LXL04_013175 | RubberDandelionOmics

Gene overview

LXL04_013175

Reference: OH-1004 Chr: Chr03 Coordinates: 25367672-25369714 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1962 bp · LXL04_013175|LXL04_013175|OH1004|cDNA

ATGGTCGCTGCTGCTTCTGCAGGAGCCACCGTCACTCACTTATCGCGCAGTAATCCTAACCTCGCTACTTTCTTCAATAAATACGTGGACACCGCCAATGTCTGGTCGTGGAATTCGGTCATCGCCGACCTTGCTCGCGCCGGTGAGTCCGTGGAGTCCCTTCTCGCCTTCTCCACCATGCGTAAGCTATCGCTTACCCCAAACCGCTCCACTTTCCCTTGCACCATCAAATCCTGCTCCGCCCTCTCTGATCTTCACTC...

CDS

Download CDS FASTA

1962 bp · LXL04_013175|LXL04_013175|OH1004|CDS

ATGGTCGCTGCTGCTTCTGCAGGAGCCACCGTCACTCACTTATCGCGCAGTAATCCTAACCTCGCTACTTTCTTCAATAAATACGTGGACACCGCCAATGTCTGGTCGTGGAATTCGGTCATCGCCGACCTTGCTCGCGCCGGTGAGTCCGTGGAGTCCCTTCTCGCCTTCTCCACCATGCGTAAGCTATCGCTTACCCCAAACCGCTCCACTTTCCCTTGCACCATCAAATCCTGCTCCGCCCTCTCTGATCTTCACTC...

Protein

Download Protein FASTA

653 aa · LXL04_013175|LXL04_013175|OH1004|PROTEIN

MVAAASAGATVTHLSRSNPNLATFFNKYVDTANVWSWNSVIADLARAGESVESLLAFSTMRKLSLTPNRSTFPCTIKSCSALSDLHSGKQTHQQALVFGFHHDVFVSSALIDMYSKCGHLDDARNLFDESPLRNVVSWTSMITGYVQNGLPNDALSLFKDFLTEENISNNEDDNVCIDSVAMVSVLAACSSTSNKSITEGVHGVVVKKGFQENTKIGNTLVDAYAKCGQVAFSRKAFNEINNKDVTTWNSMIAVCAQSGL...

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_013175`
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_013175

Location Chr03:25367672-25369714 (+)

Description Similar to PCMP-H34: Pentatricopeptide repeat-containing protein At3g26782, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g26782`	Pentatricopeptide repeat-containing protein At3g26782, mitochondrial.	No verified direct reference in this release
`At3g12770`	Pentatricopeptide repeat-containing protein At3g12770.	No verified direct reference in this release
`At1g08070`	Involved in multiple sites RNA editing events in chloroplasts.	No verified direct reference in this release
`At4g33990`	Pentatricopeptide repeat-containing protein At4g33990.	No verified direct reference in this release
`At3g23330`	Putative pentatricopeptide repeat-containing protein At3g23330.	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_013175 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0031425 chloroplast RNA processing 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:AT1G08070

ath:AT3G12770

ath:AT3G26782

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.

Mitochondrion0.588

Rank 1 · LXL04_013175 · OH-1004

Plastid0.264

Rank 2 · LXL04_013175 · OH-1004

Nucleus0.054

Rank 3 · LXL04_013175 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_013175 · OH-1004

Cell membrane0.006

Rank 5 · LXL04_013175 · 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_2133-160 aa

PF01535.27PPR136-160 aa

PF13041.13PPR_2243-293 aa

PF01535.27PPR247-273 aa

PF13041.13PPR_2346-393 aa

PF01535.27PPR349-377 aa

PF20431.5E_motif463-525 aa

PF14432.13DYW_deaminase561-653 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013175	`PF13041.13`	PPR_2	133	160	5.3e-43	145.6
LXL04_013175	`PF01535.27`	PPR	136	160	4.4e-53	174.6
LXL04_013175	`PF13041.13`	PPR_2	243	293	5.3e-43	145.6
LXL04_013175	`PF01535.27`	PPR	247	273	4.4e-53	174.6
LXL04_013175	`PF13041.13`	PPR_2	346	393	5.3e-43	145.6
LXL04_013175	`PF01535.27`	PPR	349	377	4.4e-53	174.6
LXL04_013175	`PF20431.5`	E_motif	463	525	2e-24	86.3
LXL04_013175	`PF14432.13`	DYW_deaminase	561	653	1.2e-37	128.3

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
`Q9LW32`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g26782, mitochondrial	62.074%	Swiss-Prot	strong database homology
`Q9LTV8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g12770	39.450%	Swiss-Prot	moderate database homology
`Q9LN01`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g08070, chloroplastic	40.644%	Swiss-Prot	moderate database homology
`O81767`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g33990	40.388%	Swiss-Prot	moderate database homology
`Q9LW63`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g23330	38.462%	Swiss-Prot	moderate database homology

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