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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_002611
Reference: OH-1004 Chr: Chr01 Coordinates: 52948842-52953056 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2718 bp · LXL04_002611|LXL04_002611|OH1004|cDNA

ATGCTCGCTCACTACTTCCGACGCGAGTTCTGCCGTCGCCCTACGTCCCTTCCGGCGTGCGTCTCGCGGGTTTCCGATGCGGGTTCGCCGGAATCTGCTTCTCCCCATGCGTGCGTCGTTCGGGTGTTAGCCGGTGGTGTCCGGCGATGTGGAGCTCTCTTTGAGCGAGAGGGTGGGtcgatgaagaagaagaaagCTTTCACATTTAGCATGGCTTGTCTCCGAATTCCTGTAATCCCTTTAAATCATACTTCTCCAAT...

CDS

Download CDS FASTA

2718 bp · LXL04_002611|LXL04_002611|OH1004|CDS

ATGCTCGCTCACTACTTCCGACGCGAGTTCTGCCGTCGCCCTACGTCCCTTCCGGCGTGCGTCTCGCGGGTTTCCGATGCGGGTTCGCCGGAATCTGCTTCTCCCCATGCGTGCGTCGTTCGGGTGTTAGCCGGTGGTGTCCGGCGATGTGGAGCTCTCTTTGAGCGAGAGGGTGGGTCGATGAAGAAGAAGAAAGCTTTCACATTTAGCATGGCTTGTCTCCGAATTCCTGTAATCCCTTTAAATCATACTTCTCCAAT...

Protein

Download Protein FASTA

905 aa · LXL04_002611|LXL04_002611|OH1004|PROTEIN

MLAHYFRREFCRRPTSLPACVSRVSDAGSPESASPHACVVRVLAGGVRRCGALFEREGGSMKKKKAFTFSMACLRIPVIPLNHTSPISKSPKPQTHLVKPQDNEKHHQILYNSYFKHISSVCKEGKLQEAVNILLELDSQNFEIGANVYGDLLQGCVYERNLSLGKQIHSRIIKRGESLVKNEYIETKLVVFYAKCDCLDVASSLFRRLDEKNLFSWAAIIGLYCRMGFLENALLGYREMVENGFEADNFVVPNVLKACG...

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_002611
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_002611
LocationChr01:52948842-52953056 (-)
DescriptionSimilar to CRR21: Pentatricopeptide repeat-containing protein At5g55740, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g55740 Plays a major role in chloroplast RNA editing.
Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing.2007 · DOI: 10.1073/pnas.0700865104
At1g18485 Pentatricopeptide repeat-containing protein At1g18485. No verified direct reference in this release
At1g19720 Pentatricopeptide repeat-containing protein At1g19720. No verified direct reference in this release
At4g21300 Pentatricopeptide repeat-containing protein At4g21300. No verified direct reference in this release
At3g63370 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

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_002611 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
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:AT1G18485
ath:AT1G19720
ath:AT4G21300
ath:AT5G55740
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.

Mitochondrion0.575
Rank 1 · LXL04_002611 · OH-1004
Plastid0.286
Rank 2 · LXL04_002611 · OH-1004
Nucleus0.053
Rank 3 · LXL04_002611 · OH-1004
Cytoplasm0.035
Rank 4 · LXL04_002611 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_002611 · 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_2313-360 aa
PF13812.13PPR_3313-355 aa
PF01535.27PPR316-346 aa
PF13041.13PPR_2414-457 aa
PF01535.27PPR417-444 aa
PF13041.13PPR_2516-552 aa
PF13041.13PPR_2550-598 aa
PF01535.27PPR554-583 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_002611PF13041.13PPR_23133605.1e-79260.9
LXL04_002611PF13812.13PPR_33133555e-33113.7
LXL04_002611PF01535.27PPR3163469.9e-78251.8
LXL04_002611PF13041.13PPR_24144575.1e-79260.9
LXL04_002611PF01535.27PPR4174449.9e-78251.8
LXL04_002611PF13041.13PPR_25165525.1e-79260.9
LXL04_002611PF13041.13PPR_25505985.1e-79260.9
LXL04_002611PF01535.27PPR5545839.9e-78251.8
LXL04_002611PF13812.13PPR_35756235e-33113.7
LXL04_002611PF12854.14PPR_15826143.7e-38129.6
LXL04_002611PF13041.13PPR_25886255.1e-79260.9
LXL04_002611PF01535.27PPR5886189.9e-78251.8
LXL04_002611PF13041.13PPR_26917335.1e-79260.9
LXL04_002611PF01535.27PPR6917199.9e-78251.8
LXL04_002611PF20431.5E_motif8088671.4e-2074.0

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
Q9FM64Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g55740, chloroplastic51.861%Swiss-Protstrong database homology
Q0WN60Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1848530.981%Swiss-Protmoderate database homology
Q9FXH1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1972029.916%Swiss-Protweak database homology
Q9STE1Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2130032.015%Swiss-Protmoderate database homology
Q9M1V3Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g63370, chloroplastic30.637%Swiss-Protmoderate database homology

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