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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_019989
Reference: OH-1004 Chr: Chr04 Coordinates: 46569672-46573093 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2301 bp · LXL04_019989|LXL04_019989|OH1004|cDNA

ATGGACGCCACAAAGCTAATTCCTATCATAAAAAACGCCGCTGAATCAAAAGCACTCAAACATGCCAAACTCATTCACCAGAAAGTAATCATCTCCGGCCTACAGAATAACATTGCAATATGCAAAAATCTCATTACTCTCTTCTTTTCTTGCCAATTATTCCATTCTGCAAGGCTGGTTTTTCAATCCATCGAGAACCCTACAGACATCACTTTATGGAACAGTTTAATTTCAAATTACACAAAGAACTTCATGTTCGA...

CDS

Download CDS FASTA

2301 bp · LXL04_019989|LXL04_019989|OH1004|CDS

ATGGACGCCACAAAGCTAATTCCTATCATAAAAAACGCCGCTGAATCAAAAGCACTCAAACATGCCAAACTCATTCACCAGAAAGTAATCATCTCCGGCCTACAGAATAACATTGCAATATGCAAAAATCTCATTACTCTCTTCTTTTCTTGCCAATTATTCCATTCTGCAAGGCTGGTTTTTCAATCCATCGAGAACCCTACAGACATCACTTTATGGAACAGTTTAATTTCAAATTACACAAAGAACTTCATGTTCGA...

Protein

Download Protein FASTA

766 aa · LXL04_019989|LXL04_019989|OH1004|PROTEIN

MDATKLIPIIKNAAESKALKHAKLIHQKVIISGLQNNIAICKNLITLFFSCQLFHSARLVFQSIENPTDITLWNSLISNYTKNFMFDEALQVFEKLMHFPLLKPDSYTYPSVLKACSGLGFANFGRTMHTHLVKTGFMADVVVTSSLLGMYSKCGMFRLAVQVFDEMPERDLACWNTVISCYHHDGQYEKALDLFKKMKNNHGYEPDSVSFTTAISACSKLLDLETGKEIHKEATRNNFGSDGFVQAALVDMYGKCNSLE...

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_019989
TK1151 IDTkA05G110620
OH-1004 IDLXL04_019989
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)92.900
Protein coverage (%)TK1151 100.000 / OH-1004 90.470
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_019989
LocationChr04:46569672-46573093 (-)
DescriptionSimilar to PCMP-E14: Pentatricopeptide repeat-containing protein At5g27110
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g27110 Pentatricopeptide repeat-containing protein At5g27110. 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
At5g16860 Pentatricopeptide repeat-containing protein At5g16860. No verified direct reference in this release
At3g03580 Pentatricopeptide repeat-containing protein At3g03580. No verified direct reference in this release
At4g18750 Plays a major role in single RNA editing events in chloroplasts.
Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.2013 · DOI: 10.1074/jbc.m113.485755

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_019989 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016556 mRNA modification Biological Process
GO:0099402 plant organ development 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:AT5G27110
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.

Mitochondrion0.628
Rank 1 · LXL04_019989 · OH-1004
Plastid0.219
Rank 2 · LXL04_019989 · OH-1004
Nucleus0.054
Rank 3 · LXL04_019989 · OH-1004
Cytoplasm0.035
Rank 4 · LXL04_019989 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_019989 · 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_269-116 aa
PF01535.27PPR72-96 aa
PF13041.13PPR_2140-172 aa
PF01535.27PPR145-171 aa
PF13041.13PPR_2171-220 aa
PF01535.27PPR174-201 aa
PF29070.1MSC6_N236-376 aa
PF13041.13PPR_2273-320 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_019989PF13041.13PPR_2691161.1e-70234.3
LXL04_019989PF01535.27PPR72962.8e-70228.5
LXL04_019989PF13041.13PPR_21401721.1e-70234.3
LXL04_019989PF01535.27PPR1451712.8e-70228.5
LXL04_019989PF13041.13PPR_21712201.1e-70234.3
LXL04_019989PF01535.27PPR1742012.8e-70228.5
LXL04_019989PF29070.1MSC6_N2363762.2e-2177.2
LXL04_019989PF13041.13PPR_22733201.1e-70234.3
LXL04_019989PF01535.27PPR2753022.8e-70228.5
LXL04_019989PF13041.13PPR_23734211.1e-70234.3
LXL04_019989PF13812.13PPR_33734201.2e-33115.7
LXL04_019989PF01535.27PPR3784022.8e-70228.5
LXL04_019989PF13041.13PPR_24755221.1e-70234.3
LXL04_019989PF13812.13PPR_34755211.2e-33115.7
LXL04_019989PF01535.27PPR4775062.8e-70228.5
LXL04_019989PF20431.5E_motif5936552.4e-1660.4

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
O04659Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g2711050.723%Swiss-Protstrong database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic34.320%Swiss-Protmoderate database homology
Q9LFL5Arabidopsis thalianaPentatricopeptide repeat-containing protein At5g1686033.472%Swiss-Protmoderate database homology
Q9SS60Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0358034.257%Swiss-Protmoderate database homology
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic32.035%Swiss-Protmoderate database homology

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