LXL04_006317 | RubberDandelionOmics

Gene overview

LXL04_006317

Reference: OH-1004 Chr: Chr02 Coordinates: 6783423-6787276 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

279 bp · LXL04_006317|LXL04_006317|OH1004|cDNA

ATGATCGATATGCTTGTTAAATGTGGATACAAGAAAGGAACCACATTGTTCGGATACAGATATAACTTCCGGCAAAGCAATAGTTATGATCTAGAGTCTAAGTTTTTATCGAATGATGATGGGTATGCAAAGGCTGGGAAAATAGATGATGTAGAGAAgatgttcgatgaaatgcctgaaaGAGATGTTATATCATGGAGCTCATTGATTACAGGTTATGTGCAAAATGAAAACTTAGAACAAGCACTAGACTCTTTTAA...

CDS

Download CDS FASTA

279 bp · LXL04_006317|LXL04_006317|OH1004|CDS

ATGATCGATATGCTTGTTAAATGTGGATACAAGAAAGGAACCACATTGTTCGGATACAGATATAACTTCCGGCAAAGCAATAGTTATGATCTAGAGTCTAAGTTTTTATCGAATGATGATGGGTATGCAAAGGCTGGGAAAATAGATGATGTAGAGAAGATGTTCGATGAAATGCCTGAAAGAGATGTTATATCATGGAGCTCATTGATTACAGGTTATGTGCAAAATGAAAACTTAGAACAAGCACTAGACTCTTTTAA...

Protein

Download Protein FASTA

92 aa · LXL04_006317|LXL04_006317|OH1004|PROTEIN

MIDMLVKCGYKKGTTLFGYRYNFRQSNSYDLESKFLSNDDGYAKAGKIDDVEKMFDEMPERDVISWSSLITGYVQNENLEQALDSFKRMSDL

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_006317`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006317

Location Chr02:6783423-6787276 (+)

Description Similar to PCMP-H82: Pentatricopeptide repeat-containing protein At3g62890

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g62890`	Pentatricopeptide repeat-containing protein At3g62890.	No verified direct reference in this release
`At3g05240`	Putative pentatricopeptide repeat-containing protein At3g05240.	No verified direct reference in this release
`At1g05750`	Pentatricopeptide repeat-containing protein At1g05750, chloroplastic.	No verified direct reference in this release
`At1g31430`	Pentatricopeptide repeat-containing protein At1g31430.	No verified direct reference in this release
`At2g35030`	Pentatricopeptide repeat-containing protein At2g35030, mitochondrial.	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_006317 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification 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:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G05750

ath:AT1G31430

ath:AT3G05240

ath:AT3G62890

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.

Mitochondrion0.384

Rank 1 · LXL04_006317 · OH-1004

Plastid0.186

Rank 2 · LXL04_006317 · OH-1004

Cytoplasm0.154

Rank 3 · LXL04_006317 · OH-1004

Nucleus0.081

Rank 4 · LXL04_006317 · OH-1004

Peroxisome0.049

Rank 5 · LXL04_006317 · 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.

PF01535.27PPR40-62 aa

PF13041.13PPR_261-90 aa

PF01535.27PPR64-90 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006317	`PF01535.27`	PPR	40	62	2.2e-14	53.3
LXL04_006317	`PF13041.13`	PPR_2	61	90	4.7e-10	40.1
LXL04_006317	`PF01535.27`	PPR	64	90	2.2e-14	53.3

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

Protein	Organism	Description	Identity	Database	Confidence
`Q683I9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g62890	46.067%	Swiss-Prot	moderate database homology
`Q9MA95`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g05240	39.604%	Swiss-Prot	moderate database homology
`Q9MA50`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g05750, chloroplastic	38.889%	Swiss-Prot	moderate database homology
`Q9C866`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g31430	57.143%	Swiss-Prot	moderate database homology
`O64766`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g35030, mitochondrial	48.077%	Swiss-Prot	moderate database homology

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