LXL04_026439 | RubberDandelionOmics

Gene overview

LXL04_026439

Reference: OH-1004 Chr: Chr05 Coordinates: 126351606-126354117 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1461 bp · LXL04_026439|LXL04_026439|OH1004|cDNA

ATGCACGCTCGTTTCATATCGTCTTCTCGAGATAATATACTCGATCTCATTAATGTTAATTACCCAAAAGTTGGACCACTGAAATTCACACACCATAATGAGCATGCTTTTGAAGTTGCTCAATTGTTTAAATCAATAGCTTCAAATCACGATGACTCCTCTTACCTATCTAAGGAGTATTATTCTGGATTGCTGCATTCGTCTCGTTTAAAAACTGGGTACCGTTTATTAGGCAGGCAGTGCCATGGATACCTATTGAA...

CDS

Download CDS FASTA

1461 bp · LXL04_026439|LXL04_026439|OH1004|CDS

ATGCACGCTCGTTTCATATCGTCTTCTCGAGATAATATACTCGATCTCATTAATGTTAATTACCCAAAAGTTGGACCACTGAAATTCACACACCATAATGAGCATGCTTTTGAAGTTGCTCAATTGTTTAAATCAATAGCTTCAAATCACGATGACTCCTCTTACCTATCTAAGGAGTATTATTCTGGATTGCTGCATTCGTCTCGTTTAAAAACTGGGTACCGTTTATTAGGCAGGCAGTGCCATGGATACCTATTGAA...

Protein

Download Protein FASTA

486 aa · LXL04_026439|LXL04_026439|OH1004|PROTEIN

MHARFISSSRDNILDLINVNYPKVGPLKFTHHNEHAFEVAQLFKSIASNHDDSSYLSKEYYSGLLHSSRLKTGYRLLGRQCHGYLLKSGLVLHQYVKATLARYGDLNLGRQVHKKLLMSDVTYDESVCNAIMKMYGKCKEISSARKVFDTCEPPPNVTLWTTFLAAYLENGSFKKSLLGFIDMQRSDVVPNESIFCILLTAIAELLSLSSGNMLHALIVKTGFKDCKKVKDTLINMYSRTGDIKAAKNVFLGMSIYNRDV...

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.

ID Mapping

Input ID	`LXL04_026439`
TK1151 ID	TkA06G010380
OH-1004 ID	LXL04_026439
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.800
Protein coverage (%)	TK1151 63.571 / OH-1004 18.313 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 version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_026439

Location Chr05:126351606-126354117 (+)

Description Similar to EMB2744: Pentatricopeptide repeat-containing protein At5g39680

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g39680`	Pentatricopeptide repeat-containing protein At5g39680.	No verified direct reference in this release
`At4g13650`	Pentatricopeptide repeat-containing protein At4g13650.	No verified direct reference in this release
`At3g03580`	Pentatricopeptide repeat-containing protein At3g03580.	No verified direct reference in this release
`At4g14050`	Involved in C-to-U editing of mitochondrial RNA.	The DYW Subgroup PPR Protein MEF35 Targets RNA Editing Sites in the Mitochondrial rpl16, nad4 and cob mRNAs in Arabidopsis thaliana.2015 · DOI: 10.1371/journal.pone.0140680
`At3g46790`	Required for the intergenic processing between chloroplast rsp7 and ndhB transcripts.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_026439 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0005739 mitochondrion 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:AT4G13650

ath:AT5G39680

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Mitochondrion0.685

Rank 1 · LXL04_026439 · OH-1004

Plastid0.168

Rank 2 · LXL04_026439 · OH-1004

Nucleus0.053

Rank 3 · LXL04_026439 · OH-1004

Cytoplasm0.038

Rank 4 · LXL04_026439 · OH-1004

Cell membrane0.009

Rank 5 · LXL04_026439 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13041.13PPR_2155-202 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026439	`PF13041.13`	PPR_2	155	202	1.3e-19	70.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FK93`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g39680	31.765%	Swiss-Prot	moderate database homology
`Q9SVP7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g13650	28.536%	Swiss-Prot	weak database homology
`Q9SS60`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g03580	28.142%	Swiss-Prot	weak database homology
`O23266`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g14050, mitochondrial	26.884%	Swiss-Prot	weak database homology
`Q9STF3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein CRR2, chloroplastic	28.169%	Swiss-Prot	weak database homology

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