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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_022567
Reference: OH-1004 Chr: Chr05 Coordinates: 1660531-1664421 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3228 bp · LXL04_022567|LXL04_022567|OH1004|cDNA

ATGGAAGCTTTAAAATCTTCGTTCCTAAACCCAACTCCATTGAACTCTCACTCTTCAAAATACCCCCTTCACCTCAAATCCTCATCTATCATCATCTCCTGTTCAGGGAAAGTCTCCCCTGACCCATGGTCTCTGAGCGAtggcaacaacaacaacaaaccaaaaccaaaatcaaaaaaCCGAAAAAACCCTCTTTCAGACGACAATGCACGCCGCATCATCAAAGGCAAAGCGCGTTACTTAAGCGCGTTGAGGCGCAA...

CDS

Download CDS FASTA

3228 bp · LXL04_022567|LXL04_022567|OH1004|CDS

ATGGAAGCTTTAAAATCTTCGTTCCTAAACCCAACTCCATTGAACTCTCACTCTTCAAAATACCCCCTTCACCTCAAATCCTCATCTATCATCATCTCCTGTTCAGGGAAAGTCTCCCCTGACCCATGGTCTCTGAGCGATGGCAACAACAACAACAAACCAAAACCAAAATCAAAAAACCGAAAAAACCCTCTTTCAGACGACAATGCACGCCGCATCATCAAAGGCAAAGCGCGTTACTTAAGCGCGTTGAGGCGCAA...

Protein

Download Protein FASTA

1075 aa · LXL04_022567|LXL04_022567|OH1004|PROTEIN

MEALKSSFLNPTPLNSHSSKYPLHLKSSSIIISCSGKVSPDPWSLSDGNNNNKPKPKSKNRKNPLSDDNARRIIKGKARYLSALRRNQGSRALTPAWIKRSPEQMIQYLEDDRNGHLYGRHVVAAIQRVRGLSGLPDGSYDMRRVMASFVTKLTFREMCTVLKEQRNWRQVRDFLAWMKLQVPLSTFSKLTYRPSVIVYTLVLRTYGQAGKIKLAEETFLEMLEAGCEPDEVACGTMLCAYAKWGRHNSMLSFHSALQER...

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_022567
TK1151 IDTkA06G476040
OH-1004 IDLXL04_022567
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)84.500
Protein coverage (%)TK1151 100.000 / OH-1004 100.000
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_022567
LocationChr05:1660531-1664421 (-)
DescriptionSimilar to EMB976: Pentatricopeptide repeat-containing protein At5g27270
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g27270 Pentatricopeptide repeat-containing protein At5g27270. No verified direct reference in this release
At4g31850 Plays a role in the stabilization of the primary polycistronic transcript of the petL operon encoding subunits of the cytochrome b6-f complex.
PPR motifs of the nucleus-encoded factor, PGR3, function in the selective and distinct steps of chloroplast gene expression in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02035.x
At3g06920 Pentatricopeptide repeat-containing protein At3g06920. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
UniProt: Q76C99 Reduces the expression of the cytoplasmic male sterility (CMS)-associated mitochondrial gene ORF79, encoding a cytotoxic peptide. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_022567 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000373 Group II intron splicing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0006412 translation Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0032544 plastid translation Biological Process
GO:0043489 RNA stabilization Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT4G31850
ath:AT5G27270
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.

Mitochondrion0.556
Rank 1 · LXL04_022567 · OH-1004
Plastid0.284
Rank 2 · LXL04_022567 · OH-1004
Nucleus0.072
Rank 3 · LXL04_022567 · OH-1004
Cytoplasm0.026
Rank 4 · LXL04_022567 · OH-1004
Cell membrane0.011
Rank 5 · LXL04_022567 · 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.

PF13812.13PPR_3193-230 aa
PF13041.13PPR_2194-243 aa
PF23276.3TPR_24200-330 aa
PF17177.11PPR_long288-423 aa
PF13041.13PPR_2302-349 aa
PF12854.14PPR_1302-331 aa
PF01535.27PPR305-335 aa
PF13812.13PPR_3360-421 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_022567PF13812.13PPR_31932304.5e-46155.5
LXL04_022567PF13041.13PPR_21942432.3e-88290.9
LXL04_022567PF23276.3TPR_242003305.9e-30104.6
LXL04_022567PF17177.11PPR_long2884236.5e-2691.7
LXL04_022567PF13041.13PPR_23023492.3e-88290.9
LXL04_022567PF12854.14PPR_13023311.3e-34118.3
LXL04_022567PF01535.27PPR3053354.3e-79256.1
LXL04_022567PF13812.13PPR_33604214.5e-46155.5
LXL04_022567PF29070.1MSC6_N3614691.1e-2694.5
LXL04_022567PF13041.13PPR_23724092.3e-88290.9
LXL04_022567PF01535.27PPR3764034.3e-79256.1
LXL04_022567PF13041.13PPR_24084522.3e-88290.9
LXL04_022567PF29070.1MSC6_N6498471.1e-2694.5
LXL04_022567PF13041.13PPR_27207622.3e-88290.9
LXL04_022567PF23276.3TPR_247588835.9e-30104.6
LXL04_022567PF13812.13PPR_37748344.5e-46155.5

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
O04647Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g2727050.886%Swiss-Protstrong database homology
Q9SZ52Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g31850, chloroplastic21.474%Swiss-Protweak database homology
Q9M907Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0692021.839%Swiss-Protweak database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286022.688%Swiss-Protweak database homology
Q76C99Oryza sativa subsp. indicaProtein Rf1, mitochondrial22.876%Swiss-Protweak database homology

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