LXL04_001648 | RubberDandelionOmics

Gene overview

LXL04_001648

Reference: OH-1004 Chr: Chr01 Coordinates: 30754607-30757115 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2418 bp · LXL04_001648|LXL04_001648|OH1004|cDNA

ATGCAACTGAGCACCAGTAGTCGTGAGCTATCACCCTTCATCTTCCCTCTCTCCTCTATTCCCTCCCTTGATAAAAGCTACACGGCACCCATGCGCACAACCCCATCCCTCCTCCGCTCTCTCTCCACCTCCCTCCCTAACCACCACCGCCGTATCCTCATCCAACGTACTTTCTCCCTCTTTAAACCCCACCTTGTAAACCCTCCTCGAATCTCACTCTTTTGTACTCGCTCCGCGGAACAATCGTCAGTCAGTAATTT...

CDS

Download CDS FASTA

2361 bp · LXL04_001648|LXL04_001648|OH1004|CDS

ATGCAACTGAGCACCAGTAGTCGTGAGCTATCACCCTTCATCTTCCCTCTCTCCTCTATTCCCTCCCTTGATAAAAGCTACACGGCACCCATGCGCACAACCCCATCCCTCCTCCGCTCTCTCTCCACCTCCCTCCCTAACCACCACCGCCGTATCCTCATCCAACGTACTTTCTCCCTCTTTAAACCCCACCTTGTAAACCCTCCTCGAATCTCACTCTTTTGTACTCGCTCCGCGGAACAATCGTCAGTCAGTAATTT...

Protein

Download Protein FASTA

786 aa · LXL04_001648|LXL04_001648|OH1004|PROTEIN

MQLSTSSRELSPFIFPLSSIPSLDKSYTAPMRTTPSLLRSLSTSLPNHHRRILIQRTFSLFKPHLVNPPRISLFCTRSAEQSSVSNFVELLADENEDLEFDKDNEPFTFDASFRSNDDSKNLNLSPSLDVKELDELPEQWRRSKLAWLCKELPAHKAPTLIRILNAQRKWVNQEDMTYVTVHCMRIRENETGFRVYKWMMQQHWFRFDFSLATKLADYMGKERKYLKCREIFDDIINHGLIPTEYTFHILIISYLSSSNR...

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_001648`
TK1151 ID	TkA01G520610
OH-1004 ID	LXL04_001648
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_001648

Location Chr01:30754607-30757115 (+)

Description Similar to OTP51: Pentatricopeptide repeat-containing protein At2g15820, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g15820`	Promotes the splicing of group II introns in chloroplasts.	The pentatricopeptide repeat gene OTP51 with two LAGLIDADG motifs is required for the cis-splicing of plastid ycf3 intron 2 in Arabidopsis thaliana.2008 · DOI: 10.1111/j.1365-313x.2008.03581.x
`At2g17140`	Pentatricopeptide repeat-containing protein At2g17140.	No verified direct reference in this release
`At2g15630`	Pentatricopeptide repeat-containing protein At2g15630, mitochondrial.	No verified direct reference in this release
`At1g09680`	Putative pentatricopeptide repeat-containing protein At1g09680.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0702000`	Promotes the splicing of group II introns in chloroplasts.	A mutation of OSOTP 51 leads to impairment of photosystem I complex assembly and serious photo-damage in rice.2012 · DOI: 10.1111/j.1744-7909.2012.01094.x

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001648 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:0048564 photosystem I assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0004519 endonuclease activity Molecular Function

KEGG gene cross-reference

ath:AT2G15630

ath:AT2G15820

ath:AT2G17140

dosa:Os02g0702000

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.

Mitochondrion0.722

Rank 1 · LXL04_001648 · OH-1004

Plastid0.202

Rank 2 · LXL04_001648 · OH-1004

Nucleus0.071

Rank 3 · LXL04_001648 · OH-1004

Cytoplasm0.037

Rank 4 · LXL04_001648 · OH-1004

Cell membrane0.012

Rank 5 · LXL04_001648 · 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.

PF29070.1MSC6_N261-333 aa

PF25062.2ARM_TT21_N328-484 aa

PF29070.1MSC6_N337-454 aa

PF29070.1MSC6_N471-558 aa

PF03161.19LAGLIDADG_2603-757 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001648	`PF29070.1`	MSC6_N	261	333	4.8e-20	72.7
LXL04_001648	`PF25062.2`	ARM_TT21_N	328	484	4.4e-06	27.3
LXL04_001648	`PF29070.1`	MSC6_N	337	454	4.8e-20	72.7
LXL04_001648	`PF29070.1`	MSC6_N	471	558	4.8e-20	72.7
LXL04_001648	`PF03161.19`	LAGLIDADG_2	603	757	4.3e-40	138.1

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
`Q9XIL5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g15820, chloroplastic	52.152%	Swiss-Prot	strong database homology
`Q0WPZ6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g17140	23.824%	Swiss-Prot	weak database homology
`Q9ZQF1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g15630, mitochondrial	22.782%	Swiss-Prot	weak database homology
`O04491`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At1g09680	22.456%	Swiss-Prot	weak database homology
`Q6ZHJ5`	Oryza sativa subsp. japonica	Pentatricopeptide repeat-containing protein OTP51, chloroplastic	52.000%	Swiss-Prot	strong database homology

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