LXL04_000230 | RubberDandelionOmics

Gene overview

LXL04_000230

Reference: OH-1004 Chr: Chr01 Coordinates: 4334816-4335879 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1053 bp · LXL04_000230|LXL04_000230|OH1004|cDNA

atgagGACACGTGTCGTAACCACATTCATCCTCAGCTCATTGTTCCCGCCCAAATACCTCCCAAATCCGAATTCCATAAATattgttagtgtatcccacatcggtgcgaacacgatctataagtggctatatatgttggagtatcccctctctccacaagggctcttttggagagacaatattggggctccacatatattaacaggGCATCAATCTATGATTGTTTTCGACTTAGGGTTTCATCATCATTCTGTTGGATG...

CDS

Download CDS FASTA

1053 bp · LXL04_000230|LXL04_000230|OH1004|CDS

ATGAGGACACGTGTCGTAACCACATTCATCCTCAGCTCATTGTTCCCGCCCAAATACCTCCCAAATCCGAATTCCATAAATATTGTTAGTGTATCCCACATCGGTGCGAACACGATCTATAAGTGGCTATATATGTTGGAGTATCCCCTCTCTCCACAAGGGCTCTTTTGGAGAGACAATATTGGGGCTCCACATATATTAACAGGGCATCAATCTATGATTGTTTTCGACTTAGGGTTTCATCATCATTCTGTTGGATG...

Protein

Download Protein FASTA

350 aa · LXL04_000230|LXL04_000230|OH1004|PROTEIN

MRTRVVTTFILSSLFPPKYLPNPNSINIVSVSHIGANTIYKWLYMLEYPLSPQGLFWRDNIGAPHILTGHQSMIVFDLGFHHHSVGCVVMPVGRDLGLPSLVVLVVIFVILPVVGFVIRRKLRHAAARNEEIKKLLIFASEEAARAEIEATDGYFFTANTSSSIPPPNSAWAPAPESAWVQPRASVPLVSSLKLPYQRAVCFSPTSTRCAKCKAVRYCSGRCQIVHWRQGHKDECRPYVGTKDVATSCLKKEDDKDSNKA...

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_000230`
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_000230

Location Chr01:4334816-4335879 (+)

Description Similar to UBP16: Ubiquitin carboxyl-terminal hydrolase 16

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g24560`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability.2012 · DOI: 10.1105/tpc.112.106393 UBIQUITIN-SPECIFIC PROTEASE16 interacts with a HEAVY METAL ASSOCIATED ISOPRENYLATED PLANT PROTEIN27 and modulates cadmium tolerance.2013 · DOI: 10.4161/psb.25680
`At5g65450`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At1g17110`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development.2008 · DOI: 10.1111/j.1365-313x.2008.03557.x The ubiquitin receptor DA1 regulates seed and organ size by modulating the stability of the ubiquitin-specific protease UBP15/SOD2 in Arabidopsis.2014 · DOI: 10.1105/tpc.114.122663
`At2g24640`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0244300`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Ubiquitin Specific Protease 15 Has an Important Role in Regulating Grain Width and Size in Rice.2019 · DOI: 10.1104/pp.19.00065

Functional annotation source

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Functional annotation source: OH1004 · LXL04_000230 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006508 proteolysis Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009908 flower development Biological Process

GO:0010154 fruit development Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0048364 root development Biological Process

GO:0048366 leaf development Biological Process

GO:0048367 shoot system development Biological Process

GO:0051301 cell division Biological Process

GO:1901000 regulation of response to salt stress Biological Process

GO:0005576 extracellular region Cellular Component

KEGG gene cross-reference

ath:AT1G17110

ath:AT2G24640

ath:AT4G24560

ath:AT5G65450

dosa:Os02g0244300

osa:4328857

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.322

Rank 1 · LXL04_000230 · OH-1004

Cytoplasm0.311

Rank 2 · LXL04_000230 · OH-1004

Endoplasmic reticulum0.187

Rank 3 · LXL04_000230 · OH-1004

Cell membrane0.155

Rank 4 · LXL04_000230 · OH-1004

Mitochondrion0.155

Rank 5 · LXL04_000230 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF01753.25zf-MYND200-235 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000230	`PF01753.25`	zf-MYND	200	235	1.5e-08	35.3

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
`Q9SB51`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 16	42.177%	Swiss-Prot	weak database homology
`Q9FKP5`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 17	35.714%	Swiss-Prot	weak database homology
`Q9FPS9`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 15	69.231%	Swiss-Prot	weak database homology
`Q9SJA1`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 19	44.186%	Swiss-Prot	weak database homology
`Q0E2F9`	Oryza sativa subsp. japonica	Ubiquitin C-terminal hydrolase 15	33.333%	Swiss-Prot	weak database homology

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