LXL04_028775 | RubberDandelionOmics

Gene overview

LXL04_028775

Reference: OH-1004 Chr: Chr06 Coordinates: 62480349-62483867 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1167 bp · LXL04_028775|LXL04_028775|OH1004|cDNA

ATGGCCTGGATTAAAAGGATTAGCTTACAAACACACGGATCGGGTTTCTCATTCACAAAACAGATTGAACAAAGACACGGATCGATGAATCACCTACACACCTCACTGACCTTACCCGAGAGGCGCCATTCCTCCGACACCAGCCTCGATCTTCACCAGCCTCGATCTTCACCAGCTCCTCTCCACGCTTGCACGCCGATTCCCTTGCACGCCAGACGATTTCCATCTCTATATTTACCCTCCCGATTTCAAATGGAGAT...

CDS

Download CDS FASTA

1167 bp · LXL04_028775|LXL04_028775|OH1004|CDS

ATGGCCTGGATTAAAAGGATTAGCTTACAAACACACGGATCGGGTTTCTCATTCACAAAACAGATTGAACAAAGACACGGATCGATGAATCACCTACACACCTCACTGACCTTACCCGAGAGGCGCCATTCCTCCGACACCAGCCTCGATCTTCACCAGCCTCGATCTTCACCAGCTCCTCTCCACGCTTGCACGCCGATTCCCTTGCACGCCAGACGATTTCCATCTCTATATTTACCCTCCCGATTTCAAATGGAGAT...

Protein

Download Protein FASTA

388 aa · LXL04_028775|LXL04_028775|OH1004|PROTEIN

MAWIKRISLQTHGSGFSFTKQIEQRHGSMNHLHTSLTLPERRHSSDTSLDLHQPRSSPAPLHACTPIPLHARRFPSLYLPSRFQMEMQLVSIPSQFYLRHTQHQIENDNTSKRILRLSFHFLQGIDSRFQSKGSVGNIGSSSDAAGLPWAILEVFSSKLGYSRKMSRKEVRKNGTYIFRFSILISILDFAGFIHSNSIQGLNNRLQEVKVCLFLSSQFKSVHSSNHLAFFAVYNVESTEIIAFYQMSSEKLYILFEQFCD...

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_028775`
TK1151 ID	TkA04G369180
OH-1004 ID	LXL04_028775
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	76.500
Protein coverage (%)	TK1151 93.725 / OH-1004 70.103 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_028775

Location Chr06:62480349-62483867 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_028775 · 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.

Nucleus0.458

Rank 1 · LXL04_028775 · OH-1004

Cytoplasm0.410

Rank 2 · LXL04_028775 · OH-1004

Mitochondrion0.118

Rank 3 · LXL04_028775 · OH-1004

Cell membrane0.087

Rank 4 · LXL04_028775 · OH-1004

Endoplasmic reticulum0.076

Rank 5 · LXL04_028775 · 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.

PF09737.15Det1219-297 aa

PF00574.29CLP_protease309-364 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028775	`PF09737.15`	Det1	219	297	1.8e-17	64.2
LXL04_028775	`PF00574.29`	CLP_protease	309	364	5e-11	43.5

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
`Q9XJ36`	Arabidopsis thaliana	ATP-dependent Clp protease proteolytic subunit-related protein 2, chloroplastic	68.919%	Swiss-Prot	weak database homology
`P48732`	Arabidopsis thaliana	Light-mediated development protein DET1	62.338%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card