LXL04_021241 | RubberDandelionOmics

Gene overview

LXL04_021241

Reference: OH-1004 Chr: Chr04 Coordinates: 125303884-125307387 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1236 bp · LXL04_021241|LXL04_021241|OH1004|cDNA

ATGGCCTGGATTAAAAGGATTAGCTTACAAACACACGGATCGGGTTTCTCATTCACAAAACAGATTGAACAAAGACACGGATCGATGAATCACCTACACACCTCACTGACCTTACCCGAGAGGCGCCATTCCTCCGACACCAGCCTCGATCTTCACCAGCTCCTCTCCACGCTTGCACGCCGATTCCCTTGCACGCCAGACGATTTCCATCTCTATATTTACCCTCCCGATTTCAAATGGAGATGCAATTGGTTTCGATT...

CDS

Download CDS FASTA

1236 bp · LXL04_021241|LXL04_021241|OH1004|CDS

ATGGCCTGGATTAAAAGGATTAGCTTACAAACACACGGATCGGGTTTCTCATTCACAAAACAGATTGAACAAAGACACGGATCGATGAATCACCTACACACCTCACTGACCTTACCCGAGAGGCGCCATTCCTCCGACACCAGCCTCGATCTTCACCAGCTCCTCTCCACGCTTGCACGCCGATTCCCTTGCACGCCAGACGATTTCCATCTCTATATTTACCCTCCCGATTTCAAATGGAGATGCAATTGGTTTCGATT...

Protein

Download Protein FASTA

411 aa · LXL04_021241|LXL04_021241|OH1004|PROTEIN

MAWIKRISLQTHGSGFSFTKQIEQRHGSMNHLHTSLTLPERRHSSDTSLDLHQLLSTLARRFPCTPDDFHLYIYPPDFKWRCNWFRFHPNFTSDTHRLYLPPLHVAAIPKLSLFISTANIRFPSTHQIENDNTSKRILRLSFHFLQGIDSRFQSKGSVGNIGSSSDAAGLPWAILEVFSSKLGYSRKMSRKEVRKNGTYIFRFSILISIMDFAGFIHSNSIQGLNNRLQEVKVCLFLSSQFKSVHSSNHLAFFAVYNVES...

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_021241`
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_021241

Location Chr04:125303884-125307387 (-)

Description Similar to CLPR2: ATP-dependent Clp protease proteolytic subunit-related protein 2, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g12410`	Required for chloroplast development and integrity.	Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis.2006 · DOI: 10.1105/tpc.106.042861
`At4g10180`	Component of light signal transduction machinery.	Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes.2004 · DOI: 10.1101/gad.1229504 DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis.2018 · DOI: 10.7554/elife.37892 DET1 represses a chloroplast blue light-responsive promoter in a developmental and tissue-specific manner in Arabidopsis thaliana.1998 · DOI: 10.1046/j.1365-313x.1998.00078.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021241 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0006281 DNA repair Biological Process

GO:0006515 protein quality control for misfolded or incompletely synthesized proteins Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009368 endopeptidase Clp complex Cellular Component

KEGG gene cross-reference

ath:AT1G12410

ath:AT4G10180

cyp:PCC8801_0943

pma:Pro_1388

sly:778329

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.

Nucleus0.434

Rank 1 · LXL04_021241 · OH-1004

Cytoplasm0.400

Rank 2 · LXL04_021241 · OH-1004

Mitochondrion0.136

Rank 3 · LXL04_021241 · OH-1004

Cell membrane0.086

Rank 4 · LXL04_021241 · OH-1004

Endoplasmic reticulum0.079

Rank 5 · LXL04_021241 · 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.

PF09737.15Det1242-320 aa

PF00574.29CLP_protease332-387 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021241	`PF09737.15`	Det1	242	320	1.2e-17	64.8
LXL04_021241	`PF00574.29`	CLP_protease	332	387	3.8e-12	47.2

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
`Q9XJ36`	Arabidopsis thaliana	ATP-dependent Clp protease proteolytic subunit-related protein 2, chloroplastic	70.270%	Swiss-Prot	weak database homology
`P48732`	Arabidopsis thaliana	Light-mediated development protein DET1	62.338%	Swiss-Prot	weak database homology

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