LXL04_039054 | RubberDandelionOmics

Gene overview

LXL04_039054

Reference: OH-1004 Chr: Chr09 Coordinates: 57640611-57642476 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1866 bp · LXL04_039054|LXL04_039054|OH1004|cDNA

ATGTCTCAAACAAGAGCGAGGGCATTCCAAACGGTGAAATCTGTTAATTATTACTATAAGGTATGTAGTACTACAAATGCTTCACGCAGTTATTGCTCAAGTAGTTCCTTCAAAGCCCACCCTTTTGTTAAAGAAATTAGCACTCTTAGTTCTGCGGCCAAGAATGTGAGCTCTGATTTCCGAAACCCTAATGAGTTCCCAGGTGCTGGCACAAACTATAATGGATACGGCAAAGATTGGTCTACAGAAAGTAAAAGTGA...

CDS

Download CDS FASTA

1866 bp · LXL04_039054|LXL04_039054|OH1004|CDS

ATGTCTCAAACAAGAGCGAGGGCATTCCAAACGGTGAAATCTGTTAATTATTACTATAAGGTATGTAGTACTACAAATGCTTCACGCAGTTATTGCTCAAGTAGTTCCTTCAAAGCCCACCCTTTTGTTAAAGAAATTAGCACTCTTAGTTCTGCGGCCAAGAATGTGAGCTCTGATTTCCGAAACCCTAATGAGTTCCCAGGTGCTGGCACAAACTATAATGGATACGGCAAAGATTGGTCTACAGAAAGTAAAAGTGA...

Protein

Download Protein FASTA

621 aa · LXL04_039054|LXL04_039054|OH1004|PROTEIN

MSQTRARAFQTVKSVNYYYKVCSTTNASRSYCSSSSFKAHPFVKEISTLSSAAKNVSSDFRNPNEFPGAGTNYNGYGKDWSTESKSEYERHRKQLYNLNGNYPYNIMDHSSNRLSEEGRSVKGGGNDQYLKNNVIFQENQGNYYMREDDLHRQSQYNVNGSYSGNASSNQQSSVKNYQYNVTGSSSSDASSYQQSIVVNDQLPNGSCSDMVNSQLQAVDERRLLGTIQELDAFCKNGKLKEAVEVLDLLEQNKVSVDIPR...

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_039054`
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_039054

Location Chr09:57640611-57642476 (+)

Description Similar to PCMP-H63: Pentatricopeptide repeat-containing protein At4g32450, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g32450`	Pentatricopeptide repeat-containing protein At4g32450, mitochondrial.	No verified direct reference in this release
`At2g25580`	Pentatricopeptide repeat-containing protein At2g25580.	No verified direct reference in this release
`At2g34370`	Pentatricopeptide repeat-containing protein At2g34370, mitochondrial.	No verified direct reference in this release
`At1g29710`	Pentatricopeptide repeat-containing protein At1g29710, mitochondrial.	No verified direct reference in this release
`At2g15690`	Pentatricopeptide repeat-containing protein At2g15690, 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_039054 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G29710

ath:AT2G15690

ath:AT2G25580

ath:AT2G34370

ath:AT4G32450

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.

Plastid0.446

Rank 1 · LXL04_039054 · OH-1004

Mitochondrion0.394

Rank 2 · LXL04_039054 · OH-1004

Nucleus0.096

Rank 3 · LXL04_039054 · OH-1004

Cytoplasm0.050

Rank 4 · LXL04_039054 · OH-1004

Cell membrane0.017

Rank 5 · LXL04_039054 · 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.

PF23276.3TPR_24230-318 aa

PF17177.11PPR_long261-421 aa

PF13041.13PPR_2292-325 aa

PF13041.13PPR_2323-359 aa

PF01535.27PPR326-352 aa

PF14432.13DYW_deaminase529-621 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039054	`PF23276.3`	TPR_24	230	318	1.1e-09	39.0
LXL04_039054	`PF17177.11`	PPR_long	261	421	5.2e-07	30.0
LXL04_039054	`PF13041.13`	PPR_2	292	325	4.4e-22	78.6
LXL04_039054	`PF13041.13`	PPR_2	323	359	4.4e-22	78.6
LXL04_039054	`PF01535.27`	PPR	326	352	1.1e-21	76.1
LXL04_039054	`PF14432.13`	DYW_deaminase	529	621	9.4e-42	141.5

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
`Q9SUU7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g32450, mitochondrial	51.515%	Swiss-Prot	moderate database homology
`Q680H3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g25580	50.380%	Swiss-Prot	moderate database homology
`Q8S8Q7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g34370, mitochondrial	47.000%	Swiss-Prot	moderate database homology
`Q9C6G2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g29710, mitochondrial	42.821%	Swiss-Prot	moderate database homology
`Q9ZQE5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g15690, mitochondrial	37.374%	Swiss-Prot	moderate database homology

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