LXL04_025491 | RubberDandelionOmics

Gene overview

LXL04_025491

Reference: OH-1004 Chr: Chr05 Coordinates: 112496853-112503533 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3840 bp · LXL04_025491|LXL04_025491|OH1004|cDNA

ATGGGCGGCCGTAACGATCCTAACGAGAATCCTACTGCAAACTCAAAATCATCGACGCTTCCCCCAAATCGTGATATTGAATCTGATACGACCGTTGATATCCCTTCTCATAACACCAAGGATATGAAAGCCAAGGAAAAAGAACTCCAGGATAAAGAAGCCGAATtaaaaaagaaggaagagGATCTACGGAAGAGAGAAGCGGCAATTGCACGATCTGGAGTTGTTATTGATGATAACAATTGGCCACCCTTTTACCC...

CDS

Download CDS FASTA

3840 bp · LXL04_025491|LXL04_025491|OH1004|CDS

ATGGGCGGCCGTAACGATCCTAACGAGAATCCTACTGCAAACTCAAAATCATCGACGCTTCCCCCAAATCGTGATATTGAATCTGATACGACCGTTGATATCCCTTCTCATAACACCAAGGATATGAAAGCCAAGGAAAAAGAACTCCAGGATAAAGAAGCCGAATTAAAAAAGAAGGAAGAGGATCTACGGAAGAGAGAAGCGGCAATTGCACGATCTGGAGTTGTTATTGATGATAACAATTGGCCACCCTTTTACCC...

Protein

Download Protein FASTA

1279 aa · LXL04_025491|LXL04_025491|OH1004|PROTEIN

MGGRNDPNENPTANSKSSTLPPNRDIESDTTVDIPSHNTKDMKAKEKELQDKEAELKKKEEDLRKREAAIARSGVVIDDNNWPPFYPIIHHDIKSEIPIHLQKVQYVAFGSWLGIMLCLVWNLVAVSVAWYEGEGVTIWLCAVIYVILGIPMSYYLWYRPLYRAMRADSAVKFTFFLITYSFHISFCAFASLAPPIFIEGKSIAGILPAFDLLVGNAALGGLYLVGFGLFFIETAISIWVIQQVYSYFRGSGKAAEMKRE...

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_025491`
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_025491

Location Chr05:112496853-112503533 (+)

Description Similar to At1g73710: Pentatricopeptide repeat-containing protein At1g73710

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g73710`	Pentatricopeptide repeat-containing protein At1g73710.	No verified direct reference in this release
`At3g23020`	Pentatricopeptide repeat-containing protein At3g23020.	No verified direct reference in this release
`At1g61250`	Probably involved in membrane trafficking.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2YMP7`	Probably involved in membrane trafficking.	No verified direct reference in this release
`Os07g0564600`	Probably involved in membrane trafficking.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025491 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0010343 singlet oxygen-mediated programmed cell death Biological Process

GO:0015031 protein transport Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005769 early endosome Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0030658 transport vesicle membrane Cellular Component

GO:0032588 trans-Golgi network membrane Cellular Component

GO:0055038 recycling endosome membrane Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G73710

ath:AT3G23020

dosa:Os07g0564600

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.

Plastid0.784

Rank 1 · LXL04_025491 · OH-1004

Mitochondrion0.123

Rank 2 · LXL04_025491 · OH-1004

Nucleus0.056

Rank 3 · LXL04_025491 · OH-1004

Cytoplasm0.035

Rank 4 · LXL04_025491 · OH-1004

Cell membrane0.029

Rank 5 · LXL04_025491 · 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.

PF04144.19SCAMP80-250 aa

PF17177.11PPR_long424-540 aa

PF13812.13PPR_3444-494 aa

PF13041.13PPR_2445-492 aa

PF13041.13PPR_2484-527 aa

PF01535.27PPR484-513 aa

PF13041.13PPR_2605-648 aa

PF29070.1MSC6_N605-698 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025491	`PF04144.19`	SCAMP	80	250	1.5e-50	172.5
LXL04_025491	`PF17177.11`	PPR_long	424	540	1.2e-37	130.1
LXL04_025491	`PF13812.13`	PPR_3	444	494	4.6e-54	181.1
LXL04_025491	`PF13041.13`	PPR_2	445	492	9.9e-108	352.9
LXL04_025491	`PF13041.13`	PPR_2	484	527	9.9e-108	352.9
LXL04_025491	`PF01535.27`	PPR	484	513	3.1e-87	281.6
LXL04_025491	`PF13041.13`	PPR_2	605	648	9.9e-108	352.9
LXL04_025491	`PF29070.1`	MSC6_N	605	698	9.3e-38	131.0
LXL04_025491	`PF17177.11`	PPR_long	605	787	1.2e-37	130.1
LXL04_025491	`PF01535.27`	PPR	607	636	3.1e-87	281.6
LXL04_025491	`PF12854.14`	PPR_1	607	631	3.4e-67	222.6
LXL04_025491	`PF13812.13`	PPR_3	607	651	4.6e-54	181.1
LXL04_025491	`PF23276.3`	TPR_24	607	699	6.6e-40	136.8
LXL04_025491	`PF12854.14`	PPR_1	635	667	3.4e-67	222.6
LXL04_025491	`PF13041.13`	PPR_2	639	683	9.9e-108	352.9
LXL04_025491	`PF01535.27`	PPR	641	671	3.1e-87	281.6

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
`Q9C9U0`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g73710	56.811%	Swiss-Prot	strong database homology
`Q9LS88`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g23020	37.143%	Swiss-Prot	moderate database homology
`Q9M5P2`	Arabidopsis thaliana	Secretory carrier-associated membrane protein 3	54.965%	Swiss-Prot	weak database homology
`A2YMP7`	Oryza sativa subsp. indica	Putative secretory carrier-associated membrane protein 1	60.385%	Swiss-Prot	weak database homology
`Q8H5X5`	Oryza sativa subsp. japonica	Secretory carrier-associated membrane protein 1	60.385%	Swiss-Prot	weak database homology

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