to PCMP-H61: Pentatricopeptide repeat-containing protein At5g66520

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g66520`	Pentatricopeptide repeat-containing protein At5g66520.	No verified direct reference in this release
`At5g40405`	Putative pentatricopeptide repeat-containing protein At5g40405.	No verified direct reference in this release
`At5g48910`	Pentatricopeptide repeat-containing protein At5g48910.	No verified direct reference in this release
`At1g74630`	Pentatricopeptide repeat-containing protein At1g74630.	No verified direct reference in this release
`At4g18840`	Pentatricopeptide repeat-containing protein At4g18840.	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_034743 · 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: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:AT1G74630

ath:AT4G18840

ath:AT5G40405

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.

Mitochondrion0.624

Rank 1 · LXL04_034743 · OH-1004

Plastid0.191

Rank 2 · LXL04_034743 · OH-1004

Nucleus0.050

Rank 3 · LXL04_034743 · OH-1004

Cytoplasm0.033

Rank 4 · LXL04_034743 · OH-1004

Cell membrane0.005

Rank 5 · LXL04_034743 · 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_279-127 aa

PF01535.27PPR83-109 aa

PF13041.13PPR_2181-225 aa

PF13041.13PPR_2213-271 aa

PF13041.13PPR_2324-372 aa

PF01535.27PPR328-357 aa

PF20431.5E_motif442-504 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_034743	`PF13041.13`	PPR_2	79	127	8.3e-42	141.8
LXL04_034743	`PF01535.27`	PPR	83	109	1.2e-41	138.8
LXL04_034743	`PF13041.13`	PPR_2	181	225	8.3e-42	141.8
LXL04_034743	`PF13041.13`	PPR_2	213	271	8.3e-42	141.8
LXL04_034743	`PF13041.13`	PPR_2	324	372	8.3e-42	141.8
LXL04_034743	`PF01535.27`	PPR	328	357	1.2e-41	138.8
LXL04_034743	`PF20431.5`	E_motif	442	504	4.9e-15	56.2

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
`Q9FJY7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g66520	40.125%	Swiss-Prot	moderate database homology
`Q9FND7`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At5g40405	36.948%	Swiss-Prot	moderate database homology
`Q9FI80`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g48910	37.769%	Swiss-Prot	moderate database homology
`Q9CA54`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g74630	35.067%	Swiss-Prot	moderate database homology
`O49399`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g18840	38.878%	Swiss-Prot	moderate database homology

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