TkA04G124070 | RubberDandelionOmics

Gene overview

TkA04G124070

Reference: TK1151 Chr: Chr04 Coordinates: 32234544-32237192 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

504 bp · TkA04G124070|TK1151|cDNA

ATGTCGTTGCCACCATCGTCGGGCACAATCCCCCTCCCTCAACAACTCGTTAGTGAGGGTCAATACAAGGCGACATTGGTTTGTCCTGTATGTGAGAAGATCTCCGTCACATTTGATCCGTTCATGTACCTCTCGCTGCCGCTTCAATCAACCACCACTCGCACAATGACTGTCACAATTTTCAGTTGTGATGGAAGTGCCGTCCCTTCCACCTGTACGGTAACTGTACCAAAACAGGGACGTTTTCGAAGATTCGAGAT...

CDS

Download CDS FASTA

504 bp · TkA04G124070|TK1151|CDS

ATGTCGTTGCCACCATCGTCGGGCACAATCCCCCTCCCTCAACAACTCGTTAGTGAGGGTCAATACAAGGCGACATTGGTTTGTCCTGTATGTGAGAAGATCTCCGTCACATTTGATCCGTTCATGTACCTCTCGCTGCCGCTTCAATCAACCACCACTCGCACAATGACTGTCACAATTTTCAGTTGTGATGGAAGTGCCGTCCCTTCCACCTGTACGGTAACTGTACCAAAACAGGGACGTTTTCGAAGATTCGAGAT...

Protein

Download Protein FASTA

167 aa · TkA04G124070|TK1151|PROTEIN

MSLPPSSGTIPLPQQLVSEGQYKATLVCPVCEKISVTFDPFMYLSLPLQSTTTRTMTVTIFSCDGSAVPSTCTVTVPKQGRFRRFEIDLRSDFFHLTSKSGFASADFWVCLRCHTIQVFIDLLTDLNIIGQQKDDTHLLTACGDHNIKLWDNQNKTVLEHQLDTLEL

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	`TkA04G124070`
TK1151 ID	TkA04G124070
OH-1004 ID	LXL04_019075
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	67.200
Protein coverage (%)	TK1151 73.054 / OH-1004 9.365 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 TkA04G124070

Location Chr04:32234544-32237192 (-)

Description Similar to UBP5: Ubiquitin carboxyl-terminal hydrolase 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40930`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	Ubiquitin-specific proteases from Arabidopsis thaliana: cloning of AtUBP5 and analysis of substrate specificity of AtUBP3, AtUBP4, and AtUBP5 using Escherichia coli in vivo and in vitro assays.2000 · DOI: 10.1006/abbi.2000.1874
`At4g10570`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At4g10590`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At1g32850`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At5g22030`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	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_019075 · 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:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007032 endosome organization Biological Process

GO:0007265 Ras protein signal transduction Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0141137 positive regulation of gene expression, epigenetic Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0004843 cysteine-type deubiquitinase activity Molecular Function

GO:0140950 histone H2A deubiquitinase activity Molecular Function

KEGG gene cross-reference

ath:AT1G32850

ath:AT2G40930

ath:AT4G10570

ath:AT4G10590

ath:AT5G22030

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.

Cytoplasm0.447

Rank 1 · TkA04G124070 · TK1151

Nucleus0.394

Rank 2 · TkA04G124070 · TK1151

Mitochondrion0.126

Rank 3 · TkA04G124070 · TK1151

Extracellular0.080

Rank 4 · TkA04G124070 · TK1151

Endoplasmic reticulum0.076

Rank 5 · TkA04G124070 · 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.

PF11781Zn_ribbon_RRN727-33 aa

PF25048Beta-prop_TEP1_C57-66 aa

PF00400WD4061-65 aa

PF25175Beta-prop_WDR596-159 aa

PF11781Zn_ribbon_RRN7107-116 aa

PF11715Beta-prop_Nup120_160133-159 aa

PF00400WD40134-151 aa

PF25048Beta-prop_TEP1_C135-156 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G124070	`PF11781`	Zn_ribbon_RRN7	27	33	1.1	9.7
TkA04G124070	`PF25048`	Beta-prop_TEP1_C	57	66	0.021	15.6
TkA04G124070	`PF00400`	WD40	61	65	0.019	16.3
TkA04G124070	`PF25175`	Beta-prop_WDR5	96	159	0.042	13.9
TkA04G124070	`PF11781`	Zn_ribbon_RRN7	107	116	1.1	9.7
TkA04G124070	`PF11715`	Beta-prop_Nup120_160	133	159	0.0097	15.3
TkA04G124070	`PF00400`	WD40	134	151	0.019	16.3
TkA04G124070	`PF25048`	Beta-prop_TEP1_C	135	156	0.021	15.6

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
`O22207`	Arabidopsis thaliana	sp\|O22207\|UBP5_ARATH Ubiquitin carboxyl-terminal hydrolase 5	73.100%	Swiss-Prot	Low
`Q9ZSB5`	Arabidopsis thaliana	sp\|Q9ZSB5\|UBP10_ARATH Ubiquitin carboxyl-terminal hydrolase 10	70.100%	Swiss-Prot	Low
`Q93Y01`	Arabidopsis thaliana	sp\|Q93Y01\|UBP9_ARATH Ubiquitin carboxyl-terminal hydrolase 9	68.700%	Swiss-Prot	Low
`Q9MAQ3`	Arabidopsis thaliana	sp\|Q9MAQ3\|UBP11_ARATH Putative ubiquitin carboxyl-terminal hydrolase 11	68.700%	Swiss-Prot	Low
`Q9C585`	Arabidopsis thaliana	sp\|Q9C585\|UBP8_ARATH Ubiquitin carboxyl-terminal hydrolase 8	63.600%	Swiss-Prot	Low

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