TkA07G313390 | RubberDandelionOmics

Gene overview

TkA07G313390

Reference: TK1151 Chr: Chr07 Coordinates: 78616594-78618571 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

852 bp · TkA07G313390|TK1151|cDNA

CAGGTGCAGTATCCAACATATAGCGATTTAAACACCAACGACATTTTAAGCTTAATTCAGTCTGTGCAAAGTGAGATTGATGCCAACTCAGCAACGGCAACAACCTCTACAATGGAATCAGTGCTGTCATTGAACGATGGTAGTTGGATACGTCCAAGTCAGCAGCCACATGTACAGTTTGACAGTGATGATTTCTTTTCTGGAAATATAATCAGGCAACCTTCTCCCCCTCCCGTGCTTGCCCGTGTGCAACCTCATCA...

CDS

Download CDS FASTA

852 bp · TkA07G313390|TK1151|CDS

CAGGTGCAGTATCCAACATATAGCGATTTAAACACCAACGACATTTTAAGCTTAATTCAGTCTGTGCAAAGTGAGATTGATGCCAACTCAGCAACGGCAACAACCTCTACAATGGAATCAGTGCTGTCATTGAACGATGGTAGTTGGATACGTCCAAGTCAGCAGCCACATGTACAGTTTGACAGTGATGATTTCTTTTCTGGAAATATAATCAGGCAACCTTCTCCCCCTCCCGTGCTTGCCCGTGTGCAACCTCATCA...

Protein

Download Protein FASTA

283 aa · TkA07G313390|TK1151|PROTEIN

QVQYPTYSDLNTNDILSLIQSVQSEIDANSATATTSTMESVLSLNDGSWIRPSQQPHVQFDSDDFFSGNIIRQPSPPPVLARVQPHHSPISPTRVADPRPGAAKCYGTDAPTSNGHQHLHIPLKMMQDFLRLAQENTKKNLETCGVLAEFLKNRVFHITTLIIPKQESTSDSCQTLNEEDIIEVQDKRSLFQLGWIQVNGRLVFLVFKCKLHFRSFGIIMLPEAIAIVMAPTDESCPHGIFHLSDPGGVNLIRNCDERGF...

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	`TkA07G313390`
TK1151 ID	TkA07G313390
OH-1004 ID	LXL04_012467
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	83.300
Protein coverage (%)	TK1151 71.378 / OH-1004 67.219 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

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA07G313390

Location Chr07:78616594-78618571 (-)

Description Similar to AMSH3: AMSH-like ubiquitin thioesterase 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g16144`	Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'- linked polyubiquitin chains, but is not implicated in protein degradation by the 26S proteasome, deneddylation, or desumoylation.	The deubiquitinating enzyme AMSH3 is required for intracellular trafficking and vacuole biogenesis in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.075952
`At1g48790`	Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.	No verified direct reference in this release
`At1g10600`	Zinc metalloprotease that cleaves 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012467 · 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:0000281 mitotic cytokinesis Biological Process

GO:0006508 proteolysis Biological Process

GO:0006897 endocytosis Biological Process

GO:0007033 vacuole organization Biological Process

GO:0007259 cell surface receptor signaling pathway via JAK-STAT Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0015031 protein transport Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0032511 late endosome to vacuole transport via multivesicular body sorting pathway Biological Process

GO:0043328 protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Biological Process

GO:0044090 positive regulation of vacuole organization Biological Process

GO:0045324 late endosome to vacuole transport Biological Process

KEGG gene cross-reference

ath:AT1G10600

ath:AT1G48790

hsa:10617

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.

Cytoplasm0.523

Rank 1 · TkA07G313390 · TK1151

Nucleus0.413

Rank 2 · TkA07G313390 · TK1151

Cell membrane0.097

Rank 3 · TkA07G313390 · TK1151

Mitochondrion0.078

Rank 4 · TkA07G313390 · TK1151

Endoplasmic reticulum0.077

Rank 5 · TkA07G313390 · 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.

PF15805SCNM1_acidic43-64 aa

PF01398JAB116-198 aa

PF13552DUF4127118-189 aa

PF15805SCNM1_acidic189-198 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G313390	`PF15805`	SCNM1_acidic	43	64	0.35	11.3
TkA07G313390	`PF01398`	JAB	116	198	7.4e-06	26.5
TkA07G313390	`PF13552`	DUF4127	118	189	0.36	10.0
TkA07G313390	`PF15805`	SCNM1_acidic	189	198	0.35	11.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q5PNU3`	Arabidopsis thaliana	sp\|Q5PNU3\|AMSH3_ARATH AMSH-like ubiquitin thioesterase 3	55.700%	Swiss-Prot	High
`Q8VYB5`	Arabidopsis thaliana	sp\|Q8VYB5\|AMSH1_ARATH AMSH-like ubiquitin thioesterase 1	51.100%	Swiss-Prot	High
`Q6NKP9`	Arabidopsis thaliana	sp\|Q6NKP9\|AMSH2_ARATH AMSH-like ubiquitin thioesterase 2	48.000%	Swiss-Prot	Medium

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