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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_035849
Reference: OH-1004 Chr: Chr08 Coordinates: 30546351-30549117 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2151 bp · LXL04_035849|LXL04_035849|OH1004|cDNA

ATGCCTCTGAATCTCAGCCTCCGAATCATCTTCATCTTAACAGTGGTCTGCAAGAAATTTTGGGAGATTGCTTACAGAAAGAAAGAAATCGACGGCGAGGGAGGTGGAACTCAGCATTTTTACAGGGAGTTGTTAAAGAACCCACCATTCTCTTTGGAGGGAAATTACCTTGGTTATAGCACAACCGATGAAGAAGGTATAGCACAACTGATGAAGAAAGGATGTAAAGAAAGAAGAGAAGTAGAGAAGAGTGTAGAAAG...

CDS

Download CDS FASTA

2151 bp · LXL04_035849|LXL04_035849|OH1004|CDS

ATGCCTCTGAATCTCAGCCTCCGAATCATCTTCATCTTAACAGTGGTCTGCAAGAAATTTTGGGAGATTGCTTACAGAAAGAAAGAAATCGACGGCGAGGGAGGTGGAACTCAGCATTTTTACAGGGAGTTGTTAAAGAACCCACCATTCTCTTTGGAGGGAAATTACCTTGGTTATAGCACAACCGATGAAGAAGGTATAGCACAACTGATGAAGAAAGGATGTAAAGAAAGAAGAGAAGTAGAGAAGAGTGTAGAAAG...

Protein

Download Protein FASTA

716 aa · LXL04_035849|LXL04_035849|OH1004|PROTEIN

MPLNLSLRIIFILTVVCKKFWEIAYRKKEIDGEGGGTQHFYRELLKNPPFSLEGNYLGYSTTDEEGIAQLMKKGCKERREVEKSVERGESKFRTFVPKMFSSITLVSPNLRFLQSPPPPPYLVDIHLPTSLNHNHNPLKKPRSSCSSTHEDPRFQCFSARHSKYQTRPDDKLPSCSDNIGDTYVINGKNLGNLLHFCTSIKEIKRLHAVVTKCRGDSRIFLDNNLLSGYLRMGCLIDARKVFDEMLDRNVVSWTAMLGGY...

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.

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ID Mapping

Input IDLXL04_035849
Source versionOH-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 IDLXL04_035849
LocationChr08:30546351-30549117 (-)
DescriptionSimilar to PCMP-A2: Pentatricopeptide repeat-containing protein At4g18520, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g18520 Required for proper chloroplast development.
Seedling Lethal1, a pentatricopeptide repeat protein lacking an E/E+ or DYW domain in Arabidopsis, is involved in plastid gene expression and early chloroplast development.2013 · DOI: 10.1104/pp.113.227199
PPR protein PDM1/SEL1 is involved in RNA editing and splicing of plastid genes in Arabidopsis thaliana.2015 · DOI: 10.1007/s11120-015-0171-4
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At3g09040 Pentatricopeptide repeat-containing protein At3g09040, mitochondrial. No verified direct reference in this release
At4g21300 Pentatricopeptide repeat-containing protein At4g21300. No verified direct reference in this release
At3g53360 Pentatricopeptide repeat-containing protein At3g53360, mitochondrial. 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_035849 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0008380 RNA splicing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0004519 endonuclease activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G11290
ath:AT4G18520
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.

Mitochondrion0.519
Rank 1 · LXL04_035849 · OH-1004
Plastid0.353
Rank 2 · LXL04_035849 · OH-1004
Nucleus0.058
Rank 3 · LXL04_035849 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_035849 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_035849 · 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.

PF01535.27PPR223-250 aa
PF13041.13PPR_2248-296 aa
PF01535.27PPR251-281 aa
PF13041.13PPR_2348-395 aa
PF12854.14PPR_1349-376 aa
PF13812.13PPR_3349-397 aa
PF01535.27PPR351-381 aa
PF13041.13PPR_2450-496 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_035849PF01535.27PPR2232507.5e-70227.1
LXL04_035849PF13041.13PPR_22482961.2e-73243.7
LXL04_035849PF01535.27PPR2512817.5e-70227.1
LXL04_035849PF13041.13PPR_23483951.2e-73243.7
LXL04_035849PF12854.14PPR_13493764.8e-39132.5
LXL04_035849PF13812.13PPR_33493974.5e-30104.2
LXL04_035849PF01535.27PPR3513817.5e-70227.1
LXL04_035849PF13041.13PPR_24504961.2e-73243.7
LXL04_035849PF12854.14PPR_14504784.8e-39132.5
LXL04_035849PF01535.27PPR4524827.5e-70227.1
LXL04_035849PF13041.13PPR_25505991.2e-73243.7
LXL04_035849PF13812.13PPR_35515994.5e-30104.2
LXL04_035849PF01535.27PPR5535837.5e-70227.1
LXL04_035849PF13041.13PPR_26216531.2e-73243.7
LXL04_035849PF01535.27PPR6266527.5e-70227.1
LXL04_035849PF12854.14PPR_16266484.8e-39132.5

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q0WNP3Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g18520, chloroplastic56.601%Swiss-Protstrong database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic31.953%Swiss-Protmoderate database homology
Q9SS83Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g09040, mitochondrial35.743%Swiss-Protmoderate database homology
Q9STE1Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2130031.740%Swiss-Protmoderate database homology
Q9LFI1Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g53360, mitochondrial32.609%Swiss-Protmoderate database homology

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