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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_028380
Reference: OH-1004 Chr: Chr06 Coordinates: 39464652-39467198 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2547 bp · LXL04_028380|LXL04_028380|OH1004|cDNA

ATGGAGGGCACATTCCTCCCGAACAGACCAGCGCTCCCTCTACAATTGACAAAACCCACACAATCAAACCAACAACAAAGACTCGGATTCAATCCAGTAACTCTCCCTCCACAACCACCGTCTCCGCAATCTTTCCCCATTGATCCTCTCGTCCAGCACCTTGTCCACCTCTCTTCGCCACCGCCAACCACCACCCACAAACAAAAACCTATACGATCACTAAAATCAAGCAACACCCAGTTCCCTTCTACTCGCAGCTA...

CDS

Download CDS FASTA

2547 bp · LXL04_028380|LXL04_028380|OH1004|CDS

ATGGAGGGCACATTCCTCCCGAACAGACCAGCGCTCCCTCTACAATTGACAAAACCCACACAATCAAACCAACAACAAAGACTCGGATTCAATCCAGTAACTCTCCCTCCACAACCACCGTCTCCGCAATCTTTCCCCATTGATCCTCTCGTCCAGCACCTTGTCCACCTCTCTTCGCCACCGCCAACCACCACCCACAAACAAAAACCTATACGATCACTAAAATCAAGCAACACCCAGTTCCCTTCTACTCGCAGCTA...

Protein

Download Protein FASTA

848 aa · LXL04_028380|LXL04_028380|OH1004|PROTEIN

MEGTFLPNRPALPLQLTKPTQSNQQQRLGFNPVTLPPQPPSPQSFPIDPLVQHLVHLSSPPPTTTHKQKPIRSLKSSNTQFPSTRSYSRKNALNRTHFKKNYSTSVLTLEETKVQLAGIDGDAEGSLDFLSNECKSMLDSILEQSLSSLNLFFYSVKFKLIELDMVSLLKGLDLSGNWEKALCLFEWVLEDSRTNQSFNLDNQMIELMVKMLGRESQHTIMSKLFDKFDIEDHSLDVRAFTTIIHSHSCTGKYEKAINVF...

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_028380
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_028380
LocationChr06:39464652-39467198 (+)
DescriptionSimilar to At2g18940: Pentatricopeptide repeat-containing protein At2g18940, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g18940 Pentatricopeptide repeat-containing protein At2g18940, chloroplastic. No verified direct reference in this release
At5g02860 Pentatricopeptide repeat-containing protein At5g02860. 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
At3g06920 Pentatricopeptide repeat-containing protein At3g06920. 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_028380 · 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.

Mitochondrion0.448
Rank 1 · LXL04_028380 · OH-1004
Plastid0.376
Rank 2 · LXL04_028380 · OH-1004
Nucleus0.077
Rank 3 · LXL04_028380 · OH-1004
Cytoplasm0.026
Rank 4 · LXL04_028380 · OH-1004
Cell membrane0.010
Rank 5 · LXL04_028380 · 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_3223-285 aa
PF23276.3TPR_24230-328 aa
PF13041.13PPR_2236-282 aa
PF01535.27PPR239-267 aa
PF29070.1MSC6_N241-330 aa
PF13041.13PPR_2270-319 aa
PF13812.13PPR_3295-355 aa
PF17177.11PPR_long296-431 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028380PF13812.13PPR_32232851.1e-102336.9
LXL04_028380PF23276.3TPR_242303287.3e-40136.7
LXL04_028380PF13041.13PPR_22362824.8e-130424.3
LXL04_028380PF01535.27PPR2392673.4e-96309.7
LXL04_028380PF29070.1MSC6_N2413309e-38131.1
LXL04_028380PF13041.13PPR_22703194.8e-130424.3
LXL04_028380PF13812.13PPR_32953551.1e-102336.9
LXL04_028380PF17177.11PPR_long2964311.8e-37129.5
LXL04_028380PF13041.13PPR_23073504.8e-130424.3
LXL04_028380PF23276.3TPR_243103867.3e-40136.7
LXL04_028380PF12854.14PPR_13383708.6e-90294.8
LXL04_028380PF13041.13PPR_23413824.8e-130424.3
LXL04_028380PF01535.27PPR3443743.4e-96309.7
LXL04_028380PF29070.1MSC6_N3454329e-38131.1
LXL04_028380PF13812.13PPR_33603891.1e-102336.9
LXL04_028380PF13041.13PPR_23764244.8e-130424.3

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
O64624Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g18940, chloroplastic60.731%Swiss-Protstrong database homology
Q9LYZ9Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g0286041.353%Swiss-Protmoderate database homology
Q9S7Q2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g74850, chloroplastic25.000%Swiss-Protweak database homology
Q9M907Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0692026.780%Swiss-Protweak database homology

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