LXL04_019232 | RubberDandelionOmics

Gene overview

LXL04_019232

Reference: OH-1004 Chr: Chr04 Coordinates: 26886101-26888628 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2349 bp · LXL04_019232|LXL04_019232|OH1004|cDNA

ATGAACCTCTTAATCAAATCTTTCTGCCTAAGCCGCAGATACTTTCATTCCCTTTTTTTTTACAAGAAACTCCTCCCCGTTACAAAATTAGAAGTTTCTACGTTCCCTTCAAGTCTCAAATCATGTTCTTCTCTGCCATCTCTTGATGCGGGATTCATGAAGCATGGGTACTTGATCAAATGCGGGGTTTTGAATTGCTGTGTTGATGTTGGGAATGATCTACTGAGGATGTATCTGACGCATGAAGAATTTGGGGATGC...

CDS

Download CDS FASTA

2349 bp · LXL04_019232|LXL04_019232|OH1004|CDS

ATGAACCTCTTAATCAAATCTTTCTGCCTAAGCCGCAGATACTTTCATTCCCTTTTTTTTTACAAGAAACTCCTCCCCGTTACAAAATTAGAAGTTTCTACGTTCCCTTCAAGTCTCAAATCATGTTCTTCTCTGCCATCTCTTGATGCGGGATTCATGAAGCATGGGTACTTGATCAAATGCGGGGTTTTGAATTGCTGTGTTGATGTTGGGAATGATCTACTGAGGATGTATCTGACGCATGAAGAATTTGGGGATGC...

Protein

Download Protein FASTA

782 aa · LXL04_019232|LXL04_019232|OH1004|PROTEIN

MNLLIKSFCLSRRYFHSLFFYKKLLPVTKLEVSTFPSSLKSCSSLPSLDAGFMKHGYLIKCGVLNCCVDVGNDLLRMYLTHEEFGDAYKVFDEMPMKSKGDLFDRIIHELGTNRAYKDVILAFEKMVELSIFPNVHSLCHVIKACSNLTSIKSGQFVHNFVTQNGFENQVLIMNSLISMYAKMGRLDLAQKVFNNIIHKDIVSWNSLITGYAQNQNSLKVFDLFIYLKQAEKTVPNVITFLALLSSVRKVTIGTTIHSHL...

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_019232`
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_019232

Location Chr04:26886101-26888628 (-)

Description Similar to PCMP-E36: Pentatricopeptide repeat-containing protein At4g21300

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g21300`	Pentatricopeptide repeat-containing protein At4g21300.	No verified direct reference in this release
`At3g03580`	Pentatricopeptide repeat-containing protein At3g03580.	No verified direct reference in this release
`At4g33990`	Pentatricopeptide repeat-containing protein At4g33990.	No verified direct reference in this release
`At4g18750`	Plays a major role in single RNA editing events in chloroplasts.	Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.2013 · DOI: 10.1074/jbc.m113.485755
`At4g04370`	Pentatricopeptide repeat-containing protein At4g04370.	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_019232 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0005739 mitochondrion 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:AT3G03580

ath:AT4G21300

ath:AT4G33990

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.

Mitochondrion0.669

Rank 1 · LXL04_019232 · OH-1004

Plastid0.154

Rank 2 · LXL04_019232 · OH-1004

Nucleus0.047

Rank 3 · LXL04_019232 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_019232 · OH-1004

Cell membrane0.006

Rank 5 · LXL04_019232 · 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.

PF13812.13PPR_3197-245 aa

PF13041.13PPR_2199-245 aa

PF13041.13PPR_2299-346 aa

PF01535.27PPR300-326 aa

PF13041.13PPR_2401-448 aa

PF13041.13PPR_2503-547 aa

PF01535.27PPR505-528 aa

PF13041.13PPR_2604-651 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019232	`PF13812.13`	PPR_3	197	245	1e-23	83.9
LXL04_019232	`PF13041.13`	PPR_2	199	245	1.8e-61	204.7
LXL04_019232	`PF13041.13`	PPR_2	299	346	1.8e-61	204.7
LXL04_019232	`PF01535.27`	PPR	300	326	6.7e-55	180.3
LXL04_019232	`PF13041.13`	PPR_2	401	448	1.8e-61	204.7
LXL04_019232	`PF13041.13`	PPR_2	503	547	1.8e-61	204.7
LXL04_019232	`PF01535.27`	PPR	505	528	6.7e-55	180.3
LXL04_019232	`PF13041.13`	PPR_2	604	651	1.8e-61	204.7
LXL04_019232	`PF01535.27`	PPR	607	635	6.7e-55	180.3
LXL04_019232	`PF01535.27`	PPR	641	668	6.7e-55	180.3

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
`Q9STE1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g21300	29.911%	Swiss-Prot	weak database homology
`Q9SS60`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g03580	30.769%	Swiss-Prot	moderate database homology
`O81767`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g33990	29.870%	Swiss-Prot	weak database homology
`Q9SN39`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein DOT4, chloroplastic	31.193%	Swiss-Prot	moderate database homology
`Q9XE98`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g04370	28.592%	Swiss-Prot	weak database homology

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