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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_028031
Reference: OH-1004 Chr: Chr06 Coordinates: 29388545-29390731 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2187 bp · LXL04_028031|LXL04_028031|OH1004|cDNA

ATGATACTCTCATCGTCTTCGCTTATCACTACTACACCCATTGCTCCACCACAAATTCACCACCAATCTCTGAGTCTTCTTTCAAAATGCAAGAATATGGAAGAATTCAAACAAGTTCATGCTCAAATGATAAAAGATGGCCTCCACAATTCGCATTTTGCTCTAAGCAAGATTATCCATTTTTGTGCCATCAACAGTGGTGGCGACCTGTCATACGCTGTTTCGGTATTTGACACCATTGAAGAACCGCCTGATCAGAT...

CDS

Download CDS FASTA

2187 bp · LXL04_028031|LXL04_028031|OH1004|CDS

ATGATACTCTCATCGTCTTCGCTTATCACTACTACACCCATTGCTCCACCACAAATTCACCACCAATCTCTGAGTCTTCTTTCAAAATGCAAGAATATGGAAGAATTCAAACAAGTTCATGCTCAAATGATAAAAGATGGCCTCCACAATTCGCATTTTGCTCTAAGCAAGATTATCCATTTTTGTGCCATCAACAGTGGTGGCGACCTGTCATACGCTGTTTCGGTATTTGACACCATTGAAGAACCGCCTGATCAGAT...

Protein

Download Protein FASTA

728 aa · LXL04_028031|LXL04_028031|OH1004|PROTEIN

MILSSSSLITTTPIAPPQIHHQSLSLLSKCKNMEEFKQVHAQMIKDGLHNSHFALSKIIHFCAINSGGDLSYAVSVFDTIEEPPDQIIWNTIIRGYSLNSSPFSAIDYYRFMLLSGVEPNSYTFPPLFKSCARIDGINEGKQIHGHVLKLGLGCDVFTHTSLINFYSQSGELDDARLVFDKSPLRDAVSFTALITGYITHGRFKDARKLFDEMPVRDVVSWNSIIAGHTRIKRFQDAIDLFTEMQTAKVKPNESTLVTVL...

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_028031
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_028031
LocationChr06:29388545-29390731 (-)
DescriptionSimilar to PCMP-H12: Pentatricopeptide repeat-containing protein At1g08070, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g08070 Involved in multiple sites 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
At3g12770 Pentatricopeptide repeat-containing protein At3g12770. No verified direct reference in this release
At3g23330 Putative pentatricopeptide repeat-containing protein At3g23330. No verified direct reference in this release
At4g14820 Pentatricopeptide repeat-containing protein At4g14820. No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_028031 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0080156 mitochondrial mRNA 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:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT1G08070
ath:AT2G29760
ath:AT3G12770
ath:AT3G23330
ath:AT4G14820
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.

Mitochondrion0.591
Rank 1 · LXL04_028031 · OH-1004
Plastid0.273
Rank 2 · LXL04_028031 · OH-1004
Nucleus0.049
Rank 3 · LXL04_028031 · OH-1004
Cytoplasm0.036
Rank 4 · LXL04_028031 · OH-1004
Peroxisome0.006
Rank 5 · LXL04_028031 · 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_284-133 aa
PF13041.13PPR_2186-216 aa
PF12854.14PPR_1186-213 aa
PF01535.27PPR188-216 aa
PF13041.13PPR_2216-264 aa
PF01535.27PPR219-246 aa
PF29070.1MSC6_N228-311 aa
PF13041.13PPR_2317-366 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028031PF13041.13PPR_2841335.8e-69228.7
LXL04_028031PF13041.13PPR_21862165.8e-69228.7
LXL04_028031PF12854.14PPR_11862134.4e-35119.8
LXL04_028031PF01535.27PPR1882163.5e-61200.0
LXL04_028031PF13041.13PPR_22162645.8e-69228.7
LXL04_028031PF01535.27PPR2192463.5e-61200.0
LXL04_028031PF29070.1MSC6_N2283112.3e-1970.5
LXL04_028031PF13041.13PPR_23173665.8e-69228.7
LXL04_028031PF01535.27PPR3203493.5e-61200.0
LXL04_028031PF13041.13PPR_24204675.8e-69228.7
LXL04_028031PF01535.27PPR4234523.5e-61200.0
LXL04_028031PF01535.27PPR4955193.5e-61200.0
LXL04_028031PF20431.5E_motif5376005e-1865.8
LXL04_028031PF20430.4Eplus_motif6056271.3e-1041.5
LXL04_028031PF14432.13DYW_deaminase6367281.9e-38130.9

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
Q9LN01Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g08070, chloroplastic55.977%Swiss-Protstrong database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic39.125%Swiss-Protmoderate database homology
Q9LTV8Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g1277038.710%Swiss-Protmoderate database homology
Q9LW63Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g2333037.620%Swiss-Protmoderate database homology
O23337Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g1482035.676%Swiss-Protmoderate database homology

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