LXL04_008643 | RubberDandelionOmics

Gene overview

LXL04_008643

Reference: OH-1004 Chr: Chr02 Coordinates: 105073135-105079933 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1458 bp · LXL04_008643|LXL04_008643|OH1004|cDNA

ATGGCGAGGCAAGAAAAATCTCAACATAATCCTAATCTAGGTGGTGTTGGTGGTGGTACAGTTTTTGTAGATATAGGAGGCAAAGTAGGAGAACTCTGCTCAGACCTTCCGATTGGCGCTACATCAGAGTCTCCGCAGTTCCACCGGTTCTTGGAAAAGATTAGTCTATCCAATGCTTTAATCGAAATGTATGCCAAAAGTGGAAACATCAACCAAGCACGCCAAGTGTTCGACAAAATGCTTCAAAGAGATGTAATTTC...

CDS

Download CDS FASTA

1458 bp · LXL04_008643|LXL04_008643|OH1004|CDS

ATGGCGAGGCAAGAAAAATCTCAACATAATCCTAATCTAGGTGGTGTTGGTGGTGGTACAGTTTTTGTAGATATAGGAGGCAAAGTAGGAGAACTCTGCTCAGACCTTCCGATTGGCGCTACATCAGAGTCTCCGCAGTTCCACCGGTTCTTGGAAAAGATTAGTCTATCCAATGCTTTAATCGAAATGTATGCCAAAAGTGGAAACATCAACCAAGCACGCCAAGTGTTCGACAAAATGCTTCAAAGAGATGTAATTTC...

Protein

Download Protein FASTA

485 aa · LXL04_008643|LXL04_008643|OH1004|PROTEIN

MARQEKSQHNPNLGGVGGGTVFVDIGGKVGELCSDLPIGATSESPQFHRFLEKISLSNALIEMYAKSGNINQARQVFDKMLQRDVISWSTMIVGLANHACAHSGFLEIGLKYFNSMKTDYNLNPGIQHYGCLVDLLGRTSCITRAFELVKTMPMKPDSAIWGSLLSSCRTKGNLEMAVIAVEHLLELEPEDVGNYVMLSNIYADLGRWDCVSKVRKLMREIKPFLAGKENTRAVKKNKLPLFYIKENKTPMLRMGPPGYD...

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_008643`
TK1151 ID	TkA04G507380
OH-1004 ID	LXL04_008643
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	68.600
Protein coverage (%)	TK1151 35.000 / OH-1004 12.990 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_008643

Location Chr02:105073135-105079933 (-)

Description Similar to PCMP-E78: Pentatricopeptide repeat-containing protein At2g20540

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g20540`	Pentatricopeptide repeat-containing protein At2g20540.	No verified direct reference in this release
`At5g56310`	Pentatricopeptide repeat-containing protein At5g56310.	No verified direct reference in this release
`At5g59200`	Involved in RNA editing event in chloroplasts.	A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
`At3g47530`	Pentatricopeptide repeat-containing protein At3g47530.	No verified direct reference in this release
`At5g43790`	Pentatricopeptide repeat-containing protein At5g43790.	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_008643 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0031425 chloroplast RNA processing 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

KEGG gene cross-reference

ath:AT2G20540

ath:AT5G56310

ath:AT5G59200

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.

Nucleus0.454

Rank 1 · LXL04_008643 · OH-1004

Cytoplasm0.357

Rank 2 · LXL04_008643 · OH-1004

Plastid0.100

Rank 3 · LXL04_008643 · OH-1004

Endoplasmic reticulum0.083

Rank 4 · LXL04_008643 · OH-1004

Cell membrane0.075

Rank 5 · LXL04_008643 · 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.

PF01535.27PPR58-84 aa

PF13041.13PPR_258-97 aa

PF20431.5E_motif173-220 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008643	`PF01535.27`	PPR	58	84	2.7e-11	43.6
LXL04_008643	`PF13041.13`	PPR_2	58	97	7.1e-08	33.2
LXL04_008643	`PF20431.5`	E_motif	173	220	4.2e-15	56.5

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
`Q9SIL5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g20540	52.000%	Swiss-Prot	weak database homology
`Q9FMA1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g56310	39.013%	Swiss-Prot	weak database homology
`Q9FIF7`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At5g59200, chloroplastic	40.625%	Swiss-Prot	weak database homology
`Q9SN85`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g47530	35.683%	Swiss-Prot	weak database homology
`Q9FG85`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g43790	44.271%	Swiss-Prot	weak database homology

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