LXL04_009988 | RubberDandelionOmics

Gene overview

LXL04_009988

Reference: OH-1004 Chr: Chr02 Coordinates: 137392235-137393148 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

441 bp · LXL04_009988|LXL04_009988|OH1004|cDNA

ATGGTACACGAGATCAGATCAGGATCTAGTGACCTCAGAGCACAAAGGATCAAGAAGCTAAAGATAGGAGGAAGCAGATTTGAAGAACACACTTACCGATTAGTCAACAGGCTTCCAATCCATGGTACTTCATCACAAGCGATTTCGCACATGATGTATACGTGTAATTTTTTTATGAAACAGCTGGTTGAAGAGGGTGACTTGGATAAAGCTATGGCAGTTTATGAACCTGTGAAGAAGAAAGGTTTTCGTCCAAATGC...

CDS

Download CDS FASTA

441 bp · LXL04_009988|LXL04_009988|OH1004|CDS

ATGGTACACGAGATCAGATCAGGATCTAGTGACCTCAGAGCACAAAGGATCAAGAAGCTAAAGATAGGAGGAAGCAGATTTGAAGAACACACTTACCGATTAGTCAACAGGCTTCCAATCCATGGTACTTCATCACAAGCGATTTCGCACATGATGTATACGTGTAATTTTTTTATGAAACAGCTGGTTGAAGAGGGTGACTTGGATAAAGCTATGGCAGTTTATGAACCTGTGAAGAAGAAAGGTTTTCGTCCAAATGC...

Protein

Download Protein FASTA

146 aa · LXL04_009988|LXL04_009988|OH1004|PROTEIN

MVHEIRSGSSDLRAQRIKKLKIGGSRFEEHTYRLVNRLPIHGTSSQAISHMMYTCNFFMKQLVEEGDLDKAMAVYEPVKKKGFRPNAYTYGIVVEGRCKKGYLKEVVEVFEGHVKKKGFCPILLIFDFLYIFRGFRKEFKIEEMGK

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_009988`
TK1151 ID	TkA02G576250
OH-1004 ID	LXL04_009988
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	91.900
Protein coverage (%)	TK1151 94.286 / OH-1004 67.808 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

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_009988

Location Chr02:137392235-137393148 (-)

Description Similar to At1g62910: Pentatricopeptide repeat-containing protein At1g62910

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g62910`	Pentatricopeptide repeat-containing protein At1g62910.	No verified direct reference in this release
`At1g63400`	Pentatricopeptide repeat-containing protein At1g63400.	No verified direct reference in this release
`At3g13150`	Pentatricopeptide repeat-containing protein At3g13150.	No verified direct reference in this release
`At1g62670`	Pentatricopeptide repeat-containing protein At1g62670, mitochondrial.	No verified direct reference in this release
`At4g26680`	Pentatricopeptide repeat-containing protein At4g26680, mitochondrial.	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_009988 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000966 RNA 5'-end processing Biological Process

GO:0090617 mitochondrial mRNA 5'-end processing Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G62670

ath:AT1G62910

ath:AT1G63400

ath:AT3G13150

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.

Mitochondrion0.729

Rank 1 · LXL04_009988 · OH-1004

Nucleus0.093

Rank 2 · LXL04_009988 · OH-1004

Cytoplasm0.081

Rank 3 · LXL04_009988 · OH-1004

Plastid0.050

Rank 4 · LXL04_009988 · OH-1004

Cell membrane0.016

Rank 5 · LXL04_009988 · 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_350-92 aa

PF13041.13PPR_253-99 aa

PF12854.14PPR_181-111 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009988	`PF13812.13`	PPR_3	50	92	1.2e-07	32.4
LXL04_009988	`PF13041.13`	PPR_2	53	99	2.2e-11	44.4
LXL04_009988	`PF12854.14`	PPR_1	81	111	1.6e-07	31.7

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
`Q9LQ16`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62910	31.522%	Swiss-Prot	moderate database homology
`Q9SH26`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g63400	28.866%	Swiss-Prot	weak database homology
`Q9LK58`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g13150	26.613%	Swiss-Prot	weak database homology
`Q9SXD1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62670, mitochondrial	29.293%	Swiss-Prot	weak database homology
`Q9SZ10`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g26680, mitochondrial	29.293%	Swiss-Prot	weak database homology

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