LXL04_009730 | RubberDandelionOmics

Gene overview

LXL04_009730

Reference: OH-1004 Chr: Chr02 Coordinates: 132284453-132285307 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

774 bp · LXL04_009730|LXL04_009730|OH1004|cDNA

ATGGCAATCACAAGTACGAGTTATAATCTTTCTATACAAACAAGAATGAGTTTCACAGAGTTTTGGGGACTTCCAAACTGCCCGTCACTCAAATCGGGGCAGCCGGGCAGAGGAAGTTCATGTAGTCGGATGATCCCAATGAGAGTAACAATGAGAGACCGAAGCAAAAACCGCAAACAATTACAAAAAGGACGAAATCTCAGCATTGAAGCCATTCAAACAATTCAAGCACTCAAAAGATCCCCAAAATCTAAAGAAAA...

CDS

Download CDS FASTA

774 bp · LXL04_009730|LXL04_009730|OH1004|CDS

ATGGCAATCACAAGTACGAGTTATAATCTTTCTATACAAACAAGAATGAGTTTCACAGAGTTTTGGGGACTTCCAAACTGCCCGTCACTCAAATCGGGGCAGCCGGGCAGAGGAAGTTCATGTAGTCGGATGATCCCAATGAGAGTAACAATGAGAGACCGAAGCAAAAACCGCAAACAATTACAAAAAGGACGAAATCTCAGCATTGAAGCCATTCAAACAATTCAAGCACTCAAAAGATCCCCAAAATCTAAAGAAAA...

Protein

Download Protein FASTA

257 aa · LXL04_009730|LXL04_009730|OH1004|PROTEIN

MAITSTSYNLSIQTRMSFTEFWGLPNCPSLKSGQPGRGSSCSRMIPMRVTMRDRSKNRKQLQKGRNLSIEAIQTIQALKRSPKSKEKQQQVIDSKFSRLLKFDMMAILRELLRQENYLLALTVFAEIKKEHWYKPQVLLYTDIISVLAKNNLYDDVDTIFLELKTEKGRLEAKTEGLNMLLETLMSYNITKLAMDCFELMKEVGCDPDRSTFKLLVGYLESKGEMSLSEGIRQEAYKYYGDSIEYVNEQDEMAINRT

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_009730`
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_009730

Location Chr02:132284453-132285307 (-)

Description Similar to THA8: Protein THYLAKOID ASSEMBLY 8, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g27750`	Essential protein required during embryogenesis.	A short PPR protein required for the splicing of specific group II introns in angiosperm chloroplasts.2012 · DOI: 10.1261/rna.032623.112 Structure of a PLS-class pentatricopeptide repeat protein provides insights into mechanism of RNA recognition.2013 · DOI: 10.1074/jbc.m113.496828
`At3g46870`	Binds weakly to specific single strand RNA (ssRNA).	Structure of a PLS-class pentatricopeptide repeat protein provides insights into mechanism of RNA recognition.2013 · DOI: 10.1074/jbc.m113.496828
`At1g62350`	Pentatricopeptide repeat-containing protein At1g62350.	No verified direct reference in this release
`At2g35130`	Pentatricopeptide repeat-containing protein At2g35130.	No verified direct reference in this release
`At1g74750`	Pentatricopeptide repeat-containing protein At1g74750.	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_009730 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003727 single-stranded RNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G62350

ath:AT1G74750

ath:AT2G35130

ath:AT3G27750

ath:AT3G46870

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.

Plastid0.910

Rank 1 · LXL04_009730 · OH-1004

Mitochondrion0.077

Rank 2 · LXL04_009730 · OH-1004

Nucleus0.038

Rank 3 · LXL04_009730 · OH-1004

Cytoplasm0.017

Rank 4 · LXL04_009730 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_009730 · 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_2177-216 aa

PF13812.13PPR_3178-217 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009730	`PF13041.13`	PPR_2	177	216	6.2e-08	33.3
LXL04_009730	`PF13812.13`	PPR_3	178	217	6.5e-10	39.7

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
`Q9LVW6`	Arabidopsis thaliana	Protein THYLAKOID ASSEMBLY 8, chloroplastic	32.258%	Swiss-Prot	moderate database homology
`Q9STF9`	Arabidopsis thaliana	Protein THYLAKOID ASSEMBLY 8-like, chloroplastic	31.288%	Swiss-Prot	moderate database homology
`Q1PFH7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62350	25.134%	Swiss-Prot	weak database homology
`O82178`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g35130	29.245%	Swiss-Prot	weak database homology
`Q9SSF9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g74750	21.390%	Swiss-Prot	weak database homology

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