TkA04G506680 | RubberDandelionOmics

Gene overview

TkA04G506680

Reference: TK1151 Chr: Chr04 Coordinates: 128014224-128018107 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3029 bp · TkA04G506680|TK1151|cDNA

CACGAAATCACGTCTGTTGATGCTTAGACAAATTCGTTTCTTTCTTATTTTCACCTTTTGAGTTTTTTCACACACAAAAAAAAGCCCTAAAATCTTGATCTTGCAAATTTCCGAATTTAAGTCGCGAACAACTGATTGTGGAAGTCGCCATAGCTGTTAACATTTTCTAAATTCACTTCATAAGTTTTGGTTTATGATTCATTGATACGATGTTTATGAACCATCATCATCGCAGCATCGACTTTGTGGAATAAAGGGGC...

CDS

Download CDS FASTA

2307 bp · TkA04G506680|TK1151|CDS

ATGCTTGTTGGAAGGGATCTAGGGCTTCCAAACCTGGTGGTCCTGGTAGTAATATTCGTGATTTTTCCGGTGATCGGCTTTGTTATCCGCCGAAAGTTGCGACACGCGGCGGCGAGGAACGAGGAGATTAAGAAGCTTTTGATTTTGGCATCGGAAGAGGCAGCCAGGGCTGAGATTGAGGCTACATCGGGATACTTTTTCACGGCCAACACTAGTTCATCGATTCCTCCTCCGGATTCGGCCTGGGCACCGGCTCCAGA...

Protein

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768 aa · TkA04G506680|TK1151|PROTEIN

MLVGRDLGLPNLVVLVVIFVIFPVIGFVIRRKLRHAAARNEEIKKLLILASEEAARAEIEATSGYFFTANTSSSIPPPDSAWAPAPESAWVQPTASVPLVSSLKPPYQCAVCFSPTSTRCAKCKAVRYCSGRCQIVHWRQGHKDECRPYVGTKDVATSCLKKEDDKDSNNAEVHEPETDSFIQSAFDTSPSEESCAFSSTSRSSTETSSVSSGESDDFVSVQFQSTKVKPSNEDTTSSDFWSGTIDFKKSTIDETSSNGF...

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	`TkA04G506680`
TK1151 ID	TkA04G506680
OH-1004 ID	LXL04_039136
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.300
Protein coverage (%)	TK1151 98.958 / OH-1004 96.569 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

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Basic Information and Functional Annotation

Gene ID TkA04G506680

Location Chr04:128014224-128018107 (-)

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
`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
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_039136 · 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: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.

Cytoplasm0.445

Rank 1 · TkA04G506680 · TK1151

Nucleus0.376

Rank 2 · TkA04G506680 · TK1151

Cell membrane0.118

Rank 3 · TkA04G506680 · TK1151

Mitochondrion0.103

Rank 4 · TkA04G506680 · TK1151

Endoplasmic reticulum0.099

Rank 5 · TkA04G506680 · TK1151

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.

PF01753zf-MYND109-146 aa

PF24324MYND_ZMYND11_ZMYD8109-146 aa

PF13423UCH_1170-217 aa

PF00443UCH370-666 aa

PF13423UCH_1371-648 aa

PF24324MYND_ZMYND11_ZMYD8378-387 aa

PF01753zf-MYND404-412 aa

PF01753zf-MYND496-501 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G506680	`PF01753`	zf-MYND	109	146	1.5e-08	35.3
TkA04G506680	`PF24324`	MYND_ZMYND11_ZMYD8	109	146	0.017	15.9
TkA04G506680	`PF13423`	UCH_1	170	217	4.3e-23	83.2
TkA04G506680	`PF00443`	UCH	370	666	3.7e-55	188.0
TkA04G506680	`PF13423`	UCH_1	371	648	4.3e-23	83.2
TkA04G506680	`PF24324`	MYND_ZMYND11_ZMYD8	378	387	0.017	15.9
TkA04G506680	`PF01753`	zf-MYND	404	412	1.5e-08	35.3
TkA04G506680	`PF01753`	zf-MYND	496	501	1.5e-08	35.3
TkA04G506680	`PF01753`	zf-MYND	542	551	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
`Q9FKP5`	Arabidopsis thaliana	sp\|Q9FKP5\|UBP17_ARATH Ubiquitin carboxyl-terminal hydrolase 17	43.100%	Swiss-Prot	Medium
`Q9SB51`	Arabidopsis thaliana	sp\|Q9SB51\|UBP16_ARATH Ubiquitin carboxyl-terminal hydrolase 16	38.100%	Swiss-Prot	Medium
`Q9FPS9`	Arabidopsis thaliana	sp\|Q9FPS9\|UBP15_ARATH Ubiquitin carboxyl-terminal hydrolase 15	38.100%	Swiss-Prot	Medium
`Q9SJA1`	Arabidopsis thaliana	sp\|Q9SJA1\|UBP19_ARATH Ubiquitin carboxyl-terminal hydrolase 19	53.600%	Swiss-Prot	Low
`Q67XW5`	Arabidopsis thaliana	sp\|Q67XW5\|UBP18_ARATH Ubiquitin carboxyl-terminal hydrolase 18	54.000%	Swiss-Prot	Low
`Q0E2F9`	Oryza sativa subsp. japonica	sp\|Q0E2F9\|UBP15_ORYSJ Ubiquitin C-terminal hydrolase 15	34.900%	Swiss-Prot	Medium

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