LXL04_004720 | RubberDandelionOmics

Gene overview

LXL04_004720

Reference: OH-1004 Chr: Chr01 Coordinates: 144694387-144696667 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1476 bp · LXL04_004720|LXL04_004720|OH1004|cDNA

ATGACTCGTGTGTTTGTTCAGAGAGGTTCATCTGCCGCTGGGTCTTCTTCATCGTCTAATAATGCAAACAGGTCGAGTTCTTCGTCTTCATCGAGTCAACCTCTGGCTCAGGTTACAGGGGACGACGTTCAAGAACAAGTTATTTCCGAAGATCTTCCTGTAGAAACTACTGAAATTGATCGAATCGATGCTCTCGACGTACCCACCACTGATAAAATCGAAGACGAAACTGTCTCAGAAGATCTTTTAAAAAGAATCAG...

CDS

Download CDS FASTA

1476 bp · LXL04_004720|LXL04_004720|OH1004|CDS

ATGACTCGTGTGTTTGTTCAGAGAGGTTCATCTGCCGCTGGGTCTTCTTCATCGTCTAATAATGCAAACAGGTCGAGTTCTTCGTCTTCATCGAGTCAACCTCTGGCTCAGGTTACAGGGGACGACGTTCAAGAACAAGTTATTTCCGAAGATCTTCCTGTAGAAACTACTGAAATTGATCGAATCGATGCTCTCGACGTACCCACCACTGATAAAATCGAAGACGAAACTGTCTCAGAAGATCTTTTAAAAAGAATCAG...

Protein

Download Protein FASTA

491 aa · LXL04_004720|LXL04_004720|OH1004|PROTEIN

MTRVFVQRGSSAAGSSSSSNNANRSSSSSSSSQPLAQVTGDDVQEQVISEDLPVETTEIDRIDALDVPTTDKIEDETVSEDLLKRISGLRVNEEEEEKDVKKSDDYPSQTTSVSPHPPPPPAPPTPPPKPSTTSNSRRFTPGNSASLRIGSSRRATAWPVVSTGSPRSHPENDGYNSADEQNPCYGSSYNDAERERQFEIDIRRTKGYEVKRMSEDGNCLFRAVADQVYGDSEAYDLARQMCIDYMERERDHFSQFITEG...

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_004720`
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_004720

Location Chr01:144694387-144696667 (+)

Description Similar to OTU6: OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 6

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g27350`	Hydrolase that can remove conjugated ubiquitin from proteins in vitro and may therefore play an important regulatory role at the level of protein turnover by preventing degradation.	Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression.2011 · DOI: 10.1073/pnas.1014030108 Distinct phylogenetic relationships and biochemical properties of Arabidopsis ovarian tumor-related deubiquitinases support their functional differentiation.2014 · DOI: 10.3389/fpls.2014.00084 The histone deubiquitinase OTLD1 targets euchromatin to regulate plant growth.2016 · DOI: 10.1126/scisignal.aaf6767 Activation of gene expression by histone deubiquitinase OTLD1.2017 · DOI: 10.1080/15592294.2017.1348446

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004720 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001817 regulation of cytokine production Biological Process

GO:0006508 proteolysis Biological Process

GO:0009966 regulation of signal transduction Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0030154 cell differentiation Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0032496 response to lipopolysaccharide Biological Process

GO:0032700 negative regulation of interleukin-17 production Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

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

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

KEGG gene cross-reference

ath:AT2G27350

dre:555459

mmu:54644

rno:363452

xtr:448134

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.

Cytoplasm0.570

Rank 1 · LXL04_004720 · OH-1004

Nucleus0.414

Rank 2 · LXL04_004720 · OH-1004

Cell membrane0.132

Rank 3 · LXL04_004720 · OH-1004

Golgi apparatus0.063

Rank 4 · LXL04_004720 · OH-1004

Endoplasmic reticulum0.056

Rank 5 · LXL04_004720 · 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.

PF02338.26OTU216-325 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004720	`PF02338.26`	OTU	216	325	1.1e-18	68.7

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
`Q9XIP2`	Arabidopsis thaliana	OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 6	71.164%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card