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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_003012
Reference: OH-1004 Chr: Chr01 Coordinates: 64961658-64968634 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3462 bp · LXL04_003012|LXL04_003012|OH1004|cDNA

ATGCATGATGGACATGGAACCCTAAATCAAAATCTACCTACCGCAATCAAAACAGATCGTCAAATTCAGATTTGGTTCAATTTAAGCCGGTCATACTGTCGTCCGATGGAAAATGGTGTATGGGCGACGGCGGTGGAAAATGAATTTGGGCCTTACACACCTTGTGCAACCGATTCTATGGTTACTGGCATCTCCCATTTGGTTCTCTTGGAAATCTGCATATGCCGATTAAGGGTGACAACGAAGAATTTAAAAGTGCA...

CDS

Download CDS FASTA

3462 bp · LXL04_003012|LXL04_003012|OH1004|CDS

ATGCATGATGGACATGGAACCCTAAATCAAAATCTACCTACCGCAATCAAAACAGATCGTCAAATTCAGATTTGGTTCAATTTAAGCCGGTCATACTGTCGTCCGATGGAAAATGGTGTATGGGCGACGGCGGTGGAAAATGAATTTGGGCCTTACACACCTTGTGCAACCGATTCTATGGTTACTGGCATCTCCCATTTGGTTCTCTTGGAAATCTGCATATGCCGATTAAGGGTGACAACGAAGAATTTAAAAGTGCA...

Protein

Download Protein FASTA

1153 aa · LXL04_003012|LXL04_003012|OH1004|PROTEIN

MHDGHGTLNQNLPTAIKTDRQIQIWFNLSRSYCRPMENGVWATAVENEFGPYTPCATDSMVTGISHLVLLEICICRLRVTTKNLKVQRFKLRSKIYNYLLGLLALFSTVEPLIRLIMGISVFNVDGETGLAPYEVCFFLIDLIACLNIDWLEQEPAGDHSNKIDSALLEKLYDEMISDAIELDGQLLNPRTSTVVSLILQLGNLGRAEEAEAIFEEIKEGGVIPRTRAYNAVYVKNGNLKDAESIVTEMERKGVSRPYIQ...

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_003012
TK1151 IDTkA01G404600
OH-1004 IDLXL04_003012
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)99.700
Protein coverage (%)TK1151 35.644 / OH-1004 24.978
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_003012
LocationChr01:64961658-64968634 (-)
DescriptionSimilar to At5g02860: Pentatricopeptide repeat-containing protein At5g02860
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At2g18940 Pentatricopeptide repeat-containing protein At2g18940, chloroplastic. No verified direct reference in this release
At1g74850 Involved in plastid gene expression.
pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression.2006 · DOI: 10.1105/tpc.105.036392

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_003012 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0048255 mRNA stabilization Biological Process
GO:0009507 chloroplast Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0003729 mRNA binding Molecular Function
GO:0042802 identical protein binding Molecular Function
KEGG gene cross-reference
ath:AT2G18940
ath:AT5G02860
zma:100302579
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.

Plastid0.635
Rank 1 · LXL04_003012 · OH-1004
Mitochondrion0.266
Rank 2 · LXL04_003012 · OH-1004
Nucleus0.064
Rank 3 · LXL04_003012 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_003012 · OH-1004
Cell membrane0.013
Rank 5 · LXL04_003012 · 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.

PF23276.3TPR_24510-639 aa
PF13041.13PPR_2514-555 aa
PF13812.13PPR_3529-591 aa
PF29070.1MSC6_N535-625 aa
PF12854.14PPR_1539-570 aa
PF13041.13PPR_2542-588 aa
PF01535.27PPR545-574 aa
PF13041.13PPR_2579-624 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_003012PF23276.3TPR_245106397.1e-46156.1
LXL04_003012PF13041.13PPR_25145552.5e-141460.4
LXL04_003012PF13812.13PPR_35295914e-127415.1
LXL04_003012PF29070.1MSC6_N5356252.7e-57195.3
LXL04_003012PF12854.14PPR_15395702.7e-109357.3
LXL04_003012PF13041.13PPR_25425882.5e-141460.4
LXL04_003012PF01535.27PPR5455749.4e-116371.0
LXL04_003012PF13041.13PPR_25796242.5e-141460.4
LXL04_003012PF13812.13PPR_36006604e-127415.1
LXL04_003012PF17177.11PPR_long6007351.1e-50172.7
LXL04_003012PF12854.14PPR_16096412.7e-109357.3
LXL04_003012PF01535.27PPR6156459.4e-116371.0
LXL04_003012PF13041.13PPR_26236572.5e-141460.4
LXL04_003012PF13812.13PPR_36356954e-127415.1
LXL04_003012PF12854.14PPR_16446762.7e-109357.3
LXL04_003012PF13041.13PPR_26476912.5e-141460.4

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
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286062.182%Swiss-Protmoderate database homology
O64624Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g18940, chloroplastic41.667%Swiss-Protmoderate database homology
Q9S7Q2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g74850, chloroplastic27.544%Swiss-Protweak database homology
Q76C99Oryza sativa subsp. indicaProtein Rf1, mitochondrial26.325%Swiss-Protweak database homology

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