TkA04G506630 | RubberDandelionOmics

Gene overview

TkA04G506630

Reference: TK1151 Chr: Chr04 Coordinates: 127995307-128001689 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3015 bp · TkA04G506630|TK1151|cDNA

TTTCGGGTCGGAATATTAGATGACCGACGAAATCACGTCTGTTGATGCTTAGACAAATTCGTTTCTTTCTTATTTTCACCTTTTGAGATTTTTCACACACAAAAAGCCCTAAAATCTTGATTTTGCAAATTTCCGAATTTAAGTCGCGAACAACTGATTGTGGAAGTCGCCATTAAATTTTTCCAAATTCACTTCAAAAGTTTTGGTTTATGATTCATTGATACGATGTTTATGAACCGCCATCATCATCGCAAGCATCG...

CDS

Download CDS FASTA

2163 bp · TkA04G506630|TK1151|CDS

ATGCCTGTTGGAAGGGATCTAGGGCTTCCAAGCCTGGTGGTCCTGGTAGTGATATTCGTGATATTGCCGGTGGTCGGCTTTGTTATCCGCAGAAAATTGCGACATGCGGCGGCGAGGAACGAGGAGATTAAGAAACTTTTGATATTTGCATCGGAAGAGGCAGCTAGGGCTGAGATTGAGGCTACAGATGGATACTTTTTCACGGCGAACACTAGCTCATCGATTCCTCCTCCAAATTCAGCCTGGGCACCGGCTCCAGA...

Protein

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720 aa · TkA04G506630|TK1151|PROTEIN

MPVGRDLGLPSLVVLVVIFVILPVVGFVIRRKLRHAAARNEEIKKLLIFASEEAARAEIEATDGYFFTANTSSSIPPPNSAWAPAPESAWVQPRASVPLVSSLKPPYQCAVCFSPTSTRCAKCKAVRYCSGRCQIVHWRQGHKDECRPYVGTKDVATSCLKKEDDKDSNKAKFHEPETDSFTQSASDTSPSEESCAFSSTSRSSAETSSVSSGESDDFVSVQFQSTKVKPSNEDTTSSDFWSGTIDSKKSTIDEPSSNGF...

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	`TkA04G506630`
TK1151 ID	TkA04G506630
OH-1004 ID	LXL04_039137
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	96.700
Protein coverage (%)	TK1151 88.056 / OH-1004 77.872 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 TkA04G506630

Location Chr04:127995307-128001689 (-)

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
`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_039137 · 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:0010154 fruit 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

KEGG gene cross-reference

ath:AT1G17110

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.

Cytoplasm0.411

Rank 1 · TkA04G506630 · TK1151

Nucleus0.336

Rank 2 · TkA04G506630 · TK1151

Mitochondrion0.129

Rank 3 · TkA04G506630 · TK1151

Cell membrane0.125

Rank 4 · TkA04G506630 · TK1151

Endoplasmic reticulum0.112

Rank 5 · TkA04G506630 · 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_1171-171 aa

PF00443UCH310-348 aa

PF00443UCH376-627 aa

PF13423UCH_1377-635 aa

PF24324MYND_ZMYND11_ZMYD8384-393 aa

PF01753zf-MYND410-418 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G506630	`PF01753`	zf-MYND	109	146	1.4e-08	35.4
TkA04G506630	`PF24324`	MYND_ZMYND11_ZMYD8	109	146	0.016	16.0
TkA04G506630	`PF13423`	UCH_1	171	171	2.3e-19	70.9
TkA04G506630	`PF00443`	UCH	310	348	5.6e-42	144.8
TkA04G506630	`PF00443`	UCH	376	627	5.6e-42	144.8
TkA04G506630	`PF13423`	UCH_1	377	635	2.3e-19	70.9
TkA04G506630	`PF24324`	MYND_ZMYND11_ZMYD8	384	393	0.016	16.0
TkA04G506630	`PF01753`	zf-MYND	410	418	1.4e-08	35.4
TkA04G506630	`PF01753`	zf-MYND	502	507	1.4e-08	35.4
TkA04G506630	`PF01753`	zf-MYND	548	557	1.4e-08	35.4
TkA04G506630	`PF24324`	MYND_ZMYND11_ZMYD8	552	556	0.016	16.0

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	sp\|Q9FKP5\|UBP17_ARATH Ubiquitin carboxyl-terminal hydrolase 17	45.000%	Swiss-Prot	Medium
`Q9SB51`	Arabidopsis thaliana	sp\|Q9SB51\|UBP16_ARATH Ubiquitin carboxyl-terminal hydrolase 16	37.900%	Swiss-Prot	Medium
`Q9FPS9`	Arabidopsis thaliana	sp\|Q9FPS9\|UBP15_ARATH Ubiquitin carboxyl-terminal hydrolase 15	37.800%	Swiss-Prot	Medium
`Q67XW5`	Arabidopsis thaliana	sp\|Q67XW5\|UBP18_ARATH Ubiquitin carboxyl-terminal hydrolase 18	52.900%	Swiss-Prot	Low
`Q0E2F9`	Oryza sativa subsp. japonica	sp\|Q0E2F9\|UBP15_ORYSJ Ubiquitin C-terminal hydrolase 15	33.100%	Swiss-Prot	Medium

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