LXL04_006443 | RubberDandelionOmics

Gene overview

LXL04_006443

Reference: OH-1004 Chr: Chr02 Coordinates: 10780291-10782225 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1935 bp · LXL04_006443|LXL04_006443|OH1004|cDNA

ATGAGAAATCAATGGCGTCTCCTCCTTCAACGATGCAAACCAGTTTCCGAGCTTCAATTCAAGGTACAATCATCAACTACTGTTCCTCTGTATCACAATCGCACTTTCCATTCAGTTAACCCTCACTCTCCTGCACTCCACATTCATTTCCAAAACCGTAGTTTCCCACGATTATTCACATCGTCATCTGAACTCGCTGTTGAACAAAATAAAGCCACGGATCAATCCGCCATTACATCAACATTGATTGAGCTATATTC...

CDS

Download CDS FASTA

1935 bp · LXL04_006443|LXL04_006443|OH1004|CDS

ATGAGAAATCAATGGCGTCTCCTCCTTCAACGATGCAAACCAGTTTCCGAGCTTCAATTCAAGGTACAATCATCAACTACTGTTCCTCTGTATCACAATCGCACTTTCCATTCAGTTAACCCTCACTCTCCTGCACTCCACATTCATTTCCAAAACCGTAGTTTCCCACGATTATTCACATCGTCATCTGAACTCGCTGTTGAACAAAATAAAGCCACGGATCAATCCGCCATTACATCAACATTGATTGAGCTATATTC...

Protein

Download Protein FASTA

644 aa · LXL04_006443|LXL04_006443|OH1004|PROTEIN

MRNQWRLLLQRCKPVSELQFKVQSSTTVPLYHNRTFHSVNPHSPALHIHFQNRSFPRLFTSSSELAVEQNKATDQSAITSTLIELYSDPIKSNEDVMLELRSKPDLTSTGDVTKLFENRGSEPKAAKAFYDWVMSKESDNLSSNSCNRLLGMLGANGLVKEFWDSVDFMKKKGYGVKKGASVRAMAKFEEEGLKDEVQKLKDLFALGSIDASIEKLSSKVSKIIQQTPWGDDVETKLQELGAVYSPDLVKMVLENLGSDP...

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_006443`
TK1151 ID	TkA03G037180
OH-1004 ID	LXL04_006443
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.200
Protein coverage (%)	TK1151 91.054 / OH-1004 44.255 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_006443

Location Chr02:10780291-10782225 (+)

Description Similar to At3g02490: Pentatricopeptide repeat-containing protein At3g02490, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02490`	Pentatricopeptide repeat-containing protein At3g02490, mitochondrial.	No verified direct reference in this release
`At5g15980`	Small ribosomal subunit protein mS81 (rPPR8).	No verified direct reference in this release
`At3g48250`	Pentatricopeptide repeat-containing protein At3g48250, chloroplastic.	No verified direct reference in this release
`At1g74850`	Involved in plastid gene expression.	pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression.2006 · DOI: 10.1105/tpc.105.036392
`At3g06920`	Pentatricopeptide repeat-containing protein At3g06920.	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_006443 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008380 RNA splicing Biological Process

GO:0042793 plastid transcription Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005840 ribosome Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0042644 chloroplast nucleoid Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G74850

ath:AT3G02490

ath:AT3G06920

ath:AT3G48250

ath:AT5G15980

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.

Mitochondrion0.794

Rank 1 · LXL04_006443 · OH-1004

Plastid0.136

Rank 2 · LXL04_006443 · OH-1004

Nucleus0.062

Rank 3 · LXL04_006443 · OH-1004

Cytoplasm0.039

Rank 4 · LXL04_006443 · OH-1004

Cell membrane0.013

Rank 5 · LXL04_006443 · 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.

PF29070.1MSC6_N277-411 aa

PF13041.13PPR_2279-326 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006443	`PF29070.1`	MSC6_N	277	411	1.5e-09	38.2
LXL04_006443	`PF13041.13`	PPR_2	279	326	2.4e-15	57.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9M891`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g02490, mitochondrial	40.208%	Swiss-Prot	moderate database homology
`Q8LPF1`	Arabidopsis thaliana	Small ribosomal subunit protein mS81 (rPPR8)	38.705%	Swiss-Prot	moderate database homology
`Q9STK5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g48250, chloroplastic	33.457%	Swiss-Prot	moderate database homology
`Q9S7Q2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g74850, chloroplastic	23.398%	Swiss-Prot	weak database homology
`Q9M907`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g06920	20.979%	Swiss-Prot	weak database homology

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