LXL04_030958 | RubberDandelionOmics

Gene overview

LXL04_030958

Reference: OH-1004 Chr: Chr06 Coordinates: 125653252-125658674 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2637 bp · LXL04_030958|LXL04_030958|OH1004|cDNA

ATGTCCGCCAAGGCCAGAACCCTCACCAAGCTGGTAAGTTCCGCCACCACGTACTCCGTTCGCACGGCCAATAACCTCGCCCGTTCCGCCGTCACTATCACCTCGCCTCTCAGCTCCGCCGCAGCACAGGACGTAACCTTGAAGAACTATATACAACTTACCAACGCCGCAAAATATTCTTCTTCATCATCACGTCTTAAACCCCCAAAATCAAAAaaatcttcatcttcctcaaAATCAAAGAGATCTTCATTTTCCAA...

CDS

Download CDS FASTA

2637 bp · LXL04_030958|LXL04_030958|OH1004|CDS

ATGTCCGCCAAGGCCAGAACCCTCACCAAGCTGGTAAGTTCCGCCACCACGTACTCCGTTCGCACGGCCAATAACCTCGCCCGTTCCGCCGTCACTATCACCTCGCCTCTCAGCTCCGCCGCAGCACAGGACGTAACCTTGAAGAACTATATACAACTTACCAACGCCGCAAAATATTCTTCTTCATCATCACGTCTTAAACCCCCAAAATCAAAAAAATCTTCATCTTCCTCAAAATCAAAGAGATCTTCATTTTCCAA...

Protein

Download Protein FASTA

878 aa · LXL04_030958|LXL04_030958|OH1004|PROTEIN

MSAKARTLTKLVSSATTYSVRTANNLARSAVTITSPLSSAAAQDVTLKNYIQLTNAAKYSSSSSRLKPPKSKKSSSSSKSKRSSFSKPLSELAIESIRINTSASLSDTKRALSRELSSILCDAEETETETETDDVEEPLVTLLEIPWLPPVSNTTTSQRRRELFRVKKAKWVFKSTQGNRFSKLTRMCTHNLGAKVAIEVFGKLGRETGPKEYNAMIDICIEKARNTDDEDVALEEFHRAYRVFECMREFGFEIKEQTYG...

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_030958`
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_030958

Location Chr06:125653252-125658674 (+)

Description Similar to At4g04790: Pentatricopeptide repeat-containing protein At4g04790, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g04790`	Pentatricopeptide repeat-containing protein At4g04790, mitochondrial.	No verified direct reference in this release
`At4g21880`	Pentatricopeptide repeat-containing protein At4g21880, mitochondrial.	No verified direct reference in this release
`At5g65560`	Pentatricopeptide repeat-containing protein At5g65560.	No verified direct reference in this release
`At2g31400`	Involved in nuclear gene expression via the retrograde plastid-to-nucleus signaling.	Signals from chloroplasts converge to regulate nuclear gene expression.2007 · PMID: 17395793 Plastid signals that affect photomorphogenesis in Arabidopsis thaliana are dependent on GENOMES UNCOUPLED 1 and cryptochrome 1.2009 · DOI: 10.1111/j.1469-8137.2008.02729.x The Arabidopsis plastid-signalling mutant gun1 (genomes uncoupled1) shows altered sensitivity to sucrose and abscisic acid and alterations in early seedling development.2010 · DOI: 10.1093/jxb/erq186 Timing the switch to phototrophic growth: a possible role of GUN1.2011 · DOI: 10.4161/psb.6.4.14900
`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_030958 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0004016 adenylate cyclase activity Molecular Function

KEGG gene cross-reference

ath:AT1G62590

ath:AT4G04790

ath:AT4G21880

ath:AT5G65560

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.

Mitochondrion0.739

Rank 1 · LXL04_030958 · OH-1004

Plastid0.183

Rank 2 · LXL04_030958 · OH-1004

Nucleus0.074

Rank 3 · LXL04_030958 · OH-1004

Cytoplasm0.051

Rank 4 · LXL04_030958 · OH-1004

Cell membrane0.015

Rank 5 · LXL04_030958 · 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.

PF17177.11PPR_long432-569 aa

PF13812.13PPR_3451-512 aa

PF13812.13PPR_3490-544 aa

PF13812.13PPR_3522-579 aa

PF13041.13PPR_2532-579 aa

PF29070.1MSC6_N535-624 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030958	`PF17177.11`	PPR_long	432	569	2.4e-17	63.7
LXL04_030958	`PF13812.13`	PPR_3	451	512	7.1e-19	68.4
LXL04_030958	`PF13812.13`	PPR_3	490	544	7.1e-19	68.4
LXL04_030958	`PF13812.13`	PPR_3	522	579	7.1e-19	68.4
LXL04_030958	`PF13041.13`	PPR_2	532	579	3.5e-27	95.0
LXL04_030958	`PF29070.1`	MSC6_N	535	624	8.9e-09	35.6

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
`Q6NQ81`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g04790, mitochondrial	44.804%	Swiss-Prot	moderate database homology
`O49711`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g21880, mitochondrial	43.343%	Swiss-Prot	moderate database homology
`Q9LSL9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g65560	24.586%	Swiss-Prot	weak database homology
`Q9SIC9`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein GUN1, chloroplastic	23.108%	Swiss-Prot	weak database homology
`Q9SXD8`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62590	24.468%	Swiss-Prot	weak database homology

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