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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_025492
Reference: OH-1004 Chr: Chr05 Coordinates: 112503693-112505528 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1836 bp · LXL04_025492|LXL04_025492|OH1004|cDNA

ATGAATCTCCTGATTCGGCGCCATCACAGCTCTTTCGCACCTTTGAAGCTCCAATCTACCATTGAACGCGACATTATATCACTTTGCAAAAGGGACCTACTTTTCGACGCCATACACCTCCTAAACTCCAATCAATGCCACAAAATTTTCACAAAAAAGCCAATCCTCTACGCTATTCTCTTGCAAACTTGCACAAAATCCCAAGCTTTCAACGTTGGGCTTCAACTGCACTCACATGTCATCAAGACTGGACTTGTAAC...

CDS

Download CDS FASTA

1836 bp · LXL04_025492|LXL04_025492|OH1004|CDS

ATGAATCTCCTGATTCGGCGCCATCACAGCTCTTTCGCACCTTTGAAGCTCCAATCTACCATTGAACGCGACATTATATCACTTTGCAAAAGGGACCTACTTTTCGACGCCATACACCTCCTAAACTCCAATCAATGCCACAAAATTTTCACAAAAAAGCCAATCCTCTACGCTATTCTCTTGCAAACTTGCACAAAATCCCAAGCTTTCAACGTTGGGCTTCAACTGCACTCACATGTCATCAAGACTGGACTTGTAAC...

Protein

Download Protein FASTA

611 aa · LXL04_025492|LXL04_025492|OH1004|PROTEIN

MNLLIRRHHSSFAPLKLQSTIERDIISLCKRDLLFDAIHLLNSNQCHKIFTKKPILYAILLQTCTKSQAFNVGLQLHSHVIKTGLVTDRFVGNSLLAHYFKLSSNFIETKRVFDGLYFKDVVSWTSMISGFIRVGKPRCSLDLFKEMLGLGVEPNGFTLSSVIKACSELGDVNLGRGFHGIVIRLGFDTNHVIASSLIDMYGKNYIPYDARNLFDELLEPDHICCTTVISAFTKNDLFEEALKFFHSMLSKYKISPDSST...

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_025492
TK1151 IDTkA06G056440
OH-1004 IDLXL04_025492
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)98.200
Protein coverage (%)TK1151 100.000 / OH-1004 100.000
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_025492
LocationChr05:112503693-112505528 (-)
DescriptionSimilar to PCMP-E4: Pentatricopeptide repeat-containing protein At1g03540
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g03540 Pentatricopeptide repeat-containing protein At1g03540. No verified direct reference in this release
At3g49170 May play a role in embryogenesis. No verified direct reference in this release
At3g09040 Pentatricopeptide repeat-containing protein At3g09040, mitochondrial. No verified direct reference in this release
At2g13600 Pentatricopeptide repeat-containing protein At2g13600. No verified direct reference in this release
At3g02010 Putative pentatricopeptide repeat-containing protein At2g01510. 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_025492 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G03540
ath:AT3G49170
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.

Mitochondrion0.680
Rank 1 · LXL04_025492 · OH-1004
Plastid0.173
Rank 2 · LXL04_025492 · OH-1004
Nucleus0.038
Rank 3 · LXL04_025492 · OH-1004
Cytoplasm0.029
Rank 4 · LXL04_025492 · OH-1004
Cell membrane0.005
Rank 5 · LXL04_025492 · 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_2119-167 aa
PF01535.27PPR122-152 aa
PF13041.13PPR_2220-270 aa
PF01535.27PPR224-251 aa
PF12854.14PPR_1321-351 aa
PF13041.13PPR_2322-365 aa
PF01535.27PPR325-352 aa
PF13041.13PPR_2420-467 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_025492PF13041.13PPR_21191675.2e-55184.1
LXL04_025492PF01535.27PPR1221523.3e-60196.9
LXL04_025492PF13041.13PPR_22202705.2e-55184.1
LXL04_025492PF01535.27PPR2242513.3e-60196.9
LXL04_025492PF12854.14PPR_13213516.3e-37125.7
LXL04_025492PF13041.13PPR_23223655.2e-55184.1
LXL04_025492PF01535.27PPR3253523.3e-60196.9
LXL04_025492PF13041.13PPR_24204675.2e-55184.1
LXL04_025492PF12854.14PPR_14204476.3e-37125.7
LXL04_025492PF01535.27PPR4224513.3e-60196.9
LXL04_025492PF29070.1MSC6_N4235174e-1349.9
LXL04_025492PF20431.5E_motif5446016.4e-1349.5

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
Q9LR69Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g0354052.459%Swiss-Protstrong database homology
Q5G1T1Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g49170, chloroplastic34.234%Swiss-Protmoderate database homology
Q9SS83Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g09040, mitochondrial33.935%Swiss-Protmoderate database homology
Q9SIT7Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g1360031.723%Swiss-Protmoderate database homology
Q9S7F4Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At2g0151033.673%Swiss-Protmoderate database homology

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