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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_021052
Reference: OH-1004 Chr: Chr04 Coordinates: 119983371-119985173 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1803 bp · LXL04_021052|LXL04_021052|OH1004|cDNA

ATGGCAATCCTAGTTCCAGAGGTAACTCAATTAACTTGCCCGAATACCAAACCCACGAAGACACCAAGCAAATTAATAACCGGGGAAACCAACCCACTTTCTCTACTACCCAAATGCACCtatttgaaagaaataaagCAGATCCAAGCTCATTCAATAAAAACCGACCTTCATCGCACCATGTATTGGGCCACAAAGGTGATAAATCACTGCACACTCGACCCTACTCCTTCCTCAATGAACCACGCCCACCAACTGTT...

CDS

Download CDS FASTA

1803 bp · LXL04_021052|LXL04_021052|OH1004|CDS

ATGGCAATCCTAGTTCCAGAGGTAACTCAATTAACTTGCCCGAATACCAAACCCACGAAGACACCAAGCAAATTAATAACCGGGGAAACCAACCCACTTTCTCTACTACCCAAATGCACCTATTTGAAAGAAATAAAGCAGATCCAAGCTCATTCAATAAAAACCGACCTTCATCGCACCATGTATTGGGCCACAAAGGTGATAAATCACTGCACACTCGACCCTACTCCTTCCTCAATGAACCACGCCCACCAACTGTT...

Protein

Download Protein FASTA

600 aa · LXL04_021052|LXL04_021052|OH1004|PROTEIN

MAILVPEVTQLTCPNTKPTKTPSKLITGETNPLSLLPKCTYLKEIKQIQAHSIKTDLHRTMYWATKVINHCTLDPTPSSMNHAHQLFDQIPHPDVILFNFMARGYSRSHTPLQSLLLFIRITSMGIAPDHYTFPSLLKSCANAKALQEGKQLHSLAIKHGLNQNPYLYPSLINMYTECDNIGLAQLVFDRIKEPCAVTYNAIITGLVQNNRPNDALLMFQEMQNKSLKPTDVTMLSVLQSCSLLGALNTGKWVHEYIKSN...

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_021052
TK1151 IDTkA05G346420
OH-1004 IDLXL04_021052
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)93.300
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_021052
LocationChr04:119983371-119985173 (+)
DescriptionSimilar to PCMP-H26: Pentatricopeptide repeat-containing protein At2g02980, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g02980 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
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At4g37380 Plays a major role in single RNA editing events in chloroplasts. No verified direct reference in this release
At2g29760 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_021052 · 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:0016556 mRNA modification Biological Process
GO:0031425 chloroplast RNA processing 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:0004519 endonuclease activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G11290
ath:AT2G02980
ath:AT4G37380
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.

Mitochondrion0.728
Rank 1 · LXL04_021052 · OH-1004
Plastid0.141
Rank 2 · LXL04_021052 · OH-1004
Nucleus0.050
Rank 3 · LXL04_021052 · OH-1004
Cytoplasm0.034
Rank 4 · LXL04_021052 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_021052 · 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_293-142 aa
PF13041.13PPR_2194-241 aa
PF12854.14PPR_1196-223 aa
PF01535.27PPR197-225 aa
PF13041.13PPR_2296-342 aa
PF01535.27PPR299-327 aa
PF29070.1MSC6_N303-389 aa
PF17177.11PPR_long312-389 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_021052PF13041.13PPR_2931429.6e-41138.4
LXL04_021052PF13041.13PPR_21942419.6e-41138.4
LXL04_021052PF12854.14PPR_11962232.2e-2485.6
LXL04_021052PF01535.27PPR1972256.4e-32108.3
LXL04_021052PF13041.13PPR_22963429.6e-41138.4
LXL04_021052PF01535.27PPR2993276.4e-32108.3
LXL04_021052PF29070.1MSC6_N3033891.9e-1454.3
LXL04_021052PF17177.11PPR_long3123891.7e-0834.8
LXL04_021052PF20431.5E_motif4124746.2e-1452.7
LXL04_021052PF14432.13DYW_deaminase5076005.3e-36123.0

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
Q8LK93Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g02980, chloroplastic55.232%Swiss-Protstrong database homology
Q9FJY7Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g6652038.119%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic36.349%Swiss-Protmoderate database homology
Q9SZT8Arabidopsis thalianaPentatricopeptide repeat-containing protein ELI1, chloroplastic38.710%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic36.210%Swiss-Protmoderate database homology

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