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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_001010
Reference: OH-1004 Chr: Chr01 Coordinates: 18442862-18445660 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2799 bp · LXL04_001010|LXL04_001010|OH1004|cDNA

ATGGCAATTAATTTTGGGCTCATGACTATGCCACTAACGACAGTGAAGGCTTCCATTATTGGGAAAATTAGCGACGATAATATCCAGTCTGTTTCTAAAGTCTCTCGCAATTCCGTTAACATTTATCCTCCAAGAACCCTGAATGAAGCTTTCATTTCTCTTGCAAACAATCTCATTGACCAAGACACACGTTACAACACCAGTTGTTTAGATAATGCTTATTCGTTGATTCTTGAGCGGTGTTCCACACAAGAATCTTT...

CDS

Download CDS FASTA

2799 bp · LXL04_001010|LXL04_001010|OH1004|CDS

ATGGCAATTAATTTTGGGCTCATGACTATGCCACTAACGACAGTGAAGGCTTCCATTATTGGGAAAATTAGCGACGATAATATCCAGTCTGTTTCTAAAGTCTCTCGCAATTCCGTTAACATTTATCCTCCAAGAACCCTGAATGAAGCTTTCATTTCTCTTGCAAACAATCTCATTGACCAAGACACACGTTACAACACCAGTTGTTTAGATAATGCTTATTCGTTGATTCTTGAGCGGTGTTCCACACAAGAATCTTT...

Protein

Download Protein FASTA

932 aa · LXL04_001010|LXL04_001010|OH1004|PROTEIN

MAINFGLMTMPLTTVKASIIGKISDDNIQSVSKVSRNSVNIYPPRTLNEAFISLANNLIDQDTRYNTSCLDNAYSLILERCSTQESLSQIKQVHCHVLKSCYVVDTTFLSTKLVFAYGKSGFSSDAQKVFDKMPERSIFTWNAMIGSHMTNGEHFEAIELFQNMNALGVQADASTFTSILKACGELEDLCYGIQVHGMATKLGFLSNMYVSNSLLGMYAKCNDSSSAMLMFKLISEKADVVSWNSIISSYSASGKTMEAL...

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_001010
TK1151 IDTkA01G566980
OH-1004 IDLXL04_001010
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)82.000
Protein coverage (%)TK1151 97.579 / OH-1004 66.845
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 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_001010
LocationChr01:18442862-18445660 (-)
DescriptionSimilar to PCMP-H83: Pentatricopeptide repeat-containing protein At3g63370, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g63370 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
At4g13650 Pentatricopeptide repeat-containing protein At4g13650. No verified direct reference in this release
At3g57430 Involved in RNA editing events 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
At3g03580 Pentatricopeptide repeat-containing protein At3g03580. No verified direct reference in this release
At4g18750 Plays a major role in single RNA editing events in chloroplasts.
Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.2013 · DOI: 10.1074/jbc.m113.485755

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_001010 · 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: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:AT3G57430
ath:AT3G63370
ath:AT4G13650
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.

Mitochondrion0.564
Rank 1 · LXL04_001010 · OH-1004
Plastid0.308
Rank 2 · LXL04_001010 · OH-1004
Nucleus0.045
Rank 3 · LXL04_001010 · OH-1004
Cytoplasm0.030
Rank 4 · LXL04_001010 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_001010 · 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.

PF13041.13PPR_2137-183 aa
PF01535.27PPR139-169 aa
PF23276.3TPR_24225-335 aa
PF13812.13PPR_3237-285 aa
PF12854.14PPR_1238-267 aa
PF13041.13PPR_2239-285 aa
PF01535.27PPR241-267 aa
PF13041.13PPR_2339-378 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_001010PF13041.13PPR_21371831.2e-78259.8
LXL04_001010PF01535.27PPR1391699.3e-77248.8
LXL04_001010PF23276.3TPR_242253352.4e-2176.8
LXL04_001010PF13812.13PPR_32372853e-30104.8
LXL04_001010PF12854.14PPR_12382671.2e-47160.1
LXL04_001010PF13041.13PPR_22392851.2e-78259.8
LXL04_001010PF01535.27PPR2412679.3e-77248.8
LXL04_001010PF13041.13PPR_23393781.2e-78259.8
LXL04_001010PF01535.27PPR3423699.3e-77248.8
LXL04_001010PF13041.13PPR_24414771.2e-78259.8
LXL04_001010PF01535.27PPR4434739.3e-77248.8
LXL04_001010PF13041.13PPR_25385751.2e-78259.8
LXL04_001010PF01535.27PPR5405699.3e-77248.8
LXL04_001010PF13041.13PPR_26396861.2e-78259.8
LXL04_001010PF01535.27PPR6416699.3e-77248.8
LXL04_001010PF20431.5E_motif7568184.2e-2588.5

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
Q9M1V3Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g63370, chloroplastic47.784%Swiss-Protmoderate database homology
Q9SVP7Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g1365036.895%Swiss-Protmoderate database homology
Q7Y211Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g57430, chloroplastic35.971%Swiss-Protmoderate database homology
Q9SS60Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0358034.289%Swiss-Protmoderate database homology
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic36.143%Swiss-Protmoderate database homology

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