LXL04_006690 | RubberDandelionOmics

Gene overview

LXL04_006690

Reference: OH-1004 Chr: Chr02 Coordinates: 22329358-22334110 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2979 bp · LXL04_006690|LXL04_006690|OH1004|cDNA

atgtggacaagttcggaacgtttttacccaaatgtggacaagttcggaacgtttttacccaaatGTGGACAAGACGGCTCCGGATATTCGAAACCGCTACCTCTTCTTTTTCCGGTAGTGGTTGGGAACATCGCCGGAGACGCGCCGCCACCTTTAATACTGCGGCTGTTTCTGAGCTTCCGGCTGCATGAGTTTGAGAGGGAAATCGGCGGTGGGTCACGAGCCCGAGCTGGACTAAGGCCCAAGAAAAAAGGAAGGCT...

CDS

Download CDS FASTA

2979 bp · LXL04_006690|LXL04_006690|OH1004|CDS

ATGTGGACAAGTTCGGAACGTTTTTACCCAAATGTGGACAAGTTCGGAACGTTTTTACCCAAATGTGGACAAGACGGCTCCGGATATTCGAAACCGCTACCTCTTCTTTTTCCGGTAGTGGTTGGGAACATCGCCGGAGACGCGCCGCCACCTTTAATACTGCGGCTGTTTCTGAGCTTCCGGCTGCATGAGTTTGAGAGGGAAATCGGCGGTGGGTCACGAGCCCGAGCTGGACTAAGGCCCAAGAAAAAAGGAAGGCT...

Protein

Download Protein FASTA

992 aa · LXL04_006690|LXL04_006690|OH1004|PROTEIN

MWTSSERFYPNVDKFGTFLPKCGQDGSGYSKPLPLLFPVVVGNIAGDAPPPLILRLFLSFRLHEFEREIGGGSRARAGLRPKKKGRLVTHRRFPSQTHAAASSETAAVSKVAARLRRCSHPLPEKEEVAVSNIQSRLVHIWPYKIFPSSLFRDELNFALMESLSLRVPPRPPLPSQHPDVEPIKHNLLKNGVIPTPKIIHTLRKKQLQKINRRRPPPNQTPEEEQIQDEEANFQTLKAEFKTFNRAIVKATKSKQDMDIN...

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_006690`
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_006690

Location Chr02:22329358-22334110 (-)

Description Similar to DG1: Pentatricopeptide repeat-containing protein At5g67570, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g67570`	Involved in the regulation of early chloroplast development and chloroplast gene expression in a SIGF-dependent manner.	No verified direct reference in this release
`At1g30610`	May play a role in embryogenesis.	No verified direct reference in this release
`At5g02860`	Pentatricopeptide repeat-containing protein At5g02860.	No verified direct reference in this release
`At2g18940`	Pentatricopeptide repeat-containing protein At2g18940, chloroplastic.	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_006690 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0042793 plastid transcription Biological Process

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G30610

ath:AT5G02860

ath:AT5G67570

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.

Plastid0.766

Rank 1 · LXL04_006690 · OH-1004

Mitochondrion0.114

Rank 2 · LXL04_006690 · OH-1004

Nucleus0.097

Rank 3 · LXL04_006690 · OH-1004

Cytoplasm0.026

Rank 4 · LXL04_006690 · OH-1004

Cell membrane0.016

Rank 5 · LXL04_006690 · 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.

PF17177.11PPR_long417-586 aa

PF13812.13PPR_3501-549 aa

PF13041.13PPR_2503-543 aa

PF13041.13PPR_2542-587 aa

PF13812.13PPR_3547-587 aa

PF01535.27PPR577-606 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006690	`PF17177.11`	PPR_long	417	586	2e-09	37.9
LXL04_006690	`PF13812.13`	PPR_3	501	549	7.7e-22	77.9
LXL04_006690	`PF13041.13`	PPR_2	503	543	1.6e-26	92.9
LXL04_006690	`PF13041.13`	PPR_2	542	587	1.6e-26	92.9
LXL04_006690	`PF13812.13`	PPR_3	547	587	7.7e-22	77.9
LXL04_006690	`PF01535.27`	PPR	577	606	1.1e-24	85.6

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
`Q9FJW6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g67570, chloroplastic	53.953%	Swiss-Prot	strong database homology
`Q9SA76`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g30610, chloroplastic	38.185%	Swiss-Prot	moderate database homology
`Q9LYZ9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g02860	22.863%	Swiss-Prot	weak database homology
`O64624`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g18940, chloroplastic	22.833%	Swiss-Prot	weak database homology

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