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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_004215
Reference: OH-1004 Chr: Chr01 Coordinates: 129587043-129588662 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1620 bp · LXL04_004215|LXL04_004215|OH1004|cDNA

ATGCTGTCGCGTGTTGGATCACCTTTGAACTCATTATTCGTGAAGCATAAACGCCAATACCTAACAGCAACACATCATATATTCTCTTCATTGTTAGAAAACTGCTGCAATAGCATTCACGTTTATCAAATACATGGGTTCATCTTTGTTCGAGGCCTCGATCAAGACAATCTTCTTCTCAGTCGGTTCATCGTCACTTGCTCCGACAGGCGTCTTTTGGACCATGCCACTTCAGTGTTTTTTCATAAGACTTCCAAGAA...

CDS

Download CDS FASTA

1620 bp · LXL04_004215|LXL04_004215|OH1004|CDS

ATGCTGTCGCGTGTTGGATCACCTTTGAACTCATTATTCGTGAAGCATAAACGCCAATACCTAACAGCAACACATCATATATTCTCTTCATTGTTAGAAAACTGCTGCAATAGCATTCACGTTTATCAAATACATGGGTTCATCTTTGTTCGAGGCCTCGATCAAGACAATCTTCTTCTCAGTCGGTTCATCGTCACTTGCTCCGACAGGCGTCTTTTGGACCATGCCACTTCAGTGTTTTTTCATAAGACTTCCAAGAA...

Protein

Download Protein FASTA

539 aa · LXL04_004215|LXL04_004215|OH1004|PROTEIN

MLSRVGSPLNSLFVKHKRQYLTATHHIFSSLLENCCNSIHVYQIHGFIFVRGLDQDNLLLSRFIVTCSDRRLLDHATSVFFHKTSKNIYLYNTMVKALSSNSRVKDAVFIYNEARATRLRPDSYSFPFLLKGVSRLGEDGLSLGRWIHCQVLTVGLYSDVHVGVALVQMYASCGYVSDARQVFDEMPLKDLAAWNAMISAYCKVNEVDKASALFEIMPKRNVISWTSLISGYAHVNKPSEALTLFKRMQKDGVHPDEITM...

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_004215
TK1151 IDTkA01G183060
OH-1004 IDLXL04_004215
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)82.500
Protein coverage (%)TK1151 100.000 / OH-1004 68.831
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_004215
LocationChr01:129587043-129588662 (-)
DescriptionSimilar to PCMP-E13: Pentatricopeptide repeat-containing protein At5g56310
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g56310 Pentatricopeptide repeat-containing protein At5g56310. No verified direct reference in this release
At2g20540 Pentatricopeptide repeat-containing protein At2g20540. No verified direct reference in this release
At5g59200 Involved in RNA editing event in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
At5g66520 Pentatricopeptide repeat-containing protein At5g66520. No verified direct reference in this release
At5g40405 Putative pentatricopeptide repeat-containing protein At5g40405. 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_004215 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:1900865 chloroplast RNA 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:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G20540
ath:AT5G40405
ath:AT5G56310
ath:AT5G59200
ath:AT5G66520
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.

Mitochondrion0.614
Rank 1 · LXL04_004215 · OH-1004
Plastid0.223
Rank 2 · LXL04_004215 · OH-1004
Nucleus0.047
Rank 3 · LXL04_004215 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_004215 · OH-1004
Cell membrane0.005
Rank 5 · LXL04_004215 · 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_287-134 aa
PF13041.13PPR_2190-222 aa
PF01535.27PPR193-222 aa
PF12854.14PPR_1193-217 aa
PF13041.13PPR_2220-268 aa
PF13812.13PPR_3220-267 aa
PF01535.27PPR223-253 aa
PF29070.1MSC6_N226-317 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004215PF13041.13PPR_2871349.5e-53176.8
LXL04_004215PF13041.13PPR_21902229.5e-53176.8
LXL04_004215PF01535.27PPR1932225.1e-51168.1
LXL04_004215PF12854.14PPR_11932176.3e-36122.5
LXL04_004215PF13041.13PPR_22202689.5e-53176.8
LXL04_004215PF13812.13PPR_32202675.2e-2175.2
LXL04_004215PF01535.27PPR2232535.1e-51168.1
LXL04_004215PF29070.1MSC6_N2263175.3e-1142.9
LXL04_004215PF13041.13PPR_22963219.5e-53176.8
LXL04_004215PF01535.27PPR2963215.1e-51168.1
LXL04_004215PF13041.13PPR_23223689.5e-53176.8
LXL04_004215PF01535.27PPR3243525.1e-51168.1
LXL04_004215PF20431.5E_motif4395014.9e-1969.0

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
Q9FMA1Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g5631052.033%Swiss-Protstrong database homology
Q9SIL5Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2054039.918%Swiss-Protmoderate database homology
Q9FIF7Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At5g59200, chloroplastic38.386%Swiss-Protmoderate database homology
Q9FJY7Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g6652038.492%Swiss-Protmoderate database homology
Q9FND7Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At5g4040537.984%Swiss-Protmoderate database homology

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