LXL04_018095 | RubberDandelionOmics

Gene overview

LXL04_018095

Reference: OH-1004 Chr: Chr04 Coordinates: 6584774-6594383 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5001 bp · LXL04_018095|LXL04_018095|OH1004|cDNA

ATGGCTCCGAAAGCTAGTAAAGGAAAACCGCACAAAGCgaagggggagaagaagaagaaggaagagaaaGCATTGCCGACAGTGGTAGAAATAGCAATAGAAACGTCTGATGACTCCACAGTGACACTTAAGGGCATATCTACTGATAGAATATTAGATGTTCGAAAGCTACTCGCAGTACATGTTGAGACATGTCATGTGACCAACTACTCCTTAACACATGAGGTACGAGGTCCAAGGCTTAAAGATACGGTCGAAGT...

CDS

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5001 bp · LXL04_018095|LXL04_018095|OH1004|CDS

ATGGCTCCGAAAGCTAGTAAAGGAAAACCGCACAAAGCGAAGGGGGAGAAGAAGAAGAAGGAAGAGAAAGCATTGCCGACAGTGGTAGAAATAGCAATAGAAACGTCTGATGACTCCACAGTGACACTTAAGGGCATATCTACTGATAGAATATTAGATGTTCGAAAGCTACTCGCAGTACATGTTGAGACATGTCATGTGACCAACTACTCCTTAACACATGAGGTACGAGGTCCAAGGCTTAAAGATACGGTCGAAGT...

Protein

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1666 aa · LXL04_018095|LXL04_018095|OH1004|PROTEIN

MAPKASKGKPHKAKGEKKKKEEKALPTVVEIAIETSDDSTVTLKGISTDRILDVRKLLAVHVETCHVTNYSLTHEVRGPRLKDTVEVVALKPCQLTVVEEDYTEESAVAHIRRLLDIVACTTAFGGSSNSPKNTSTAAPTRSKESGSSDGEIGQDKKSNVETKSPKTDGEISSDLSEKGDAAAEIYPPPKLGQFYDFFSFSHLTPPIQYIRRSARPFLEDKTDDDFFQIDVRVSGGKPMTIVASRKGFYPAGKRILSSHS...

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_018095`
TK1151 ID	TkA08G026970
OH-1004 ID	LXL04_018095
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_018095

Location Chr04:6584774-6594383 (-)

Description Similar to TSS: Protein TSS

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g28080`	Negatively regulates meristematic tissue proliferation by integrating developmental signals with carbon source availability.	No verified direct reference in this release
`At1g01320`	May act as the scaffold of a protein complex, which sequesters key factors that are required for the G2 to M transition in meristematic tissues (By similarity).	REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.2016 · DOI: 10.1073/pnas.1515741113
`At1g15290`	May act as the scaffold of a protein complex, which sequesters key factors that are required for the G2 to M transition in meristematic tissues (By similarity).	No verified direct reference in this release
`At3g52140`	mRNA-binding protein involved in proper cytoplasmic distribution of mitochondria (By similarity).	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_018095 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007005 mitochondrion organization Biological Process

GO:0010636 positive regulation of mitochondrial fusion Biological Process

GO:0010906 regulation of glucose metabolic process Biological Process

GO:0019750 chloroplast localization Biological Process

GO:0048312 intracellular distribution of mitochondria Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G01320

ath:AT1G15290

ath:AT3G52140

ath:AT4G28080

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.

Cytoplasm0.431

Rank 1 · LXL04_018095 · OH-1004

Nucleus0.226

Rank 2 · LXL04_018095 · OH-1004

Cell membrane0.203

Rank 3 · LXL04_018095 · OH-1004

Golgi apparatus0.151

Rank 4 · LXL04_018095 · OH-1004

Endoplasmic reticulum0.127

Rank 5 · LXL04_018095 · 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.

PF15044.12CLU_N48-118 aa

PF12807.13eIF3_p135691-774 aa

PF13424.13TPR_12868-929 aa

PF24885.2TPR_NPHP3868-967 aa

PF13374.13TPR_10897-938 aa

PF13424.13TPR_12897-967 aa

PF24885.2TPR_NPHP3957-1056 aa

PF13374.13TPR_10981-1021 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018095	`PF15044.12`	CLU_N	48	118	7.4e-10	39.8
LXL04_018095	`PF12807.13`	eIF3_p135	691	774	1.4e-20	74.8
LXL04_018095	`PF13424.13`	TPR_12	868	929	2.9e-26	92.2
LXL04_018095	`PF24885.2`	TPR_NPHP3	868	967	2.8e-12	47.3
LXL04_018095	`PF13374.13`	TPR_10	897	938	1.2e-26	92.6
LXL04_018095	`PF13424.13`	TPR_12	897	967	2.9e-26	92.2
LXL04_018095	`PF24885.2`	TPR_NPHP3	957	1056	2.8e-12	47.3
LXL04_018095	`PF13374.13`	TPR_10	981	1021	1.2e-26	92.6
LXL04_018095	`PF13424.13`	TPR_12	981	1055	2.9e-26	92.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4JKH6`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 2	68.852%	Swiss-Prot	strong database homology
`F4HS99`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 1	50.190%	Swiss-Prot	strong database homology
`F4HZK4`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 3	47.607%	Swiss-Prot	moderate database homology
`F4J5S1`	Arabidopsis thaliana	Clustered mitochondria protein	37.657%	Swiss-Prot	weak database homology

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