TkA01G118410 | RubberDandelionOmics

Gene overview

TkA01G118410

Reference: TK1151 Chr: Chr01 Coordinates: 30023787-30027216 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2532 bp · TkA01G118410|TK1151|cDNA

CTCTATGCCGTACCCAAATACTCCATCCAAGCTTCATTACCATTAAATTCATATAAATTTCAAAATACAATGACATTTGTATCAAGTATTATGTCTTTGTCGTATATTTGTACGAAGAGATCTTAGAGCAAAGATCCAGTTCTAAGGCTATGTCCGAGAGTCTCACAGCTCTCCTCCGTCAACCCTGACAACCACGTGCTTCATAAAATTCCGCCACCTGGCCGCTAAATCGCAGCCTCCCATTTTCATCTCTACATGTA...

CDS

Download CDS FASTA

1476 bp · TkA01G118410|TK1151|CDS

ATGACTCGTGTGTTTGTTCAGAGAGGTTCTTCTGCCGCTGGGTCTTCTTCATCGTCTAATAATGTAAACAGGTCGAGTTCTTCGTCTTCATCGAGTCAACCTCAGGCTCAGGTTACAGGGGATGACGTTCAAGAACAAGTTATTTCCGAAGATCTTCCTGTAGAAACTACTGAAATTGATCGAATCGATGCTCTCGACGTACCCACCACTGATAAAATCGAAGACGAAACTGTCTCAGAAGATCTTCTAAAAAGAATCAG...

Protein

Download Protein FASTA

491 aa · TkA01G118410|TK1151|PROTEIN

MTRVFVQRGSSAAGSSSSSNNVNRSSSSSSSSQPQAQVTGDDVQEQVISEDLPVETTEIDRIDALDVPTTDKIEDETVSEDLLKRISGLRVNEEEEEKDVKKSDDYPSQTTSVSPHPPPPPAPPTPPPKPSTTSNSRRFTPGNSASLRIGSSRRATAWPVVSTGSPRSHPENDGYNSADEQNPCYGSSYNDAERERQFEIDIRRTKGYEVKRMSEDGNCLFRAVADQVYGDSEAYDLARQMCIDYMERERDHFSQFITEG...

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	`TkA01G118410`
TK1151 ID	TkA01G118410
OH-1004 ID	LXL04_004720
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G118410

Location Chr01:30023787-30027216 (-)

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

Arabidopsis / Rice Reference Genes and Papers

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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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Cytoplasm0.568

Rank 1 · TkA01G118410 · TK1151

Nucleus0.417

Rank 2 · TkA01G118410 · TK1151

Cell membrane0.135

Rank 3 · TkA01G118410 · TK1151

Golgi apparatus0.061

Rank 4 · TkA01G118410 · TK1151

Endoplasmic reticulum0.056

Rank 5 · TkA01G118410 · TK1151

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.

PF16101PRIMA1101-131 aa

PF22812CR_prot_dom_plant115-161 aa

PF10275Peptidase_C65208-225 aa

PF29258OTU_Vertnin214-235 aa

PF02338OTU216-325 aa

PF10275Peptidase_C65240-328 aa

PF29258OTU_Vertnin240-292 aa

PF10275Peptidase_C65357-390 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G118410	`PF16101`	PRIMA1	101	131	5.9	7.4
TkA01G118410	`PF22812`	CR_prot_dom_plant	115	161	1.9	9.7
TkA01G118410	`PF10275`	Peptidase_C65	208	225	8.7e-05	22.8
TkA01G118410	`PF29258`	OTU_Vertnin	214	235	0.0068	17.2
TkA01G118410	`PF02338`	OTU	216	325	1.1e-18	68.6
TkA01G118410	`PF10275`	Peptidase_C65	240	328	8.7e-05	22.8
TkA01G118410	`PF29258`	OTU_Vertnin	240	292	0.0068	17.2
TkA01G118410	`PF10275`	Peptidase_C65	357	390	8.7e-05	22.8
TkA01G118410	`PF29258`	OTU_Vertnin	380	391	0.0068	17.2
TkA01G118410	`PF02338`	OTU	382	405	1.1e-18	68.6
TkA01G118410	`PF22567`	UBA_9	448	479	0.02	15.4

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	sp\|Q9XIP2\|OTU6_ARATH OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 6	71.300%	Swiss-Prot	High

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