LXL04_012934 | RubberDandelionOmics

Gene overview

LXL04_012934

Reference: OH-1004 Chr: Chr03 Coordinates: 21202194-21216851 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6075 bp · LXL04_012934|LXL04_012934|OH1004|cDNA

ATGCTCAGGACAATAAGCGAGAGTGCTTTCGCTATTCCGCACACAaaacCACCGTTGATCGGACGTCATCTCCTGACGAGAACCACGACCATGGTCACTCCACAACCATTAGATCAAGAAGACGAGGATATGCTTGTGCCGCACGCGGAGCTACCGGAAGGGCCTCAACCGGTGCAAGGTCCTGTGGCTTTCGATGGTACTCCGCCAATTGAAGTCCCTCAGCCTATGGAAGGTCAAGAAGGGGCTAACACAGCAGAGAA...

CDS

Download CDS FASTA

6075 bp · LXL04_012934|LXL04_012934|OH1004|CDS

ATGCTCAGGACAATAAGCGAGAGTGCTTTCGCTATTCCGCACACAAAACCACCGTTGATCGGACGTCATCTCCTGACGAGAACCACGACCATGGTCACTCCACAACCATTAGATCAAGAAGACGAGGATATGCTTGTGCCGCACGCGGAGCTACCGGAAGGGCCTCAACCGGTGCAAGGTCCTGTGGCTTTCGATGGTACTCCGCCAATTGAAGTCCCTCAGCCTATGGAAGGTCAAGAAGGGGCTAACACAGCAGAGAA...

Protein

Download Protein FASTA

2024 aa · LXL04_012934|LXL04_012934|OH1004|PROTEIN

MLRTISESAFAIPHTKPPLIGRHLLTRTTTMVTPQPLDQEDEDMLVPHAELPEGPQPVQGPVAFDGTPPIEVPQPMEGQEGANTAENQAVEEPQASRFTWKIETFSRQTNKKLYSDVFVVGGFKWRVLIFPKGNNVDHLSMYLDVADSTSLPYGWSRYAQFSLSVVNQIHNRSTIKKDTQHQFHARESDWGFTSFMALSELYDPGKGFIVNDTCIIEADVAVRKVVDYWTYDSKKETGYVGLKNQGATCYMNSLLQTLYH...

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	`LXL04_012934`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012934

Location Chr03:21202194-21216851 (+)

Description Similar to UBP12: Ubiquitin carboxyl-terminal hydrolase 12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06600`	Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin.	No verified direct reference in this release
`At3g11910`	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_012934 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006508 proteolysis Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0016579 protein deubiquitination Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0070646 protein modification by small protein removal Biological Process

GO:2000280 regulation of root development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0004843 cysteine-type deubiquitinase activity Molecular Function

KEGG gene cross-reference

ath:AT3G11910

ath:AT5G06600

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.

Cytoplasm0.573

Rank 1 · LXL04_012934 · OH-1004

Nucleus0.335

Rank 2 · LXL04_012934 · OH-1004

Cell membrane0.132

Rank 3 · LXL04_012934 · OH-1004

Mitochondrion0.086

Rank 4 · LXL04_012934 · OH-1004

Endoplasmic reticulum0.076

Rank 5 · LXL04_012934 · OH-1004

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.

PF22486.3MATH_297-220 aa

PF00917.33MATH104-222 aa

PF00443.36UCH240-561 aa

PF13423.13UCH_1240-515 aa

PF12436.15USP7_ICP0_bdg666-918 aa

PF14533.13USP7_C2928-1138 aa

PF14111.13DUF42831314-1393 aa

PF12436.15USP7_ICP0_bdg1607-1859 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012934	`PF22486.3`	MATH_2	97	220	9.2e-77	256.6
LXL04_012934	`PF00917.33`	MATH	104	222	3e-34	118.4
LXL04_012934	`PF00443.36`	UCH	240	561	2e-58	198.7
LXL04_012934	`PF13423.13`	UCH_1	240	515	2.7e-14	54.3
LXL04_012934	`PF12436.15`	USP7_ICP0_bdg	666	918	2e-154	512.6
LXL04_012934	`PF14533.13`	USP7_C2	928	1138	3.2e-55	187.8
LXL04_012934	`PF14111.13`	DUF4283	1314	1393	2.1e-11	44.1
LXL04_012934	`PF12436.15`	USP7_ICP0_bdg	1607	1859	2e-154	512.6
LXL04_012934	`PF22486.3`	MATH_2	1875	1998	9.2e-77	256.6
LXL04_012934	`PF00917.33`	MATH	1882	1998	3e-34	118.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FPT1`	Arabidopsis thaliana	Ubiquitin C-terminal hydrolase 12	80.851%	Swiss-Prot	moderate database homology
`Q84WU2`	Arabidopsis thaliana	Ubiquitin C-terminal hydrolase 13	79.433%	Swiss-Prot	moderate database homology

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