LXL04_024570 | RubberDandelionOmics

Gene overview

LXL04_024570

Reference: OH-1004 Chr: Chr05 Coordinates: 93977172-93979473 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1569 bp · LXL04_024570|LXL04_024570|OH1004|cDNA

CTCCAAACGAACAAAGGCCCTAGGGTTTCGATAACAATAATTCGTTCATTCATTTATAGTTTTTTTGTATGATTTGAATCTGTTTCACTTTTGACAATGTCTTCATCGCTGTTTATTCAACGGTTTGGAAAGACAAAGAGCTTAACGAAGAGGTCTACTAAGAAGTATTTGGAAGAAGCACTATACAGGCGGCTCCTCAAAGATGGCGGATCAGATGTTAGCGTTAGACAAAATTTGAATCAGTTCCTTAAATCCAGAAA...

CDS

Download CDS FASTA

1479 bp · LXL04_024570|LXL04_024570|OH1004|CDS

TTGACAATGTCTTCATCGCTGTTTATTCAACGGTTTGGAAAGACAAAGAGCTTAACGAAGAGGTCTACTAAGAAGTATTTGGAAGAAGCACTATACAGGCGGCTCCTCAAAGATGGCGGATCAGATGTTAGCGTTAGACAAAATTTGAATCAGTTCCTTAAATCCAGAAAGAAAGCTTACAAATGGGAGGTGGATCATTCCCTCAAAACCCTTCGCAGTCGCAAGCGATACGCCTCTGCCCTCAAGCTATCAGAAACCAT...

Protein

Download Protein FASTA

492 aa · LXL04_024570|LXL04_024570|OH1004|PROTEIN

MTMSSSLFIQRFGKTKSLTKRSTKKYLEEALYRRLLKDGGSDVSVRQNLNQFLKSRKKAYKWEVDHSLKTLRSRKRYASALKLSETMAERGMNKTITDQAVHIDLISKARGITAAESYFINLPEQSKNHFTYGPLLNHYCKHQMTEKAESMFQKMKELNLTLTSLHYNSILTLYEKSQQHEKIPQIILEMKSTEVNPDVLTYNIWMRAVSAMNDISGVERVINEMLRDENVSPDWTTYSNLASIYIDANLTGKAETALKE...

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_024570`
TK1151 ID	TkA06G130950
OH-1004 ID	LXL04_024570
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	98.800
Protein coverage (%)	TK1151 100.000 / OH-1004 99.593 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_024570

Location Chr05:93977172-93979473 (+)

Description Similar to At1g60770: Pentatricopeptide repeat-containing protein At1g60770

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g60770`	Large ribosomal subunit protein mL101 (rPPR4).	No verified direct reference in this release
`At1g02370`	Pentatricopeptide repeat-containing protein At1g02370, mitochondrial.	No verified direct reference in this release
`At4g01990`	Pentatricopeptide repeat-containing protein At4g01990, mitochondrial.	No verified direct reference in this release
`At1g02150`	Pentatricopeptide repeat-containing protein At1g02150.	No verified direct reference in this release
`At4g02820`	Pentatricopeptide repeat-containing protein At4g02820, 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_024570 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000963 mitochondrial RNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:1902775 mitochondrial large ribosomal subunit assembly Biological Process

GO:1903427 negative regulation of reactive oxygen species biosynthetic process Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005840 ribosome Cellular Component

GO:0009507 chloroplast Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0140978 mitochondrial large ribosomal subunit binding Molecular Function

KEGG gene cross-reference

ath:AT1G02150

ath:AT1G02370

ath:AT1G60770

ath:AT4G01990

ath:AT4G02820

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.

Mitochondrion0.842

Rank 1 · LXL04_024570 · OH-1004

Plastid0.078

Rank 2 · LXL04_024570 · OH-1004

Nucleus0.062

Rank 3 · LXL04_024570 · OH-1004

Cytoplasm0.037

Rank 4 · LXL04_024570 · OH-1004

Cell membrane0.010

Rank 5 · LXL04_024570 · 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_2128-161 aa

PF12854.14PPR_1128-156 aa

PF01535.27PPR130-159 aa

PF29070.1MSC6_N137-259 aa

PF17177.11PPR_long138-292 aa

PF13812.13PPR_3151-208 aa

PF13041.13PPR_2166-208 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024570	`PF13041.13`	PPR_2	128	161	2.8e-29	101.7
LXL04_024570	`PF12854.14`	PPR_1	128	156	4.5e-06	27.0
LXL04_024570	`PF01535.27`	PPR	130	159	1e-23	82.5
LXL04_024570	`PF29070.1`	MSC6_N	137	259	4e-10	40.1
LXL04_024570	`PF17177.11`	PPR_long	138	292	2e-10	41.1
LXL04_024570	`PF13812.13`	PPR_3	151	208	7.4e-12	45.9
LXL04_024570	`PF13041.13`	PPR_2	166	208	2.8e-29	101.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O22714`	Arabidopsis thaliana	Large ribosomal subunit protein mL101 (rPPR4)	57.377%	Swiss-Prot	strong database homology
`Q9FZ24`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g02370, mitochondrial	37.419%	Swiss-Prot	moderate database homology
`Q93WC5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g01990, mitochondrial	34.461%	Swiss-Prot	moderate database homology
`Q8LPS6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g02150	33.493%	Swiss-Prot	moderate database homology
`Q9SY07`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g02820, mitochondrial	34.660%	Swiss-Prot	moderate database homology

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