LXL04_032129 | RubberDandelionOmics

Gene overview

LXL04_032129

Reference: OH-1004 Chr: Chr07 Coordinates: 17213921-17216499 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1950 bp · LXL04_032129|LXL04_032129|OH1004|cDNA

ATGCTGATTCGAGTTACCGCGACAGCGAAGCTCAAGAGATCGTCACCTTCACAACACAAACTCTTCTTTTCCTCCCTCACCTCAATCGTTGATTCTGATTATTCATCTACTTCTCATCACCAATGTCGATCTTCATCTCACCCACAAAAACCACCGACGACCCACCATCGACATCTTCCTCCGAAGCTCCACCTGACCAACCGCTCGCAATTAGATTATCAACTTATCCTAAAAACATTCATCGCTCGAAGGGCGATTCA...

CDS

Download CDS FASTA

1950 bp · LXL04_032129|LXL04_032129|OH1004|CDS

ATGCTGATTCGAGTTACCGCGACAGCGAAGCTCAAGAGATCGTCACCTTCACAACACAAACTCTTCTTTTCCTCCCTCACCTCAATCGTTGATTCTGATTATTCATCTACTTCTCATCACCAATGTCGATCTTCATCTCACCCACAAAAACCACCGACGACCCACCATCGACATCTTCCTCCGAAGCTCCACCTGACCAACCGCTCGCAATTAGATTATCAACTTATCCTAAAAACATTCATCGCTCGAAGGGCGATTCA...

Protein

Download Protein FASTA

649 aa · LXL04_032129|LXL04_032129|OH1004|PROTEIN

MLIRVTATAKLKRSSPSQHKLFFSSLTSIVDSDYSSTSHHQCRSSSHPQKPPTTHHRHLPPKLHLTNRSQLDYQLILKTFIARRAIQPGRQLHAHLCLIGLGNDTILGTKLVNLYCSCNHMYNAHLLFDRISKRNVFLWNVMIRWYAWNGPFNAAVSLYYEMIDNGIVPDNFTFPFVLKACSNLSAVDVGRDVHDNVVRTGWEKDVFVGAALIDMYAKCGNVSSARQVFDKILQRDVVLWNSMLTAYSQNSHPEDCLALC...

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_032129`
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_032129

Location Chr07:17213921-17216499 (+)

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
`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
`At3g12770`	Pentatricopeptide repeat-containing protein At3g12770.	No verified direct reference in this release
`At3g23330`	Putative pentatricopeptide repeat-containing protein At3g23330.	No verified direct reference in this release
`At3g46790`	Required for the intergenic processing between chloroplast rsp7 and ndhB transcripts.	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_032129 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009451 RNA modification Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT3G12770

ath:AT4G21065

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.

Mitochondrion0.612

Rank 1 · LXL04_032129 · OH-1004

Plastid0.250

Rank 2 · LXL04_032129 · OH-1004

Nucleus0.050

Rank 3 · LXL04_032129 · OH-1004

Cytoplasm0.035

Rank 4 · LXL04_032129 · OH-1004

Cell membrane0.006

Rank 5 · LXL04_032129 · 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_2134-182 aa

PF01535.27PPR138-167 aa

PF13041.13PPR_2235-281 aa

PF01535.27PPR339-366 aa

PF13041.13PPR_2339-382 aa

PF12854.14PPR_1339-365 aa

PF20431.5E_motif453-515 aa

PF14432.13DYW_deaminase551-637 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032129	`PF13041.13`	PPR_2	134	182	6.6e-39	132.5
LXL04_032129	`PF01535.27`	PPR	138	167	5.9e-42	139.7
LXL04_032129	`PF13041.13`	PPR_2	235	281	6.6e-39	132.5
LXL04_032129	`PF01535.27`	PPR	339	366	5.9e-42	139.7
LXL04_032129	`PF13041.13`	PPR_2	339	382	6.6e-39	132.5
LXL04_032129	`PF12854.14`	PPR_1	339	365	3e-18	66.0
LXL04_032129	`PF20431.5`	E_motif	453	515	1e-19	71.2
LXL04_032129	`PF14432.13`	DYW_deaminase	551	637	1e-35	122.2

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	40.799%	Swiss-Prot	moderate database homology
`Q9SN39`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein DOT4, chloroplastic	39.831%	Swiss-Prot	moderate database homology
`Q9LTV8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g12770	39.054%	Swiss-Prot	moderate database homology
`Q9LW63`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g23330	41.699%	Swiss-Prot	moderate database homology
`Q9STF3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein CRR2, chloroplastic	37.801%	Swiss-Prot	moderate database homology

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