LXL04_039136 | RubberDandelionOmics

Gene overview

LXL04_039136

Reference: OH-1004 Chr: Chr09 Coordinates: 60107976-60111174 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2364 bp · LXL04_039136|LXL04_039136|OH1004|cDNA

ATGCTTGTTGGAAGGGATCTAGGGCTTCCAAACCTGGTGGTCCTGGTAGTAATATTCGTGATTTTTCCGGTGATCGGCTTTGTTATCCGCCGAAAGTTGCGACACGCGGCGGCGAGGAACGAGGAGATTAAGAAGCTTTTGATTTTGGCATCGGAAGAGGCAGCCAGGGCTGAGATTGAGGCTACATCGGGATACTTTTTCACGGCCAACACTAGTTCATCGATTCCTCCTCCGGATTCGGCCTGGGCACCGGCTCCAGA...

CDS

Download CDS FASTA

2364 bp · LXL04_039136|LXL04_039136|OH1004|CDS

ATGCTTGTTGGAAGGGATCTAGGGCTTCCAAACCTGGTGGTCCTGGTAGTAATATTCGTGATTTTTCCGGTGATCGGCTTTGTTATCCGCCGAAAGTTGCGACACGCGGCGGCGAGGAACGAGGAGATTAAGAAGCTTTTGATTTTGGCATCGGAAGAGGCAGCCAGGGCTGAGATTGAGGCTACATCGGGATACTTTTTCACGGCCAACACTAGTTCATCGATTCCTCCTCCGGATTCGGCCTGGGCACCGGCTCCAGA...

Protein

Download Protein FASTA

787 aa · LXL04_039136|LXL04_039136|OH1004|PROTEIN

MLVGRDLGLPNLVVLVVIFVIFPVIGFVIRRKLRHAAARNEEIKKLLILASEEAARAEIEATSGYFFTANTSSSIPPPDSAWAPAPESAWVQPTASVPLVSSLKPPYQCAVCFSPTSTRCAKCKAVRYCSGRCQIVHWRQGHKDECRPYVGTKDVATSCLKKEDDKDSNNAEVHEPETDSFIQSAFDTSPSEESCAFSSTSRSSTETSSVSSGESDDFVSVQFQSTKVKPSNEDTTSSDFWSGTIDSKKSTIDETSSNGF...

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_039136`
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_039136

Location Chr09:60107976-60111174 (+)

Description Similar to UBP17: Ubiquitin carboxyl-terminal hydrolase 17

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65450`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`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
`At2g24640`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At4g31670`	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_039136 · 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: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

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G24640

ath:AT4G24560

ath:AT5G65450

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.

Cytoplasm0.446

Rank 1 · LXL04_039136 · OH-1004

Nucleus0.374

Rank 2 · LXL04_039136 · OH-1004

Cell membrane0.124

Rank 3 · LXL04_039136 · OH-1004

Mitochondrion0.107

Rank 4 · LXL04_039136 · OH-1004

Endoplasmic reticulum0.096

Rank 5 · LXL04_039136 · 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-MYND109-146 aa

PF00443.36UCH370-666 aa

PF13423.13UCH_1371-648 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039136	`PF01753.25`	zf-MYND	109	146	1.5e-08	35.2
LXL04_039136	`PF00443.36`	UCH	370	666	3.1e-55	188.2
LXL04_039136	`PF13423.13`	UCH_1	371	648	4.7e-23	83.0

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
`Q9FKP5`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 17	44.934%	Swiss-Prot	moderate database homology
`Q9SB51`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 16	59.481%	Swiss-Prot	weak database homology
`Q9SJA1`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 19	53.550%	Swiss-Prot	weak database homology
`Q67XW5`	Arabidopsis thaliana	Ubiquitin carboxyl-terminal hydrolase 18	53.012%	Swiss-Prot	weak database homology
`Q0E2F9`	Oryza sativa subsp. japonica	Ubiquitin C-terminal hydrolase 15	53.550%	Swiss-Prot	weak database homology

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