LXL04_021116 | RubberDandelionOmics

Gene overview

LXL04_021116

Reference: OH-1004 Chr: Chr04 Coordinates: 122011033-122012361 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1329 bp · LXL04_021116|LXL04_021116|OH1004|cDNA

ATGATCAAAGCGTCTCTGCTTCGTAACGAACTAAACACGTCGTTTCGCTTATACAAACGCCTGCTTGAAAACGGCATGCATCCTGATAATTATACACTTCCTTACATCTTAAAAGCTTGTGCGTACATGGAAAGCTTCCGTCTCGGAGAGCTGGTTCATGGCCATTGTTTGCAATTGGGGTTTTTGTTCGATAGTTTTGTCGGTAACACTTTGATAATGATGTATTCTCTATTCGGCAACATGGAAAACGCACGGTacgt...

CDS

Download CDS FASTA

1329 bp · LXL04_021116|LXL04_021116|OH1004|CDS

ATGATCAAAGCGTCTCTGCTTCGTAACGAACTAAACACGTCGTTTCGCTTATACAAACGCCTGCTTGAAAACGGCATGCATCCTGATAATTATACACTTCCTTACATCTTAAAAGCTTGTGCGTACATGGAAAGCTTCCGTCTCGGAGAGCTGGTTCATGGCCATTGTTTGCAATTGGGGTTTTTGTTCGATAGTTTTGTCGGTAACACTTTGATAATGATGTATTCTCTATTCGGCAACATGGAAAACGCACGGTACGT...

Protein

Download Protein FASTA

442 aa · LXL04_021116|LXL04_021116|OH1004|PROTEIN

MIKASLLRNELNTSFRLYKRLLENGMHPDNYTLPYILKACAYMESFRLGELVHGHCLQLGFLFDSFVGNTLIMMYSLFGNMENARYVFDEMPTHCVISWTVLISGYAKIGDIDLARVTFDEAPVKDRGIWGSIISGYVQNNCFKEGLHMFRLMQSTNIIPDEAILVSILGACAHLGTLEIGIWIHKQLNAIKLRSSVKLTTALMDMYCKCGKLDLALKLFDEMPERDTISWNVMISGLAIHGEGQHALRLFSQMETTNIP...

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_021116`
TK1151 ID	TkA05G355260
OH-1004 ID	LXL04_021116
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	98.200
Protein coverage (%)	TK1151 88.224 / 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_021116

Location Chr04:122011033-122012361 (+)

Description Similar to PCMP-E51: Putative pentatricopeptide repeat-containing protein At3g15930

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g15930`	Putative pentatricopeptide repeat-containing protein At3g15930.	No verified direct reference in this release
`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
`At2g22410`	Pentatricopeptide repeat-containing protein At2g22410, 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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021116 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G20540

ath:AT3G15930

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.

Mitochondrion0.629

Rank 1 · LXL04_021116 · OH-1004

Plastid0.218

Rank 2 · LXL04_021116 · OH-1004

Nucleus0.041

Rank 3 · LXL04_021116 · OH-1004

Cytoplasm0.038

Rank 4 · LXL04_021116 · OH-1004

Peroxisome0.007

Rank 5 · LXL04_021116 · 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.

PF01535.27PPR129-155 aa

PF13041.13PPR_2200-226 aa

PF01535.27PPR201-226 aa

PF12854.14PPR_1201-223 aa

PF13041.13PPR_2227-274 aa

PF01535.27PPR229-255 aa

PF20431.5E_motif348-409 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021116	`PF01535.27`	PPR	129	155	2.1e-40	134.8
LXL04_021116	`PF13041.13`	PPR_2	200	226	6.5e-40	135.7
LXL04_021116	`PF01535.27`	PPR	201	226	2.1e-40	134.8
LXL04_021116	`PF12854.14`	PPR_1	201	223	2.2e-19	69.6
LXL04_021116	`PF13041.13`	PPR_2	227	274	6.5e-40	135.7
LXL04_021116	`PF01535.27`	PPR	229	255	2.1e-40	134.8
LXL04_021116	`PF20431.5`	E_motif	348	409	7.7e-13	49.2

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
`Q9LSB8`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g15930	38.776%	Swiss-Prot	moderate database homology
`Q9SIL5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g20540	39.394%	Swiss-Prot	moderate database homology
`Q9FJY7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g66520	37.020%	Swiss-Prot	moderate database homology
`Q9SJZ3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g22410, mitochondrial	35.104%	Swiss-Prot	moderate database homology
`Q9SZT8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein ELI1, chloroplastic	36.259%	Swiss-Prot	moderate database homology

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