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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_003609
Reference: OH-1004 Chr: Chr01 Coordinates: 88678947-88681209 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2070 bp · LXL04_003609|LXL04_003609|OH1004|cDNA

ATGCCATTAAACACTGTTTCTTTGAATTCCTCTAAGCTACCTTCGTTTCTCTATGCTGCTAATGGCGAAACCAAGAAAAAGTCTCTTTCAAAACATCTCATATTCAACATTTTTTATGTTGGCTTGGTTACGTTATGTAGGTTTGTGATGTCCAACTCCAAACACCATGCCCTAGATTCCGAAAACGGCTCGATACAGGGTCTTTATCTGCTTAAGCTCTCTGATGAAGTTTTTTTTGTCAACCCAGTCCAGCTCCATCA...

CDS

Download CDS FASTA

2070 bp · LXL04_003609|LXL04_003609|OH1004|CDS

ATGCCATTAAACACTGTTTCTTTGAATTCCTCTAAGCTACCTTCGTTTCTCTATGCTGCTAATGGCGAAACCAAGAAAAAGTCTCTTTCAAAACATCTCATATTCAACATTTTTTATGTTGGCTTGGTTACGTTATGTAGGTTTGTGATGTCCAACTCCAAACACCATGCCCTAGATTCCGAAAACGGCTCGATACAGGGTCTTTATCTGCTTAAGCTCTCTGATGAAGTTTTTTTTGTCAACCCAGTCCAGCTCCATCA...

Protein

Download Protein FASTA

689 aa · LXL04_003609|LXL04_003609|OH1004|PROTEIN

MPLNTVSLNSSKLPSFLYAANGETKKKSLSKHLIFNIFYVGLVTLCRFVMSNSKHHALDSENGSIQGLYLLKLSDEVFFVNPVQLHQGLESCSTMKELRQYHSQIIKLGLSCDNDAIGRVIKFCAISKTGDLGYALKVFDKLPEPDPFIYNTMFRGYVQFQLAKECISLYSQMLQSCVTPNKFSFPPVTRACSFHNTTEEGKQVHAQIFKFGYSSDGFSQNNLIHMYVSFKHLKEARRVFDKMPHRDPISWTTLITGYSQ...

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_003609
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_003609
LocationChr01:88678947-88681209 (-)
DescriptionSimilar to PCMP-H61: Pentatricopeptide repeat-containing protein At5g66520
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g66520 Pentatricopeptide repeat-containing protein At5g66520. No verified direct reference in this release
At5g48910 Pentatricopeptide repeat-containing protein At5g48910. No verified direct reference in this release
At5g06540 Pentatricopeptide repeat-containing protein At5g06540. 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
At4g37380 Plays a major role in single RNA editing events in chloroplasts. 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_003609 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G29760
ath:AT5G06540
ath:AT5G48910
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.

Mitochondrion0.584
Rank 1 · LXL04_003609 · OH-1004
Plastid0.284
Rank 2 · LXL04_003609 · OH-1004
Nucleus0.056
Rank 3 · LXL04_003609 · OH-1004
Cytoplasm0.035
Rank 4 · LXL04_003609 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_003609 · 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_2145-185 aa
PF13041.13PPR_2247-278 aa
PF12854.14PPR_1247-274 aa
PF01535.27PPR249-278 aa
PF13041.13PPR_2279-324 aa
PF01535.27PPR281-308 aa
PF29070.1MSC6_N281-373 aa
PF23276.3TPR_24282-374 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_003609PF13041.13PPR_21451853.8e-47158.9
LXL04_003609PF13041.13PPR_22472783.8e-47158.9
LXL04_003609PF12854.14PPR_12472746.2e-2793.7
LXL04_003609PF01535.27PPR2492782.2e-52172.4
LXL04_003609PF13041.13PPR_22793243.8e-47158.9
LXL04_003609PF01535.27PPR2813082.2e-52172.4
LXL04_003609PF29070.1MSC6_N2813735e-1762.8
LXL04_003609PF23276.3TPR_242823742.4e-0937.9
LXL04_003609PF29070.1MSC6_N3353915e-1762.8
LXL04_003609PF29070.1MSC6_N3654825e-1762.8
LXL04_003609PF13041.13PPR_23844343.8e-47158.9
LXL04_003609PF01535.27PPR3874142.2e-52172.4
LXL04_003609PF20431.5E_motif5035658.4e-1658.7
LXL04_003609PF14432.13DYW_deaminase6086892.3e-34117.8

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
Q9FJY7Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g6652045.634%Swiss-Protmoderate database homology
Q9FI80Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g4891040.446%Swiss-Protmoderate database homology
Q9FG16Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0654040.426%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic43.640%Swiss-Protmoderate database homology
Q9SZT8Arabidopsis thalianaPentatricopeptide repeat-containing protein ELI1, chloroplastic40.554%Swiss-Protmoderate database homology

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