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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_028421
Reference: OH-1004 Chr: Chr06 Coordinates: 41354668-41356428 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1761 bp · LXL04_028421|LXL04_028421|OH1004|cDNA

ATGGGACCTGAAGTTCTTGGTTCGATTTTGCACCAATGTTCCAAAACAAGAGCATTTCGGTCTGGGTTTTCCCTCCATGCTATTGCTGTCAAGATGGGTCTTCTCGAATCCAATGTTATCATCTCCAATCATGTTCTCAACATGTACGCAAAATGCGGGAAAATAGACTTCGCTCGCCAAGTGTTCGATGATATGTCTGAAAGAAACCTCGTAAGTTGGTCTGCTATGATCTCTGGTTACGATCAATCCGGGAAACCCAT...

CDS

Download CDS FASTA

1761 bp · LXL04_028421|LXL04_028421|OH1004|CDS

ATGGGACCTGAAGTTCTTGGTTCGATTTTGCACCAATGTTCCAAAACAAGAGCATTTCGGTCTGGGTTTTCCCTCCATGCTATTGCTGTCAAGATGGGTCTTCTCGAATCCAATGTTATCATCTCCAATCATGTTCTCAACATGTACGCAAAATGCGGGAAAATAGACTTCGCTCGCCAAGTGTTCGATGATATGTCTGAAAGAAACCTCGTAAGTTGGTCTGCTATGATCTCTGGTTACGATCAATCCGGGAAACCCAT...

Protein

Download Protein FASTA

586 aa · LXL04_028421|LXL04_028421|OH1004|PROTEIN

MGPEVLGSILHQCSKTRAFRSGFSLHAIAVKMGLLESNVIISNHVLNMYAKCGKIDFARQVFDDMSERNLVSWSAMISGYDQSGKPINALKLFTQMTELPNEFVFASAISSCASLLAIKVGKQIHTKTLTLGYSSISFVSNSLVSMYMKCSHLNDAISVFTKSSEPNTVTYNAIITGLVDNKQVQKAYEMFKLMCQQGLVPNRFTLVPLLGNCTTTDDLWIGMELHCQAIKLNLDSIPFVGNMLITMYSKLNSIKESETI...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_028421
TK1151 IDTkA07G154650
OH-1004 IDLXL04_028421
Relationship / confidenceRbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)98.900
Protein coverage (%)TK1151 100.000 / OH-1004 61.092
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_028421
LocationChr06:41354668-41356428 (-)
DescriptionSimilar to PCMP-E43: Putative pentatricopeptide repeat-containing protein At3g47840
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
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
At4g33170 Pentatricopeptide repeat-containing protein At4g33170. No verified direct reference in this release
At3g47840 Putative pentatricopeptide repeat-containing protein At3g47840. No verified direct reference in this release
At2g33680 Pentatricopeptide repeat-containing protein At2g33680. No verified direct reference in this release
At2g13600 Pentatricopeptide repeat-containing protein At2g13600. 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_028421 · 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: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:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT3G47840
ath:AT4G18750
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.

Mitochondrion0.695
Rank 1 · LXL04_028421 · OH-1004
Plastid0.157
Rank 2 · LXL04_028421 · OH-1004
Nucleus0.040
Rank 3 · LXL04_028421 · OH-1004
Cytoplasm0.031
Rank 4 · LXL04_028421 · OH-1004
Cell membrane0.005
Rank 5 · LXL04_028421 · 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_238-70 aa
PF12854.14PPR_1164-194 aa
PF13812.13PPR_3165-213 aa
PF13041.13PPR_2166-206 aa
PF01535.27PPR169-198 aa
PF13041.13PPR_2267-315 aa
PF13041.13PPR_2370-416 aa
PF01535.27PPR372-401 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_028421PF13041.13PPR_238702.1e-51172.5
LXL04_028421PF12854.14PPR_11641942.3e-30104.7
LXL04_028421PF13812.13PPR_31652139.8e-2071.1
LXL04_028421PF13041.13PPR_21662062.1e-51172.5
LXL04_028421PF01535.27PPR1691982.2e-45150.5
LXL04_028421PF13041.13PPR_22673152.1e-51172.5
LXL04_028421PF13041.13PPR_23704162.1e-51172.5
LXL04_028421PF01535.27PPR3724012.2e-45150.5
LXL04_028421PF29070.1MSC6_N3754668.2e-1039.0
LXL04_028421PF20431.5E_motif4875495.7e-1452.8

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
Q9SN39Arabidopsis thalianaPentatricopeptide repeat-containing protein DOT4, chloroplastic34.336%Swiss-Protmoderate database homology
Q9SMZ2Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g3317034.946%Swiss-Protmoderate database homology
Q9STS9Arabidopsis thalianaPutative pentatricopeptide repeat-containing protein At3g4784035.478%Swiss-Protmoderate database homology
P93005Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g3368034.095%Swiss-Protmoderate database homology
Q9SIT7Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g1360031.040%Swiss-Protmoderate database homology

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