LXL04_038201 | RubberDandelionOmics

Gene overview

LXL04_038201

Reference: OH-1004 Chr: Chr09 Coordinates: 34070889-34071227 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

339 bp · LXL04_038201|LXL04_038201|OH1004|cDNA

ATGACGAGCTCGAATGCACGCTATTTCATGGCGCCTGATGTTGCTatttacaaaagtttaataAACGGGTATTTTAACGTTTCGAAGATGGAAGAGGCGATGAGTTTGTTTGACAAGATGATGAAAAAGTGCGTTGAATATGGTGCGATCATCTACGACAACATCGGGTTGTCTTTTCGATTTGTAAAGCCTAAATGTTCTGTGGAATTGTTAAAACAATATGCACTAGTAGCGGTACCGGATGAATGCACTTTCAAGAT...

CDS

Download CDS FASTA

339 bp · LXL04_038201|LXL04_038201|OH1004|CDS

ATGACGAGCTCGAATGCACGCTATTTCATGGCGCCTGATGTTGCTATTTACAAAAGTTTAATAAACGGGTATTTTAACGTTTCGAAGATGGAAGAGGCGATGAGTTTGTTTGACAAGATGATGAAAAAGTGCGTTGAATATGGTGCGATCATCTACGACAACATCGGGTTGTCTTTTCGATTTGTAAAGCCTAAATGTTCTGTGGAATTGTTAAAACAATATGCACTAGTAGCGGTACCGGATGAATGCACTTTCAAGAT...

Protein

Download Protein FASTA

112 aa · LXL04_038201|LXL04_038201|OH1004|PROTEIN

MTSSNARYFMAPDVAIYKSLINGYFNVSKMEEAMSLFDKMMKKCVEYGAIIYDNIGLSFRFVKPKCSVELLKQYALVAVPDECTFKIVMEGLCNNNRVDEALSLFQSIDDEE

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_038201`
TK1151 ID	TkAUNG028860
OH-1004 ID	LXL04_038201
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	88.600
Protein coverage (%)	TK1151 30.792 / OH-1004 93.750 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_038201

Location Chr09:34070889-34071227 (-)

Description Similar to Rf1: Protein Rf1, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g62720`	Pentatricopeptide repeat-containing protein At1g62720.	No verified direct reference in this release
`At5g41170`	Pentatricopeptide repeat-containing protein At5g41170, mitochondrial.	No verified direct reference in this release
`At1g12700`	Putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial.	No verified direct reference in this release
`At3g16710`	Putative pentatricopeptide repeat-containing protein At3g16710, mitochondrial.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q76C99`	Reduces the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene ORF79, encoding a cytotoxic peptide.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038201 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009555 pollen development Biological Process

GO:0009845 seed germination Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G62720

ath:AT5G41170

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.

Mitochondrion0.340

Rank 1 · LXL04_038201 · OH-1004

Cytoplasm0.228

Rank 2 · LXL04_038201 · OH-1004

Nucleus0.130

Rank 3 · LXL04_038201 · OH-1004

Plastid0.062

Rank 4 · LXL04_038201 · OH-1004

Extracellular0.044

Rank 5 · LXL04_038201 · 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.

PF12854.14PPR_111-40 aa

PF13041.13PPR_212-44 aa

PF01535.27PPR16-44 aa

PF12854.14PPR_179-106 aa

PF13041.13PPR_280-107 aa

PF01535.27PPR84-107 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038201	`PF12854.14`	PPR_1	11	40	2.8e-17	62.9
LXL04_038201	`PF13041.13`	PPR_2	12	44	1.2e-15	58.0
LXL04_038201	`PF01535.27`	PPR	16	44	2.3e-13	50.1
LXL04_038201	`PF12854.14`	PPR_1	79	106	2.8e-17	62.9
LXL04_038201	`PF13041.13`	PPR_2	80	107	1.2e-15	58.0
LXL04_038201	`PF01535.27`	PPR	84	107	2.3e-13	50.1

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
`Q9SI78`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62720	31.373%	Swiss-Prot	moderate database homology
`Q9FLL3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g41170, mitochondrial	32.039%	Swiss-Prot	moderate database homology
`P0C7Q7`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At1g12700, mitochondrial	30.000%	Swiss-Prot	moderate database homology
`Q9LUR2`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g16710, mitochondrial	30.097%	Swiss-Prot	moderate database homology
`Q76C99`	Oryza sativa subsp. indica	Protein Rf1, mitochondrial	34.314%	Swiss-Prot	moderate database homology

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