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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_028255
Reference: OH-1004 Chr: Chr06 Coordinates: 35978299-35981073 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2775 bp · LXL04_028255|LXL04_028255|OH1004|cDNA

ATGGCTTCAATAAAATGCTGTGTTCATTTAGACAGTTATGATGCGAAGAAACTTAACTCCGTTTTGCAGTTCTCAGATCGAGCTTTGATCTTTTCCTTTAATGGTGTAAATAACAACCCCTTCGGTAAGTTAAAGCAAGTTAGGGTTTCTAAGTTAGATACTGAGTTTTCAGATGTTTTACAATCGAATAATGTTGACAGACCTTTGGATTTAAGTAATGAGAATGTAGTTTCACGAAGCCCTAAATTATACGGGGAGTT...

CDS

Download CDS FASTA

2775 bp · LXL04_028255|LXL04_028255|OH1004|CDS

ATGGCTTCAATAAAATGCTGTGTTCATTTAGACAGTTATGATGCGAAGAAACTTAACTCCGTTTTGCAGTTCTCAGATCGAGCTTTGATCTTTTCCTTTAATGGTGTAAATAACAACCCCTTCGGTAAGTTAAAGCAAGTTAGGGTTTCTAAGTTAGATACTGAGTTTTCAGATGTTTTACAATCGAATAATGTTGACAGACCTTTGGATTTAAGTAATGAGAATGTAGTTTCACGAAGCCCTAAATTATACGGGGAGTT...

Protein

Download Protein FASTA

924 aa · LXL04_028255|LXL04_028255|OH1004|PROTEIN

MASIKCCVHLDSYDAKKLNSVLQFSDRALIFSFNGVNNNPFGKLKQVRVSKLDTEFSDVLQSNNVDRPLDLSNENVVSRSPKLYGEFRKGKKRSIWKRLDGMRNVAKTSNVMHNSTNESEKQQEIMSDHEIGNVDVLFRNDNAFYENLSSNGLESSLHHCNLILEKLENSNRDDEVLKFFKWMRINGTLKHNTNAYKLALRVLGRRQDWEEAERLIQEMQTESSCQLTFQIFNTLIFACHKRGLVTAGRKWFQMMLNKQI...

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_028255
TK1151 IDTkA07G134350
OH-1004 IDLXL04_028255
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)99.600
Protein coverage (%)TK1151 85.482 / OH-1004 85.498
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_028255
LocationChr06:35978299-35981073 (-)
DescriptionSimilar to At4g30825: Pentatricopeptide repeat-containing protein At4g30825, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g30825 Pentatricopeptide repeat-containing protein At4g30825, chloroplastic. 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
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. No verified direct reference in this release
At3g06920 Pentatricopeptide repeat-containing protein At3g06920. 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

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_028255 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006281 DNA repair Biological Process
GO:0006357 regulation of transcription by RNA polymerase II Biological Process
GO:0006412 translation Biological Process
GO:0032544 plastid translation Biological Process
GO:0043489 RNA stabilization Biological Process
GO:0005675 transcription factor TFIIH holo complex Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT4G30825
ath:AT4G31850
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.

Mitochondrion0.524
Rank 1 · LXL04_028255 · OH-1004
Plastid0.314
Rank 2 · LXL04_028255 · OH-1004
Nucleus0.069
Rank 3 · LXL04_028255 · OH-1004
Cytoplasm0.029
Rank 4 · LXL04_028255 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_028255 · 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.

PF17177.11PPR_long193-350 aa
PF13041.13PPR_2231-272 aa
PF17177.11PPR_long285-414 aa
PF23276.3TPR_24300-393 aa
PF23276.3TPR_24305-428 aa
PF29070.1MSC6_N326-428 aa
PF01535.27PPR336-364 aa
PF13812.13PPR_3339-380 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028255PF17177.11PPR_long1933504.5e-32111.9
LXL04_028255PF13041.13PPR_22312721.2e-81269.3
LXL04_028255PF17177.11PPR_long2854144.5e-32111.9
LXL04_028255PF23276.3TPR_243003933.1e-37128.2
LXL04_028255PF23276.3TPR_243054283.1e-37128.2
LXL04_028255PF29070.1MSC6_N3264283.3e-2176.6
LXL04_028255PF01535.27PPR3363643.4e-83269.0
LXL04_028255PF13812.13PPR_33393801.6e-50169.7
LXL04_028255PF13041.13PPR_23664121.2e-81269.3
LXL04_028255PF01535.27PPR3693983.4e-83269.0
LXL04_028255PF12854.14PPR_13984292.3e-52175.1
LXL04_028255PF01535.27PPR4044333.4e-83269.0
LXL04_028255PF29070.1MSC6_N5777413.3e-2176.6
LXL04_028255PF17177.11PPR_long6718174.5e-32111.9
LXL04_028255PF13812.13PPR_36797311.6e-50169.7
LXL04_028255PF13041.13PPR_26847291.2e-81269.3

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
O65567Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g30825, chloroplastic54.797%Swiss-Protstrong database homology
Q9SZ52Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g31850, chloroplastic23.231%Swiss-Protweak database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286023.223%Swiss-Protweak database homology
Q9M907Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0692020.201%Swiss-Protweak database homology
Q9S7Q2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g74850, chloroplastic27.778%Swiss-Protweak database homology

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