LXL04_009579 | RubberDandelionOmics

Gene overview

LXL04_009579

Reference: OH-1004 Chr: Chr02 Coordinates: 129234298-129236013 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1716 bp · LXL04_009579|LXL04_009579|OH1004|cDNA

ATGCATGGAACTCTGCGATTCAAAGTTGAAATCTTTAAGCAGTTTTTCAGGTTTTCAGCTTCTCATAACTTTTGTTCATTAAAATCCAATATACCCATCAATTTGAATGTAAAAACACTTAACCAGCTGCTTAATCAGCGACCACCGTTGTCCCAACTTAAGCAAGTACATGCGCAAGTCATCTCCCAATCACTTTCATCGTACTCCATTCTGATCGACTCTTTAATTCATTGCTATCTATCAACTAATAGCCTCACCTC...

CDS

Download CDS FASTA

1716 bp · LXL04_009579|LXL04_009579|OH1004|CDS

ATGCATGGAACTCTGCGATTCAAAGTTGAAATCTTTAAGCAGTTTTTCAGGTTTTCAGCTTCTCATAACTTTTGTTCATTAAAATCCAATATACCCATCAATTTGAATGTAAAAACACTTAACCAGCTGCTTAATCAGCGACCACCGTTGTCCCAACTTAAGCAAGTACATGCGCAAGTCATCTCCCAATCACTTTCATCGTACTCCATTCTGATCGACTCTTTAATTCATTGCTATCTATCAACTAATAGCCTCACCTC...

Protein

Download Protein FASTA

571 aa · LXL04_009579|LXL04_009579|OH1004|PROTEIN

MHGTLRFKVEIFKQFFRFSASHNFCSLKSNIPINLNVKTLNQLLNQRPPLSQLKQVHAQVISQSLSSYSILIDSLIHCYLSTNSLTSARTLFDQYPNYPPPILLWNLVIRSYSKLQHSPEPINLFRQLNALQNNPLVVPDKYTFTFLITSCTHQNSELLGTIVHGILIKNGHVSNLYIANSLINLYAVFRILHEARKVFDEMPERDVFSWTSLLGGHVKQGEMTTASKIFTMMPIRNTVSWAVLISGFLDCGRYIDVLSY...

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_009579`
TK1151 ID	TkA03G449710
OH-1004 ID	LXL04_009579
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.000
Protein coverage (%)	TK1151 97.416 / OH-1004 72.154 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_009579

Location Chr02:129234298-129236013 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g66520`	Pentatricopeptide repeat-containing protein At5g66520.	No verified direct reference in this release
`At2g20540`	Pentatricopeptide repeat-containing protein At2g20540.	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
`At2g29760`	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
`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_009579 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0016554 cytidine to uridine editing 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

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G20540

ath:AT2G29760

ath:AT4G37380

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.

Mitochondrion0.586

Rank 1 · LXL04_009579 · OH-1004

Plastid0.209

Rank 2 · LXL04_009579 · OH-1004

Nucleus0.057

Rank 3 · LXL04_009579 · OH-1004

Cytoplasm0.037

Rank 4 · LXL04_009579 · OH-1004

Cell membrane0.005

Rank 5 · LXL04_009579 · 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.

PF12854.14PPR_1339-368 aa

PF13041.13PPR_2340-387 aa

PF01535.27PPR345-373 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009579	`PF12854.14`	PPR_1	339	368	8.5e-17	61.3
LXL04_009579	`PF13041.13`	PPR_2	340	387	9.4e-32	109.6
LXL04_009579	`PF01535.27`	PPR	345	373	1.7e-32	110.0

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	38.690%	Swiss-Prot	moderate database homology
`Q9SIL5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g20540	34.930%	Swiss-Prot	moderate database homology
`Q9SZT8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein ELI1, chloroplastic	34.034%	Swiss-Prot	moderate database homology
`O82380`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g29760, chloroplastic	33.267%	Swiss-Prot	moderate database homology
`O49399`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g18840	33.200%	Swiss-Prot	moderate database homology

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