LXL04_038232 | RubberDandelionOmics

Gene overview

LXL04_038232

Reference: OH-1004 Chr: Chr09 Coordinates: 34795761-34797473 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1713 bp · LXL04_038232|LXL04_038232|OH1004|cDNA

ATGGAGATCGCAACAATGGCGGAAGCGACACAGCTACACGCCCAATTACTAAAACACCAACAAACCGATCACCAAAACCTAAGCAAAATCTTCAATTTCACTGCTCTATCACCCTCCGGCAGCCTCACCTACGCTCGCCACATTCTCAAAACCCTAAAAACCCCAACCAACTCCTATTTCCACAACACCATGATACGAGCTTACTCCGACTCATCCGACCCGTTCCAGTCCATCTCCCTCTTCCTCGCCTGGCATAATTC...

CDS

Download CDS FASTA

1713 bp · LXL04_038232|LXL04_038232|OH1004|CDS

ATGGAGATCGCAACAATGGCGGAAGCGACACAGCTACACGCCCAATTACTAAAACACCAACAAACCGATCACCAAAACCTAAGCAAAATCTTCAATTTCACTGCTCTATCACCCTCCGGCAGCCTCACCTACGCTCGCCACATTCTCAAAACCCTAAAAACCCCAACCAACTCCTATTTCCACAACACCATGATACGAGCTTACTCCGACTCATCCGACCCGTTCCAGTCCATCTCCCTCTTCCTCGCCTGGCATAATTC...

Protein

Download Protein FASTA

570 aa · LXL04_038232|LXL04_038232|OH1004|PROTEIN

MEIATMAEATQLHAQLLKHQQTDHQNLSKIFNFTALSPSGSLTYARHILKTLKTPTNSYFHNTMIRAYSDSSDPFQSISLFLAWHNSEDPFSPTPDRFTYPFVLKACSKLKQKRFGKQLHGLIYKSGFAPDMYIQNALIHFYSGCNQMGFASKVFDKMHHRDVVSWTSVINGYVDNKMTIEGLRLFDKMVIEGFEPNDVTVLSVLRACADTGALNVGMKLNEFLNRKGGVLKKNIVTALIDMYSKCGSIDNATRIFNEAQ...

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_038232`
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_038232

Location Chr09:34795761-34797473 (+)

Description Similar to PCMP-H28: Pentatricopeptide repeat-containing protein At4g21065

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21065`	Pentatricopeptide repeat-containing protein At4g21065.	No verified direct reference in this release
`At5g66520`	Pentatricopeptide repeat-containing protein At5g66520.	No verified direct reference in this release
`At1g31920`	Pentatricopeptide repeat-containing protein At1g31920.	No verified direct reference in this release
`At3g47530`	Pentatricopeptide repeat-containing protein At3g47530.	No verified direct reference in this release
`At2g02980`	Involved in RNA editing event in chloroplasts.	A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038232 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0016554 cytidine to uridine editing Biological Process

GO:0031425 chloroplast RNA processing Biological Process

GO:1900865 chloroplast RNA modification 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:AT1G31920

ath:AT2G02980

ath:AT3G47530

ath:AT4G21065

ath:AT5G66520

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.

Mitochondrion0.703

Rank 1 · LXL04_038232 · OH-1004

Plastid0.144

Rank 2 · LXL04_038232 · OH-1004

Nucleus0.064

Rank 3 · LXL04_038232 · OH-1004

Cytoplasm0.034

Rank 4 · LXL04_038232 · OH-1004

Cell membrane0.007

Rank 5 · LXL04_038232 · 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_2161-209 aa

PF01535.27PPR164-194 aa

PF29070.1MSC6_N185-272 aa

PF13041.13PPR_2262-309 aa

PF01535.27PPR266-292 aa

PF29070.1MSC6_N266-359 aa

PF20431.5E_motif380-442 aa

PF14432.13DYW_deaminase478-570 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038232	`PF13041.13`	PPR_2	161	209	3.2e-36	123.9
LXL04_038232	`PF01535.27`	PPR	164	194	7.8e-33	111.1
LXL04_038232	`PF29070.1`	MSC6_N	185	272	3.4e-13	50.2
LXL04_038232	`PF13041.13`	PPR_2	262	309	3.2e-36	123.9
LXL04_038232	`PF01535.27`	PPR	266	292	7.8e-33	111.1
LXL04_038232	`PF29070.1`	MSC6_N	266	359	3.4e-13	50.2
LXL04_038232	`PF20431.5`	E_motif	380	442	1.1e-08	35.9
LXL04_038232	`PF14432.13`	DYW_deaminase	478	570	1.7e-36	124.6

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
`A8MQA3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g21065	38.287%	Swiss-Prot	moderate database homology
`Q9FJY7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g66520	38.358%	Swiss-Prot	moderate database homology
`Q9C6T2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g31920	38.448%	Swiss-Prot	moderate database homology
`Q9SN85`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g47530	39.437%	Swiss-Prot	moderate database homology
`Q8LK93`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g02980, chloroplastic	36.268%	Swiss-Prot	moderate database homology

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