LXL04_021698 | RubberDandelionOmics

Gene overview

LXL04_021698

Reference: OH-1004 Chr: Chr04 Coordinates: 135515287-135516885 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1599 bp · LXL04_021698|LXL04_021698|OH1004|cDNA

ATGATAGAAGCCCGCGGGTTTTTGAAATCAATCGCGCGCTTAATAGACGACTGCAAAAACATCAAACACCTGAAACAAATCCATTCCCAAATCATAACATCACCATACTTCTCCAAATCCGATCACCTCTTCCTCATTTCTCGCCTCATCTTCTTCTGCACTGTTACATCTCCCGGTTCTTTCAATTACGCTGCTCGTGTTTTTCAAGCCACCGAAAACCCCAATCTCTTTATCTACAACGCCATGATCAGATCATACTC...

CDS

Download CDS FASTA

1599 bp · LXL04_021698|LXL04_021698|OH1004|CDS

ATGATAGAAGCCCGCGGGTTTTTGAAATCAATCGCGCGCTTAATAGACGACTGCAAAAACATCAAACACCTGAAACAAATCCATTCCCAAATCATAACATCACCATACTTCTCCAAATCCGATCACCTCTTCCTCATTTCTCGCCTCATCTTCTTCTGCACTGTTACATCTCCCGGTTCTTTCAATTACGCTGCTCGTGTTTTTCAAGCCACCGAAAACCCCAATCTCTTTATCTACAACGCCATGATCAGATCATACTC...

Protein

Download Protein FASTA

532 aa · LXL04_021698|LXL04_021698|OH1004|PROTEIN

MIEARGFLKSIARLIDDCKNIKHLKQIHSQIITSPYFSKSDHLFLISRLIFFCTVTSPGSFNYAARVFQATENPNLFIYNAMIRSYSNKNETPHSSLVLYKQMLLNSIVPDCITLPFLMKECTTRPDFISGQTIHAHSIKFGFADDVYVGNSMINFYSACGVLTCARKVFDEMSKRDTVSWNSIITGCLKHMELDSGVELFTKMDNKNIITWNTIITGLVHGNRPKPAIDFFNKMITSRNHNTIHPDKITLASVISACAS...

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_021698`
TK1151 ID	TkA05G416440
OH-1004 ID	LXL04_021698
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.400
Protein coverage (%)	TK1151 100.000 / OH-1004 57.331 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_021698

Location Chr04:135515287-135516885 (-)

Description Similar to PCMP-H61: Pentatricopeptide repeat-containing protein At5g66520

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g66520`	Pentatricopeptide repeat-containing protein At5g66520.	No verified direct reference in this release
`At5g06540`	Pentatricopeptide repeat-containing protein At5g06540.	No verified direct reference in this release
`At3g62890`	Pentatricopeptide repeat-containing protein At3g62890.	No verified direct reference in this release
`At5g48910`	Pentatricopeptide repeat-containing protein At5g48910.	No verified direct reference in this release
`At2g42920`	Pentatricopeptide repeat-containing protein At2g42920, chloroplastic.	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_021698 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:AT2G42920

ath:AT3G62890

ath:AT5G06540

ath:AT5G48910

ath:AT5G66520

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.

Mitochondrion0.622

Rank 1 · LXL04_021698 · OH-1004

Plastid0.190

Rank 2 · LXL04_021698 · OH-1004

Nucleus0.046

Rank 3 · LXL04_021698 · OH-1004

Cytoplasm0.036

Rank 4 · LXL04_021698 · OH-1004

Cell membrane0.005

Rank 5 · LXL04_021698 · 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_274-122 aa

PF13041.13PPR_2176-209 aa

PF01535.27PPR179-209 aa

PF13041.13PPR_2207-259 aa

PF13041.13PPR_2312-360 aa

PF13812.13PPR_3313-360 aa

PF01535.27PPR316-344 aa

PF20431.5E_motif430-493 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021698	`PF13041.13`	PPR_2	74	122	1.7e-42	144.0
LXL04_021698	`PF13041.13`	PPR_2	176	209	1.7e-42	144.0
LXL04_021698	`PF01535.27`	PPR	179	209	4.4e-41	137.0
LXL04_021698	`PF13041.13`	PPR_2	207	259	1.7e-42	144.0
LXL04_021698	`PF13041.13`	PPR_2	312	360	1.7e-42	144.0
LXL04_021698	`PF13812.13`	PPR_3	313	360	1.7e-14	54.3
LXL04_021698	`PF01535.27`	PPR	316	344	4.4e-41	137.0
LXL04_021698	`PF20431.5`	E_motif	430	493	5.6e-08	33.6

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
`Q9FJY7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g66520	38.370%	Swiss-Prot	moderate database homology
`Q9FG16`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g06540	36.566%	Swiss-Prot	moderate database homology
`Q683I9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g62890	38.901%	Swiss-Prot	moderate database homology
`Q9FI80`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g48910	34.087%	Swiss-Prot	moderate database homology
`Q9SJG6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g42920, chloroplastic	36.673%	Swiss-Prot	moderate database homology

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