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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_004744
Reference: OH-1004 Chr: Chr01 Coordinates: 145260220-145263041 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2445 bp · LXL04_004744|LXL04_004744|OH1004|cDNA

ATGTTGCTCCAAAGGAATGCCACGAAAATTCGATCTTTATCAGACGCAATCAATGTCTCCGGAGCTCTCAGTACTACTCGTTCTTCATGGTCACAGAACATTCAACCACTCGAGCATGGTAATGGTATTTCTCTGGATGATGTTACCTACACCAAACTGATTCAATCATCCACGCAATCAGGATGTTCAACTCACGGGAAACTAGCTCAATTGCATATGGTGAAAACGGGTTACACTCCAACCTTGTTTTTACACAATAC...

CDS

Download CDS FASTA

2445 bp · LXL04_004744|LXL04_004744|OH1004|CDS

ATGTTGCTCCAAAGGAATGCCACGAAAATTCGATCTTTATCAGACGCAATCAATGTCTCCGGAGCTCTCAGTACTACTCGTTCTTCATGGTCACAGAACATTCAACCACTCGAGCATGGTAATGGTATTTCTCTGGATGATGTTACCTACACCAAACTGATTCAATCATCCACGCAATCAGGATGTTCAACTCACGGGAAACTAGCTCAATTGCATATGGTGAAAACGGGTTACACTCCAACCTTGTTTTTACACAATAC...

Protein

Download Protein FASTA

814 aa · LXL04_004744|LXL04_004744|OH1004|PROTEIN

MLLQRNATKIRSLSDAINVSGALSTTRSSWSQNIQPLEHGNGISLDDVTYTKLIQSSTQSGCSTHGKLAQLHMVKTGYTPTLFLHNTLLNMYFKCNESDLALQLFDEMPERNVVSWNSLISGYIHLGQYPLAKEAISKARIANINLSKHTYASMLTICSQTGDLELGKVIHSLIIVTGIGVGIDAFLTNPLIAMYSKCGRIDQARLTFDKSDQLDDVSWNSMISGYIQAGLHNEMLKILIKMHQCGVRFSNYVLGSVLKT...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_004744
TK1151 IDTkA01G116260
OH-1004 IDLXL04_004744
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)75.100
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_004744
LocationChr01:145260220-145263041 (-)
DescriptionSimilar to PCMP-E89: Pentatricopeptide repeat-containing protein At3g13880
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At3g13880 Pentatricopeptide repeat-containing protein At3g13880. No verified direct reference in this release
At2g27610 Pentatricopeptide repeat-containing protein At2g27610. No verified direct reference in this release
At4g33170 Pentatricopeptide repeat-containing protein At4g33170. No verified direct reference in this release
At4g13650 Pentatricopeptide repeat-containing protein At4g13650. No verified direct reference in this release
At3g57430 Involved in RNA editing events 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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_004744 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:1900864 mitochondrial RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G27610
ath:AT3G13880
ath:AT4G33170
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.

Mitochondrion0.657
Rank 1 · LXL04_004744 · OH-1004
Plastid0.189
Rank 2 · LXL04_004744 · OH-1004
Nucleus0.054
Rank 3 · LXL04_004744 · OH-1004
Cytoplasm0.032
Rank 4 · LXL04_004744 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_004744 · 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_177-108 aa
PF13041.13PPR_284-113 aa
PF01535.27PPR85-113 aa
PF13041.13PPR_2111-158 aa
PF13041.13PPR_2215-262 aa
PF01535.27PPR217-247 aa
PF13041.13PPR_2317-362 aa
PF13812.13PPR_3318-362 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_004744PF12854.14PPR_1771088.6e-2690.1
LXL04_004744PF13041.13PPR_2841131.3e-63211.6
LXL04_004744PF01535.27PPR851132.7e-48159.6
LXL04_004744PF13041.13PPR_21111581.3e-63211.6
LXL04_004744PF13041.13PPR_22152621.3e-63211.6
LXL04_004744PF01535.27PPR2172472.7e-48159.6
LXL04_004744PF13041.13PPR_23173621.3e-63211.6
LXL04_004744PF13812.13PPR_33183621e-2487.1
LXL04_004744PF13041.13PPR_24174641.3e-63211.6
LXL04_004744PF01535.27PPR4194492.7e-48159.6
LXL04_004744PF13041.13PPR_25185651.3e-63211.6
LXL04_004744PF20431.5E_motif6356979.2e-1658.6
LXL04_004744PF20430.4Eplus_motif7037295.7e-0936.3
LXL04_004744PF14432.13DYW_deaminase7358143.1e-32111.0

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
Q9LRV9Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1388049.929%Swiss-Protmoderate database homology
Q9ZUW3Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g2761037.453%Swiss-Protmoderate database homology
Q9SMZ2Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3317037.326%Swiss-Protmoderate database homology
Q9SVP7Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g1365034.571%Swiss-Protmoderate database homology
Q7Y211Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g57430, chloroplastic33.913%Swiss-Protmoderate database homology

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