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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_030572
Reference: OH-1004 Chr: Chr06 Coordinates: 118812526-118814094 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1569 bp · LXL04_030572|LXL04_030572|OH1004|cDNA

ATGCCTCGACCTTCTCCGCCGTTAATGGCGGCTCATCTTCGGATCCTACTCCGCCGTCGTTACTTCTCCACATCATTATCACCCCTGACGCCGCTGCAATCAATCCACCATTCTCTCCACCCCCATAAACCCTCACTCCCTAAACCCTACTCCCTTTGTACACCATTTTCACCTTTCTCTAAATTCTTCTCTTCCCAAACGGAAATCGAAACACCGGTTGAAGATTCACAAGACATTGCGAAATCTCTCTCGTATGAGCT...

CDS

Download CDS FASTA

1569 bp · LXL04_030572|LXL04_030572|OH1004|CDS

ATGCCTCGACCTTCTCCGCCGTTAATGGCGGCTCATCTTCGGATCCTACTCCGCCGTCGTTACTTCTCCACATCATTATCACCCCTGACGCCGCTGCAATCAATCCACCATTCTCTCCACCCCCATAAACCCTCACTCCCTAAACCCTACTCCCTTTGTACACCATTTTCACCTTTCTCTAAATTCTTCTCTTCCCAAACGGAAATCGAAACACCGGTTGAAGATTCACAAGACATTGCGAAATCTCTCTCGTATGAGCT...

Protein

Download Protein FASTA

522 aa · LXL04_030572|LXL04_030572|OH1004|PROTEIN

MPRPSPPLMAAHLRILLRRRYFSTSLSPLTPLQSIHHSLHPHKPSLPKPYSLCTPFSPFSKFFSSQTEIETPVEDSQDIAKSLSYELLKDPNDQPIPLPHRLDLSFSHITLTSDIILATLNLSPESGRTALDFHKWVSTRTDFKLTDETLAYFIDYFGRRKDFKATHELLIASKGISGIKTFESSIDRLVRAGRPTQVVSFFDKMESDYAFVRNMDSLKFIVSKLCEHGYASYAEKMVTNLANEFFPDEFICDTLIKGWC...

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_030572
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_030572
LocationChr06:118812526-118814094 (-)
DescriptionSimilar to PNM1: Pentatricopeptide repeat-containing protein PNM1, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g60960 RNA-binding protein that functions in both mitochondrion and nucleus.
An Arabidopsis dual-localized pentatricopeptide repeat protein interacts with nuclear proteins involved in gene expression regulation.2011 · DOI: 10.1105/tpc.110.081638
At5g61370 Pentatricopeptide repeat-containing protein At5g61370, mitochondrial. No verified direct reference in this release
At1g20300 Pentatricopeptide repeat-containing protein At1g20300, mitochondrial. No verified direct reference in this release
At2g13420 Pentatricopeptide repeat-containing protein At2g13420, mitochondrial. No verified direct reference in this release
At3g53700 May be involved in female gametophyte development. 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_030572 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006351 DNA-templated transcription Biological Process
GO:0006417 regulation of translation Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0010239 chloroplast mRNA processing Biological Process
GO:0005634 nucleus Cellular Component
GO:0005739 mitochondrion Cellular Component
GO:0005759 mitochondrial matrix Cellular Component
GO:0005840 ribosome Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0042644 chloroplast nucleoid Cellular Component
GO:1990904 ribonucleoprotein complex Cellular Component
GO:0003723 RNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G20300
ath:AT3G53700
ath:AT5G60960
ath:AT5G61370
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.

Mitochondrion0.778
Rank 1 · LXL04_030572 · OH-1004
Plastid0.103
Rank 2 · LXL04_030572 · OH-1004
Nucleus0.073
Rank 3 · LXL04_030572 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_030572 · OH-1004
Cell membrane0.011
Rank 5 · LXL04_030572 · 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.

PF12854.14PPR_1245-275 aa
PF13041.13PPR_2247-296 aa
PF13041.13PPR_2309-338 aa
PF13812.13PPR_3313-369 aa
PF12854.14PPR_1321-353 aa
PF13041.13PPR_2325-371 aa
PF01535.27PPR328-357 aa
PF29070.1MSC6_N347-440 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_030572PF12854.14PPR_12452753.6e-2381.7
LXL04_030572PF13041.13PPR_22472961.1e-37128.6
LXL04_030572PF13041.13PPR_23093381.1e-37128.6
LXL04_030572PF13812.13PPR_33133695.7e-1762.3
LXL04_030572PF12854.14PPR_13213533.6e-2381.7
LXL04_030572PF13041.13PPR_23253711.1e-37128.6
LXL04_030572PF01535.27PPR3283574e-2380.7
LXL04_030572PF29070.1MSC6_N3474402.4e-0937.5
LXL04_030572PF13812.13PPR_34014425.7e-1762.3
LXL04_030572PF13041.13PPR_24044441.1e-37128.6

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
Q9FME4Arabidopsis thalianaSmall ribosomal subunit protein mL104 (rPPR9)61.155%Swiss-Protstrong database homology
Q9FLJ6Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g61370, mitochondrial27.660%Swiss-Protweak database homology
Q9LN22Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g20300, mitochondrial27.386%Swiss-Protweak database homology
Q0WP85Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g13420, mitochondrial26.216%Swiss-Protweak database homology
Q9LFF1Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g53700, chloroplastic27.378%Swiss-Protweak database homology

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