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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_012056
Reference: OH-1004 Chr: Chr03 Coordinates: 5617762-5622159 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3516 bp · LXL04_012056|LXL04_012056|OH1004|cDNA

ATGGGAACGTTTAGACACCAACTATCTGATCATTATGCTTCTCTAATTCAAAGAACCCTAGTTAACAAAGACCCATATGCTGGGAAAGGGATTCATGGTCGTATAATCAAGTCGGGTGTTCATGTCGGTGTGTTCCTCATGAACAACCTGATGAATATGTACGCAAAAACAGGGTTTCTCGCCGATGCCAGTCAGTtattcgatgaaatgcctgttAAGAACGCATCTTCGTGGAACACGCTTATCTCTGCTTACGCAAA...

CDS

Download CDS FASTA

3516 bp · LXL04_012056|LXL04_012056|OH1004|CDS

ATGGGAACGTTTAGACACCAACTATCTGATCATTATGCTTCTCTAATTCAAAGAACCCTAGTTAACAAAGACCCATATGCTGGGAAAGGGATTCATGGTCGTATAATCAAGTCGGGTGTTCATGTCGGTGTGTTCCTCATGAACAACCTGATGAATATGTACGCAAAAACAGGGTTTCTCGCCGATGCCAGTCAGTTATTCGATGAAATGCCTGTTAAGAACGCATCTTCGTGGAACACGCTTATCTCTGCTTACGCAAA...

Protein

Download Protein FASTA

1171 aa · LXL04_012056|LXL04_012056|OH1004|PROTEIN

MGTFRHQLSDHYASLIQRTLVNKDPYAGKGIHGRIIKSGVHVGVFLMNNLMNMYAKTGFLADASQLFDEMPVKNASSWNTLISAYAKQGRVDHARHLFEEMPEPDSVSWTAMMVGYNQIGRFENAIRMLTDMLSSKVIPTQYTFTIALASCAAINTLDIGKKVHSLIIRVGLSNYTSVSNSLLNMYAKSGDLLTAESIFTKMKSKTTSSWNTMISMHMQCRRFDLALSQFEKMTDRDIVTWNSMISGYNQHGFDSESLLM...

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_012056
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_012056
LocationChr03:5617762-5622159 (-)
DescriptionSimilar to PCMP-H41: Pentatricopeptide repeat-containing protein At2g22070
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g22070 Pentatricopeptide repeat-containing protein At2g22070. No verified direct reference in this release
At1g25360 Pentatricopeptide repeat-containing protein At1g25360. No verified direct reference in this release
At1g68930 Putative pentatricopeptide repeat-containing protein At1g68930. No verified direct reference in this release
At4g02750 Pentatricopeptide repeat-containing protein At4g02750. No verified direct reference in this release
At5g16860 Pentatricopeptide repeat-containing protein At5g16860. 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_012056 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0010214 seed coat development Biological Process
GO:0140547 acquisition of seed longevity Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G25360
ath:AT1G68930
ath:AT2G22070
ath:AT4G02750
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_012056 · OH-1004
Plastid0.242
Rank 2 · LXL04_012056 · OH-1004
Cytoplasm0.047
Rank 3 · LXL04_012056 · OH-1004
Nucleus0.036
Rank 4 · LXL04_012056 · OH-1004
Peroxisome0.015
Rank 5 · LXL04_012056 · 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_274-102 aa
PF12854.14PPR_174-101 aa
PF01535.27PPR77-102 aa
PF13041.13PPR_2104-152 aa
PF01535.27PPR209-237 aa
PF13041.13PPR_2236-286 aa
PF01535.27PPR239-268 aa
PF13041.13PPR_2372-412 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_012056PF13041.13PPR_2741026.5e-74244.6
LXL04_012056PF12854.14PPR_1741014.6e-41139.0
LXL04_012056PF01535.27PPR771029.2e-72233.1
LXL04_012056PF13041.13PPR_21041526.5e-74244.6
LXL04_012056PF01535.27PPR2092379.2e-72233.1
LXL04_012056PF13041.13PPR_22362866.5e-74244.6
LXL04_012056PF01535.27PPR2392689.2e-72233.1
LXL04_012056PF13041.13PPR_23724126.5e-74244.6
LXL04_012056PF01535.27PPR3754049.2e-72233.1
LXL04_012056PF29070.1MSC6_N3794672.2e-1660.7
LXL04_012056PF13041.13PPR_24755226.5e-74244.6
LXL04_012056PF01535.27PPR4775079.2e-72233.1
LXL04_012056PF20431.5E_motif5926541.2e-1971.0
LXL04_012056PF14432.13DYW_deaminase6907714.3e-31107.3
LXL04_012056PF08240.18ADH_N8709522.6e-1454.0
LXL04_012056PF00107.33ADH_zinc_N99411227.8e-2588.0

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
Q9SHZ8Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2207059.067%Swiss-Protmoderate database homology
Q9FRI5Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g2536036.340%Swiss-Protmoderate database homology
Q9CAA8Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At1g6893037.008%Swiss-Protmoderate database homology
Q9SY02Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0275036.277%Swiss-Protmoderate database homology
Q9LFL5Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g1686036.074%Swiss-Protmoderate database homology

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