LXL04_006138 | RubberDandelionOmics

Gene overview

LXL04_006138

Reference: OH-1004 Chr: Chr02 Coordinates: 2204038-2204986 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

810 bp · LXL04_006138|LXL04_006138|OH1004|cDNA

ATGTCAGCAATTGGGAGCACACTACGATCCAAATTACGGTTATCCATTTCCTCATTTCTCCACCATGACCTAACTCGAACACCCATCTTCAAACACTACATCTCTTCTTCCtactcttcttcttcttcaattaCATCACCATTATCATTCAATCACACAACCAAAACCATCAGCGACATACTATACTCACAACACCCCCGCCATTACCACGATGGTAGACCCAGAGGATCTCTCTGGAGAGGAAAGAAAATGATTGGCAA...

CDS

Download CDS FASTA

810 bp · LXL04_006138|LXL04_006138|OH1004|CDS

ATGTCAGCAATTGGGAGCACACTACGATCCAAATTACGGTTATCCATTTCCTCATTTCTCCACCATGACCTAACTCGAACACCCATCTTCAAACACTACATCTCTTCTTCCTACTCTTCTTCTTCTTCAATTACATCACCATTATCATTCAATCACACAACCAAAACCATCAGCGACATACTATACTCACAACACCCCCGCCATTACCACGATGGTAGACCCAGAGGATCTCTCTGGAGAGGAAAGAAAATGATTGGCAA...

Protein

Download Protein FASTA

269 aa · LXL04_006138|LXL04_006138|OH1004|PROTEIN

MSAIGSTLRSKLRLSISSFLHHDLTRTPIFKHYISSSYSSSSSITSPLSFNHTTKTISDILYSQHPRHYHDGRPRGSLWRGKKMIGKEALFVILGIKRVKHDEQNLENFIKIHVSRLLKMDMVAVLNELERQEEVDLAVKMFWVIQKQDWYTPDVYLYKDLIISLSKSKKMEEAMKLWESMKKENLYPDSQTYTEVIRGFLRFGSPGDAMNIYEDMKQSPDPPEELPFRILLKGLLPHPLLRNKVKQDFEEIFPDQSIYD...

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_006138`
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_006138

Location Chr02:2204038-2204986 (-)

Description Similar to THA8L: Protein THYLAKOID ASSEMBLY 8-like, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g46870`	Binds weakly to specific single strand RNA (ssRNA).	Structure of a PLS-class pentatricopeptide repeat protein provides insights into mechanism of RNA recognition.2013 · DOI: 10.1074/jbc.m113.496828
`At1g62350`	Pentatricopeptide repeat-containing protein At1g62350.	No verified direct reference in this release
`At5g41170`	Pentatricopeptide repeat-containing protein At5g41170, mitochondrial.	No verified direct reference in this release
`At3g16710`	Putative pentatricopeptide repeat-containing protein At3g16710, mitochondrial.	No verified direct reference in this release
`At1g62590`	Pentatricopeptide repeat-containing protein At1g62590.	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_006138 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009555 pollen development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003727 single-stranded RNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:1990825 sequence-specific mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G62350

ath:AT3G16710

ath:AT3G46870

ath:AT5G41170

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.

Mitochondrion0.752

Rank 1 · LXL04_006138 · OH-1004

Plastid0.178

Rank 2 · LXL04_006138 · OH-1004

Nucleus0.047

Rank 3 · LXL04_006138 · OH-1004

Cytoplasm0.033

Rank 4 · LXL04_006138 · OH-1004

Cell membrane0.010

Rank 5 · LXL04_006138 · 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.

PF29070.1MSC6_N133-214 aa

PF13041.13PPR_2153-201 aa

PF01535.27PPR158-185 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006138	`PF29070.1`	MSC6_N	133	214	2.9e-06	27.4
LXL04_006138	`PF13041.13`	PPR_2	153	201	2.5e-17	63.4
LXL04_006138	`PF01535.27`	PPR	158	185	1.1e-10	41.7

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
`Q9STF9`	Arabidopsis thaliana	Protein THYLAKOID ASSEMBLY 8-like, chloroplastic	65.217%	Swiss-Prot	strong database homology
`Q1PFH7`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62350	45.856%	Swiss-Prot	moderate database homology
`Q9FLL3`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g41170, mitochondrial	32.331%	Swiss-Prot	weak database homology
`Q9LUR2`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At3g16710, mitochondrial	28.696%	Swiss-Prot	weak database homology
`Q9SXD8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62590	30.435%	Swiss-Prot	weak database homology

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