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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_009678
Reference: OH-1004 Chr: Chr02 Coordinates: 131108263-131110662 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2400 bp · LXL04_009678|LXL04_009678|OH1004|cDNA

atgACAACGATTTTGTCACTTAATTCATCTTTGAGGTTCGTTGTTTGTGAAAATACCCCACGAAGAGAACCCAAAAAAGCTTCAGAATTCATCAACCAGTACGACCCGATTAAGCAGAAATTTTCCACTTCTGTTAGAAGTAATTTCCAATCGAACTCTTTAATCGCGAAATCAAATTTGTCACGTCAGATGGAACATCTAGTTTCGTACGTGGAATGTGGGTCTGTTGAAGTTGCACTccaactgctcgatgaaatgaA...

CDS

Download CDS FASTA

2400 bp · LXL04_009678|LXL04_009678|OH1004|CDS

ATGACAACGATTTTGTCACTTAATTCATCTTTGAGGTTCGTTGTTTGTGAAAATACCCCACGAAGAGAACCCAAAAAAGCTTCAGAATTCATCAACCAGTACGACCCGATTAAGCAGAAATTTTCCACTTCTGTTAGAAGTAATTTCCAATCGAACTCTTTAATCGCGAAATCAAATTTGTCACGTCAGATGGAACATCTAGTTTCGTACGTGGAATGTGGGTCTGTTGAAGTTGCACTCCAACTGCTCGATGAAATGAA...

Protein

Download Protein FASTA

799 aa · LXL04_009678|LXL04_009678|OH1004|PROTEIN

MTTILSLNSSLRFVVCENTPRREPKKASEFINQYDPIKQKFSTSVRSNFQSNSLIAKSNLSRQMEHLVSYVECGSVEVALQLLDEMNKRSSFVWNIAIRVLTNNGYFTEALDLYHQMCTKGVQPDKFTFPFVLKACGGCLDILSGQKVHSNLFKVGLYSDLHVSNSLISMYAKVGRIGFAEQVFDEMPVRDLVSWNSMINGYILANEGLSSLTCFSKMQQSEIKPDRFTIVSALHASSLIHSSPNGKQIHAKIIKSKFES...

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_009678
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_009678
LocationChr02:131108263-131110662 (-)
DescriptionSimilar to PCMP-H27: Pentatricopeptide repeat-containing protein At4g35130, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g35130 Pentatricopeptide repeat-containing protein At4g35130, chloroplastic. 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
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
At4g33990 Pentatricopeptide repeat-containing protein At4g33990. No verified direct reference in this release
At1g15510 Regulates the RNA editing of the chloroplast transcript accD, and is essential for the early stages of chloroplast biogenesis.
AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana.2009 · DOI: 10.1111/j.1365-313x.2009.03930.x
Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsis vanilla cream1 mutant.2010 · DOI: 10.1007/s11103-010-9616-5
A point mutation in the pentatricopeptide repeat motif of the AtECB2 protein causes delayed chloroplast development.2011 · DOI: 10.1111/j.1744-7909.2011.01030.x

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_009678 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0010087 phloem or xylem histogenesis Biological Process
GO:0010305 leaf vascular tissue pattern formation Biological Process
GO:0010588 cotyledon vascular tissue pattern formation Biological Process
GO:0016556 mRNA modification Biological Process
GO:0048366 leaf development 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
KEGG gene cross-reference
ath:AT1G11290
ath:AT4G18750
ath:AT4G35130
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.

Mitochondrion0.624
Rank 1 · LXL04_009678 · OH-1004
Plastid0.206
Rank 2 · LXL04_009678 · OH-1004
Nucleus0.058
Rank 3 · LXL04_009678 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_009678 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_009678 · 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_290-136 aa
PF01535.27PPR93-122 aa
PF01535.27PPR165-190 aa
PF13041.13PPR_2191-231 aa
PF13041.13PPR_2294-330 aa
PF01535.27PPR295-324 aa
PF13041.13PPR_2393-437 aa
PF13041.13PPR_2493-540 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_009678PF13041.13PPR_2901361.8e-58195.2
LXL04_009678PF01535.27PPR931221.9e-54178.9
LXL04_009678PF01535.27PPR1651901.9e-54178.9
LXL04_009678PF13041.13PPR_21912311.8e-58195.2
LXL04_009678PF13041.13PPR_22943301.8e-58195.2
LXL04_009678PF01535.27PPR2953241.9e-54178.9
LXL04_009678PF13041.13PPR_23934371.8e-58195.2
LXL04_009678PF13041.13PPR_24935401.8e-58195.2
LXL04_009678PF17177.11PPR_long5146518.1e-1039.2
LXL04_009678PF20431.5E_motif6116762.3e-1350.9
LXL04_009678PF14432.13DYW_deaminase7317991.4e-2383.2

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
O49619Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g35130, chloroplastic50.612%Swiss-Protstrong database homology
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic34.908%Swiss-Protmoderate database homology
Q3E6Q1Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g11290, chloroplastic35.246%Swiss-Protmoderate database homology
O81767Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3399034.590%Swiss-Protmoderate database homology
Q9M9E2Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g15510, chloroplastic34.667%Swiss-Protmoderate database homology

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