LXL04_017959 | RubberDandelionOmics

Gene overview

LXL04_017959

Reference: OH-1004 Chr: Chr04 Coordinates: 4294387-4296225 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1839 bp · LXL04_017959|LXL04_017959|OH1004|cDNA

ATGATAATCTTCAAAACTCAATTCACCAACTTCACTCGCAGCTTTTCATCTATCCCAAACCTCACACAATGCGTTTCGTCCCTCCAATCATCTGCCAAACATGCCAACTTACAGGAAGGAAAAAAACTCCATTCCTACATGCTCATCAATGGCTTCCTCACCTCCCCGGTCTCCATCACCAGCCTCATCAACATGTACTCCAAATGCAACTCCATCTCCGACGCCTTTCTACTTTTCACTTCGTCGTCAACTTCTCACCT...

CDS

Download CDS FASTA

1839 bp · LXL04_017959|LXL04_017959|OH1004|CDS

ATGATAATCTTCAAAACTCAATTCACCAACTTCACTCGCAGCTTTTCATCTATCCCAAACCTCACACAATGCGTTTCGTCCCTCCAATCATCTGCCAAACATGCCAACTTACAGGAAGGAAAAAAACTCCATTCCTACATGCTCATCAATGGCTTCCTCACCTCCCCGGTCTCCATCACCAGCCTCATCAACATGTACTCCAAATGCAACTCCATCTCCGACGCCTTTCTACTTTTCACTTCGTCGTCAACTTCTCACCT...

Protein

Download Protein FASTA

612 aa · LXL04_017959|LXL04_017959|OH1004|PROTEIN

MIIFKTQFTNFTRSFSSIPNLTQCVSSLQSSAKHANLQEGKKLHSYMLINGFLTSPVSITSLINMYSKCNSISDAFLLFTSSSTSHLNVFAYNAIIAGFIFNELPKPALQVYEKMRVAGVTMDKYTFPCVVTAFSGCGDVVGLKIVHGLVFKFGMDHDLFVGSAAVHGYLKFGLMADAQRVFDEMPDRDIVLWNAMINGYADIGEHHNALDCLQRLHTEGKVVPSRFTITGILPILAMKGDLHNGKSIHGFATKIGYSSG...

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_017959`
Source version	OH-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 ID LXL04_017959

Location Chr04:4294387-4296225 (-)

Description Similar to PCMP-E31: Pentatricopeptide repeat-containing protein At3g14730

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14730`	Pentatricopeptide repeat-containing protein At3g14730.	No verified direct reference in this release
`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
`At2g13600`	Pentatricopeptide repeat-containing protein At2g13600.	No verified direct reference in this release
`At1g08070`	Involved in multiple sites RNA editing events in chloroplasts.	No verified direct reference in this release
`At3g23330`	Putative pentatricopeptide repeat-containing protein At3g23330.	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_017959 · 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:0010182 sugar mediated signaling pathway 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:0080156 mitochondrial mRNA modification 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

KEGG gene cross-reference

ath:AT2G13600

ath:AT3G14730

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.

Mitochondrion0.691

Rank 1 · LXL04_017959 · OH-1004

Plastid0.167

Rank 2 · LXL04_017959 · OH-1004

Nucleus0.045

Rank 3 · LXL04_017959 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_017959 · OH-1004

Cell membrane0.006

Rank 5 · LXL04_017959 · 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_288-134 aa

PF13041.13PPR_2291-339 aa

PF01535.27PPR293-323 aa

PF17177.11PPR_long306-460 aa

PF01535.27PPR369-394 aa

PF13041.13PPR_2395-443 aa

PF01535.27PPR398-424 aa

PF12854.14PPR_1463-492 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017959	`PF13041.13`	PPR_2	88	134	1.1e-55	186.2
LXL04_017959	`PF13041.13`	PPR_2	291	339	1.1e-55	186.2
LXL04_017959	`PF01535.27`	PPR	293	323	1.6e-53	176.0
LXL04_017959	`PF17177.11`	PPR_long	306	460	2e-09	37.9
LXL04_017959	`PF01535.27`	PPR	369	394	1.6e-53	176.0
LXL04_017959	`PF13041.13`	PPR_2	395	443	1.1e-55	186.2
LXL04_017959	`PF01535.27`	PPR	398	424	1.6e-53	176.0
LXL04_017959	`PF12854.14`	PPR_1	463	492	5.5e-29	100.3
LXL04_017959	`PF20431.5`	E_motif	512	574	6.6e-21	75.0

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
`Q9LUC2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g14730	49.408%	Swiss-Prot	moderate database homology
`Q9SN39`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein DOT4, chloroplastic	36.177%	Swiss-Prot	moderate database homology
`Q9SIT7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g13600	33.483%	Swiss-Prot	moderate database homology
`Q9LN01`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g08070, chloroplastic	34.110%	Swiss-Prot	moderate database homology
`Q9LW63`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g23330	33.673%	Swiss-Prot	moderate database homology

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