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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_028485
Reference: OH-1004 Chr: Chr06 Coordinates: 43307501-43309864 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2364 bp · LXL04_028485|LXL04_028485|OH1004|cDNA

atgATTTGTAGAGCCGTCGGAAAGCGTGATCGGAACTTCTTTCTAAACTTGATCGGAAATGTCGCCACGCAATCCCATCTCCGGCAAACCCATGCCCAACTCATCCTCAACGGCCTAAAATCCGACATAGCCACCGTCACAAAGCTCATTCAAAAACTCTCCGACCTCGGTGCCATCTCCGACGCAACCCTCATCTGTTCGACATTTCCAAACCCTGACCTTTTTCTGTACAATGTTATCATCAAAGGATTCTCTCACAA...

CDS

Download CDS FASTA

2364 bp · LXL04_028485|LXL04_028485|OH1004|CDS

ATGATTTGTAGAGCCGTCGGAAAGCGTGATCGGAACTTCTTTCTAAACTTGATCGGAAATGTCGCCACGCAATCCCATCTCCGGCAAACCCATGCCCAACTCATCCTCAACGGCCTAAAATCCGACATAGCCACCGTCACAAAGCTCATTCAAAAACTCTCCGACCTCGGTGCCATCTCCGACGCAACCCTCATCTGTTCGACATTTCCAAACCCTGACCTTTTTCTGTACAATGTTATCATCAAAGGATTCTCTCACAA...

Protein

Download Protein FASTA

787 aa · LXL04_028485|LXL04_028485|OH1004|PROTEIN

MICRAVGKRDRNFFLNLIGNVATQSHLRQTHAQLILNGLKSDIATVTKLIQKLSDLGAISDATLICSTFPNPDLFLYNVIIKGFSHNNCYSKAVSVYRQLRETTTLKPDNFTYVFVISAASKLQCSKLGSSLHGHVIVGGAGSDLFVGSAIVDMYLNFGKVGYAYKVFDKIPEPDTVLCNSMISGSVKNDCFEESVSIFKDMILRETRFDSTTFAAVLTAASELQELKLGMAIQSSSIKLGFHSHVHVLTGLISFYAKHG...

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_028485
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_028485
LocationChr06:43307501-43309864 (-)
DescriptionSimilar to DYW9: Pentatricopeptide repeat-containing protein At4g30700
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g30700 Pentatricopeptide repeat-containing protein At4g30700. No verified direct reference in this release
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At4g33990 Pentatricopeptide repeat-containing protein At4g33990. No verified direct reference in this release
At3g12770 Pentatricopeptide repeat-containing protein At3g12770. No verified direct reference in this release
At3g26782 Pentatricopeptide repeat-containing protein At3g26782, mitochondrial. 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_028485 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000963 mitochondrial RNA processing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0016556 mRNA modification Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0004519 endonuclease activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G11290
ath:AT3G12770
ath:AT4G30700
ath:AT4G33990
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.

Mitochondrion0.713
Rank 1 · LXL04_028485 · OH-1004
Plastid0.142
Rank 2 · LXL04_028485 · OH-1004
Nucleus0.052
Rank 3 · LXL04_028485 · OH-1004
Cytoplasm0.036
Rank 4 · LXL04_028485 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_028485 · 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_272-119 aa
PF13041.13PPR_2174-220 aa
PF01535.27PPR177-203 aa
PF29070.1MSC6_N261-428 aa
PF13041.13PPR_2275-318 aa
PF01535.27PPR279-304 aa
PF13041.13PPR_2379-424 aa
PF01535.27PPR380-407 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028485PF13041.13PPR_2721191.6e-63211.3
LXL04_028485PF13041.13PPR_21742201.6e-63211.3
LXL04_028485PF01535.27PPR1772035.1e-58190.1
LXL04_028485PF29070.1MSC6_N2614282.6e-1660.4
LXL04_028485PF13041.13PPR_22753181.6e-63211.3
LXL04_028485PF01535.27PPR2793045.1e-58190.1
LXL04_028485PF13041.13PPR_23794241.6e-63211.3
LXL04_028485PF01535.27PPR3804075.1e-58190.1
LXL04_028485PF01535.27PPR4524785.1e-58190.1
LXL04_028485PF13041.13PPR_24775251.6e-63211.3
LXL04_028485PF12854.14PPR_14785045.3e-36122.8
LXL04_028485PF29070.1MSC6_N4785762.6e-1660.4
LXL04_028485PF01535.27PPR4805075.1e-58190.1
LXL04_028485PF20431.5E_motif5976598.3e-1349.1
LXL04_028485PF14432.13DYW_deaminase6957876.1e-40135.7

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
Q9SUH6Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3070057.841%Swiss-Protstrong database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic36.187%Swiss-Protmoderate database homology
O81767Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3399036.268%Swiss-Protmoderate database homology
Q9LTV8Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1277036.667%Swiss-Protmoderate database homology
Q9LW32Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g26782, mitochondrial39.936%Swiss-Protmoderate database homology

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