LXL04_000872 | RubberDandelionOmics

Gene overview

LXL04_000872

Reference: OH-1004 Chr: Chr01 Coordinates: 15985858-15988294 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1437 bp · LXL04_000872|LXL04_000872|OH1004|cDNA

ATGTTGCTATGCTTTCTTGAAAAGAAAGATAACGAGAAAAGCTTCAAAACCCTGTCTCAGATCCCTCATTTTCTTCATCCATACACAAGCAAATCAATCATGGGTCAGGGAACTCCCGGAGGTATGAACCGGCAAGGTATGCCCGGCGATCGGAAGAACGATGgcgagaagaaggagaagaaatttGAGCCAGCAGCACCACCTGCTCGTGTTGGACGAAAACAGCGGAAGCAGAAGGGACCAGAGGCAGCTGCTAGGTT...

CDS

Download CDS FASTA

1437 bp · LXL04_000872|LXL04_000872|OH1004|CDS

ATGTTGCTATGCTTTCTTGAAAAGAAAGATAACGAGAAAAGCTTCAAAACCCTGTCTCAGATCCCTCATTTTCTTCATCCATACACAAGCAAATCAATCATGGGTCAGGGAACTCCCGGAGGTATGAACCGGCAAGGTATGCCCGGCGATCGGAAGAACGATGGCGAGAAGAAGGAGAAGAAATTTGAGCCAGCAGCACCACCTGCTCGTGTTGGACGAAAACAGCGGAAGCAGAAGGGACCAGAGGCAGCTGCTAGGTT...

Protein

Download Protein FASTA

478 aa · LXL04_000872|LXL04_000872|OH1004|PROTEIN

MLLCFLEKKDNEKSFKTLSQIPHFLHPYTSKSIMGQGTPGGMNRQGMPGDRKNDGEKKEKKFEPAAPPARVGRKQRKQKGPEAAARLPTVTPHSKCRLRLLKLERIKDYLLMEEEFVANQERLKPQEEKTEEDRSKVDDLRGSPMSVGNLEELIDENHAIVSSSVGPEYYVGILSFVDKDQLEPGCAILMHNKVLSVVGLLQDDVDPMVSVMKVEKAPLESYADIGGLDAQIQEIKEAVELPLTHPELYEDIGIKPPKGV...

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_000872`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_000872

Location Chr01:15985858-15988294 (+)

Description Similar to RPT2A: 26S proteasome regulatory subunit 4 homolog A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g29040`	The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins.	The HALTED ROOT gene encoding the 26S proteasome subunit RPT2a is essential for the maintenance of Arabidopsis meristems.2004 · DOI: 10.1242/dev.01096 26S proteasome regulatory particle mutants have increased oxidative stress tolerance.2008 · DOI: 10.1111/j.1365-313x.2007.03322.x Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs.2009 · DOI: 10.1104/pp.109.135970 Regulation of leaf organ size by the Arabidopsis RPT2a 19S proteasome subunit.2009 · DOI: 10.1111/j.1365-313x.2009.03932.x Control of endoreduplication of trichome by RPT2a, a subunit of the 19S proteasome in Arabidopsis.2010 · DOI: 10.1007/s10265-010-0321-x Arabidopsis thaliana 26S proteasome subunits RPT2a and RPT5a are crucial for zinc deficiency-tolerance.2011 · DOI: 10.1271/bbb.100794 Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b.2011 · DOI: 10.1093/pcp/pcr093 RPT2a, a 26S proteasome AAA-ATPase, is directly involved in Arabidopsis CC-NBS-LRR protein uni-1D-induced signaling pathways.2011 · DOI: 10.1093/pcp/pcr099 The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis.2011 · DOI: 10.1105/tpc.111.089482 RPN1a, a 26S proteasome subunit, is required for innate immunity in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05048.x Arabidopsis RPT2a, 19S proteasome subunit, regulates gene silencing via DNA methylation.2012 · DOI: 10.1371/journal.pone.0037086 Proteomic analysis of the 26S proteasome reveals its direct interaction with transit peptides of plastid protein precursors for their degradation.2014 · DOI: 10.1021/pr401245g
`At2g20140`	The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins.	Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b.2011 · DOI: 10.1093/pcp/pcr093 The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis.2011 · DOI: 10.1105/tpc.111.089482

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0691800`	The 26S proteasome is involved in the ATP-dependent degradation of ubiquitinated proteins.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000872 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007292 female gamete generation Biological Process

GO:0009408 response to heat Biological Process

GO:0009933 meristem structural organization Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010311 lateral root formation Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0035266 meristem growth Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

KEGG gene cross-reference

ath:AT2G20140

ath:AT4G29040

dme:Dmel_CG5289

dosa:Os07g0691800

rno:117263

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.

Nucleus0.531

Rank 1 · LXL04_000872 · OH-1004

Cytoplasm0.488

Rank 2 · LXL04_000872 · OH-1004

Cell membrane0.064

Rank 3 · LXL04_000872 · OH-1004

Mitochondrion0.054

Rank 4 · LXL04_000872 · OH-1004

Endoplasmic reticulum0.053

Rank 5 · LXL04_000872 · 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.

PF16450.12Prot_ATP_ID_OB_C147-201 aa

PF00004.36AAA260-393 aa

PF17862.8AAA_lid_3415-459 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000872	`PF16450.12`	Prot_ATP_ID_OB_C	147	201	2.3e-10	40.9
LXL04_000872	`PF00004.36`	AAA	260	393	3.1e-41	141.6
LXL04_000872	`PF17862.8`	AAA_lid_3	415	459	1.1e-11	44.8

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
`Q9SZD4`	Arabidopsis thaliana	26S proteasome regulatory subunit 4 homolog A	95.067%	Swiss-Prot	strong database homology
`Q9SL67`	Arabidopsis thaliana	26S proteasome regulatory subunit 4 homolog B	94.619%	Swiss-Prot	strong database homology
`P46466`	Oryza sativa subsp. japonica	26S proteasome regulatory subunit 4 homolog	92.188%	Swiss-Prot	strong database homology

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