LXL04_010977 | RubberDandelionOmics

Gene overview

LXL04_010977

Reference: OH-1004 Chr: Chr02 Coordinates: 156030672-156037943 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3631 bp · LXL04_010977|LXL04_010977|OH1004|cDNA

CCAATCCCTCGGAGGACCCTACCGAAGTTCCGTCGGGGGGTGCCCGGTGAATAAAACCAACCATACCTTCTCATATCCCTTTCTGAGTGGAATTCGGCTCCAGTTCGTCATGGCAGAAATAGCAGCGCCATATCCTCAACTGAGCTTCCTTCGTTTTGATAAAAGTGCAATTACGCCTCCTAATTATGCCCAAAGACTACATTTTTCATCTAGGTTTCTGACAAGTGTTCCTGATGTCACCGGAAAACGGAGAAGAATCA...

CDS

Download CDS FASTA

3549 bp · LXL04_010977|LXL04_010977|OH1004|CDS

CTGAGTGGAATTCGGCTCCAGTTCGTCATGGCAGAAATAGCAGCGCCATATCCTCAACTGAGCTTCCTTCGTTTTGATAAAAGTGCAATTACGCCTCCTAATTATGCCCAAAGACTACATTTTTCATCTAGGTTTCTGACAAGTGTTCCTGATGTCACCGGAAAACGGAGAAGAATCATAAAAATTGCTGTGGTGAGAGCAAAGTCAGGTACGGTGATTGAGAAAGAACAGGAATTCAAGCCTTCATTTGAAGAGTATTT...

Protein

Download Protein FASTA

1182 aa · LXL04_010977|LXL04_010977|OH1004|PROTEIN

MSGIRLQFVMAEIAAPYPQLSFLRFDKSAITPPNYAQRLHFSSRFLTSVPDVTGKRRRIIKIAVVRAKSGTVIEKEQEFKPSFEEYLKAMETVKSRREKRKVSTETPPSPSRSPSRKIDEGSFELKDSQDQITSRKVGNLEQGEVKKTWHRKKSDPKEPQLAANVKDINISPTIDEKHSKLQGQSFNTKRGSHINSVSSHDYARDTAVHDQSRVLLNSKQNEAMKKWTRKKLDSKESQVDTTTSFEKNEERYAKFQRQSF...

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_010977`
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_010977

Location Chr02:156030672-156037943 (+)

Description Similar to EMB2279: Pentatricopeptide repeat-containing protein At1g30610, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g30610`	May play a role in embryogenesis.	No verified direct reference in this release
`At5g67570`	Involved in the regulation of early chloroplast development and chloroplast gene expression in a SIGF-dependent manner.	No verified direct reference in this release
`At1g28590`	GDSL esterase/lipase At1g28590.	No verified direct reference in this release
`At1g28580`	GDSL esterase/lipase At1g28580.	No verified direct reference in this release
`At1g28570`	GDSL esterase/lipase At1g28570.	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_010977 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005976 polysaccharide metabolic process Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0016042 lipid catabolic process Biological Process

GO:0042793 plastid transcription Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005576 extracellular region Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0016788 hydrolase activity, acting on ester bonds Molecular Function

KEGG gene cross-reference

ath:AT1G28570

ath:AT1G28580

ath:AT1G28590

ath:AT1G30610

ath:AT5G67570

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.

Plastid0.938

Rank 1 · LXL04_010977 · OH-1004

Mitochondrion0.038

Rank 2 · LXL04_010977 · OH-1004

Cytoplasm0.037

Rank 3 · LXL04_010977 · OH-1004

Nucleus0.035

Rank 4 · LXL04_010977 · OH-1004

Cell membrane0.035

Rank 5 · LXL04_010977 · 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_3471-520 aa

PF13041.13PPR_2473-517 aa

PF01535.27PPR477-505 aa

PF13812.13PPR_3613-658 aa

PF12854.14PPR_1644-673 aa

PF13041.13PPR_2646-678 aa

PF01535.27PPR649-678 aa

PF00657.29Lipase_GDSL844-1151 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010977	`PF13812.13`	PPR_3	471	520	3.1e-21	75.9
LXL04_010977	`PF13041.13`	PPR_2	473	517	9.3e-38	128.8
LXL04_010977	`PF01535.27`	PPR	477	505	2.6e-32	109.5
LXL04_010977	`PF13812.13`	PPR_3	613	658	3.1e-21	75.9
LXL04_010977	`PF12854.14`	PPR_1	644	673	1.8e-17	63.5
LXL04_010977	`PF13041.13`	PPR_2	646	678	9.3e-38	128.8
LXL04_010977	`PF01535.27`	PPR	649	678	2.6e-32	109.5
LXL04_010977	`PF00657.29`	Lipase_GDSL	844	1151	4.1e-24	86.6

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
`Q9SA76`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g30610, chloroplastic	55.556%	Swiss-Prot	weak database homology
`Q9FJW6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g67570, chloroplastic	38.986%	Swiss-Prot	weak database homology
`Q8RXT9`	Arabidopsis thaliana	GDSL esterase/lipase At1g28590	49.570%	Swiss-Prot	weak database homology
`Q9FXJ2`	Arabidopsis thaliana	GDSL esterase/lipase At1g28580	48.138%	Swiss-Prot	weak database homology
`Q9FXJ1`	Arabidopsis thaliana	GDSL esterase/lipase At1g28570	48.433%	Swiss-Prot	weak database homology

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