LXL04_000237 | RubberDandelionOmics

Gene overview

LXL04_000237

Reference: OH-1004 Chr: Chr01 Coordinates: 4425159-4427473 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1809 bp · LXL04_000237|LXL04_000237|OH1004|cDNA

ATGTGGGCGCTCCGACGAACCTCCTCTATCGCTCTCAGGTCACAAACATTTTCAGCAGTCACCTTTCGTCCATCATTTCCGGAACACAAAACACCATTTTCAACATATACAGACAAAACAAGATCCCACAACCCACTACCACACCCAAGTGGGTCCCGAATCCTAAATACATATTCTTCAAGTTCAAGTACACATTCCAACACCACCTCAAATCACACCTACTCTTCAATAGCTGGCACAATAACCAATGGGGAGaaaga...

CDS

Download CDS FASTA

1809 bp · LXL04_000237|LXL04_000237|OH1004|CDS

ATGTGGGCGCTCCGACGAACCTCCTCTATCGCTCTCAGGTCACAAACATTTTCAGCAGTCACCTTTCGTCCATCATTTCCGGAACACAAAACACCATTTTCAACATATACAGACAAAACAAGATCCCACAACCCACTACCACACCCAAGTGGGTCCCGAATCCTAAATACATATTCTTCAAGTTCAAGTACACATTCCAACACCACCTCAAATCACACCTACTCTTCAATAGCTGGCACAATAACCAATGGGGAGAAAGA...

Protein

Download Protein FASTA

602 aa · LXL04_000237|LXL04_000237|OH1004|PROTEIN

MWALRRTSSIALRSQTFSAVTFRPSFPEHKTPFSTYTDKTRSHNPLPHPSGSRILNTYSSSSSTHSNTTSNHTYSSIAGTITNGEKEQEEEDDDNKLEDGFSELEDESDNESISENDTEVMGPKVTKTNQQKRAFSEIFKAIMDSPFQPVQKTLDNWLEKGDSITRSDISIAMLEFRRRKMYGKALHLSEWLQSRKQLQFNEKDYSSHVDLISKVHGLQAAEKYISKIPKSFQGELVYRTLLANCVITTDTTKAEQIFNK...

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_000237`
TK1151 ID	TkA01G626810
OH-1004 ID	LXL04_000237
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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

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_000237

Location Chr01:4425159-4427473 (-)

Description Similar to At1g80270: Pentatricopeptide repeat-containing protein At1g80270, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80270`	Pentatricopeptide repeat-containing protein At1g80270, mitochondrial.	No verified direct reference in this release
`At1g15480`	Pentatricopeptide repeat-containing protein At1g15480, mitochondrial.	No verified direct reference in this release
`At3g15590`	Pentatricopeptide repeat-containing protein At3g15590, mitochondrial.	No verified direct reference in this release
`At1g60770`	Large ribosomal subunit protein mL101 (rPPR4).	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_000237 · 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:0032543 mitochondrial translation Biological Process

GO:0080156 mitochondrial mRNA modification 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:0005761 mitochondrial ribosome Cellular Component

GO:0005840 ribosome Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009941 chloroplast envelope Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

KEGG gene cross-reference

ath:AT1G15480

ath:AT1G60770

ath:AT1G80270

ath:AT3G15590

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.

Mitochondrion0.765

Rank 1 · LXL04_000237 · OH-1004

Plastid0.167

Rank 2 · LXL04_000237 · OH-1004

Nucleus0.058

Rank 3 · LXL04_000237 · OH-1004

Cytoplasm0.035

Rank 4 · LXL04_000237 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_000237 · 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_long236-395 aa

PF29070.1MSC6_N242-363 aa

PF13812.13PPR_3273-315 aa

PF01535.27PPR514-542 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000237	`PF17177.11`	PPR_long	236	395	3.6e-16	59.9
LXL04_000237	`PF29070.1`	MSC6_N	242	363	1.3e-07	31.8
LXL04_000237	`PF13812.13`	PPR_3	273	315	9.8e-13	48.7
LXL04_000237	`PF01535.27`	PPR	514	542	1.6e-21	75.7

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
`Q9C977`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g80270, mitochondrial	50.998%	Swiss-Prot	strong database homology
`Q9XI21`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g15480, mitochondrial	45.649%	Swiss-Prot	moderate database homology
`Q9LRP6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g15590, mitochondrial	47.945%	Swiss-Prot	moderate database homology
`O22714`	Arabidopsis thaliana	Large ribosomal subunit protein mL101 (rPPR4)	28.698%	Swiss-Prot	weak database homology
`Q9SY07`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g02820, mitochondrial	29.070%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card