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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_026174
Reference: OH-1004 Chr: Chr05 Coordinates: 122139416-122141371 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1956 bp · LXL04_026174|LXL04_026174|OH1004|cDNA

ATGAGCGTGGAGATGCCGAGATGGAAGGTACTAAACTCAACTATCCCAACGGTAAAACACCCGATGGCTGCTGGTAAGATCGTTAAACTCTCCCAACCCATTGAAAAATTTCGAGAAATCCATAAGAATCTCTCCCTTAGATCATCACCAAAGCTTTGGCATGATCACGACAAGGAGGATGAAGGTGTACCCATTTTACGCCTAAACCATTACGTCTTACGCAAATTAGAGTCATGTTCTACCGTTACACTAACACAATT...

CDS

Download CDS FASTA

1956 bp · LXL04_026174|LXL04_026174|OH1004|CDS

ATGAGCGTGGAGATGCCGAGATGGAAGGTACTAAACTCAACTATCCCAACGGTAAAACACCCGATGGCTGCTGGTAAGATCGTTAAACTCTCCCAACCCATTGAAAAATTTCGAGAAATCCATAAGAATCTCTCCCTTAGATCATCACCAAAGCTTTGGCATGATCACGACAAGGAGGATGAAGGTGTACCCATTTTACGCCTAAACCATTACGTCTTACGCAAATTAGAGTCATGTTCTACCGTTACACTAACACAATT...

Protein

Download Protein FASTA

651 aa · LXL04_026174|LXL04_026174|OH1004|PROTEIN

MSVEMPRWKVLNSTIPTVKHPMAAGKIVKLSQPIEKFREIHKNLSLRSSPKLWHDHDKEDEGVPILRLNHYVLRKLESCSTVTLTQFNQVHAQLILSGLFQHSLAAGRVMKKLCSSPSTVSHAVKLFHGVDEPDSFLCNTIMRGFVNANEPLKALEFYHREMVAKFVSPNHYTFPLLVKICADLGLVREGEKAHTRILKEGFELDLYVRNALIHMYAVSGRIRDAQIVFDLSPESDMVTWNSMIDGYVKNGMVVSARRLF...

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_026174
TK1151 IDTkA06G023220
OH-1004 IDLXL04_026174
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)85.400
Protein coverage (%)TK1151 100.000 / OH-1004 99.693
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_026174
LocationChr05:122139416-122141371 (-)
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
At3g29230 Pentatricopeptide repeat-containing protein At3g29230. No verified direct reference in this release
At5g37570 Putative pentatricopeptide repeat-containing protein At5g37570. No verified direct reference in this release
At2g45350 Plays a major role in chloroplast RNA editing.
A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing.2006 · DOI: 10.1074/jbc.m608184200
Two interacting proteins are necessary for the editing of the NdhD-1 site in Arabidopsis plastids.2012 · DOI: 10.1105/tpc.112.099507
At4g02750 Pentatricopeptide repeat-containing protein At4g02750. 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_026174 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0010214 seed coat development Biological Process
GO:0016556 mRNA modification Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0140547 acquisition of seed longevity Biological Process
GO:1900865 chloroplast RNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0005773 vacuole Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G08070
ath:AT2G45350
ath:AT3G29230
ath:AT4G02750
ath:AT5G37570
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.

Mitochondrion0.573
Rank 1 · LXL04_026174 · OH-1004
Plastid0.249
Rank 2 · LXL04_026174 · OH-1004
Nucleus0.072
Rank 3 · LXL04_026174 · OH-1004
Cytoplasm0.036
Rank 4 · LXL04_026174 · OH-1004
Cell membrane0.007
Rank 5 · LXL04_026174 · 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_2133-182 aa
PF13041.13PPR_2236-267 aa
PF12854.14PPR_1236-263 aa
PF01535.27PPR238-267 aa
PF13041.13PPR_2266-299 aa
PF12854.14PPR_1266-294 aa
PF01535.27PPR269-298 aa
PF13041.13PPR_2297-329 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_026174PF13041.13PPR_21331826e-61203.1
LXL04_026174PF13041.13PPR_22362676e-61203.1
LXL04_026174PF12854.14PPR_12362632.7e-32110.9
LXL04_026174PF01535.27PPR2382672.4e-63206.7
LXL04_026174PF13041.13PPR_22662996e-61203.1
LXL04_026174PF12854.14PPR_12662942.7e-32110.9
LXL04_026174PF01535.27PPR2692982.4e-63206.7
LXL04_026174PF13041.13PPR_22973296e-61203.1
LXL04_026174PF13041.13PPR_23283786e-61203.1
LXL04_026174PF01535.27PPR3313592.4e-63206.7
LXL04_026174PF29070.1MSC6_N3344262.3e-0937.6
LXL04_026174PF13041.13PPR_24324796e-61203.1
LXL04_026174PF01535.27PPR4344632.4e-63206.7
LXL04_026174PF20431.5E_motif5496081.3e-1867.7

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, chloroplastic39.384%Swiss-Protmoderate database homology
Q9LS72Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g2923039.421%Swiss-Protmoderate database homology
Q9FHR3Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At5g3757037.363%Swiss-Protmoderate database homology
O22137Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g45350, chloroplastic37.782%Swiss-Protmoderate database homology
Q9SY02Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0275038.710%Swiss-Protmoderate database homology

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