LXL04_033262 | RubberDandelionOmics

Gene overview

LXL04_033262

Reference: OH-1004 Chr: Chr07 Coordinates: 39599663-39602849 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1326 bp · LXL04_033262|LXL04_033262|OH1004|cDNA

ATGGCTTTTGATATCAAATTTTGCAACTTAAAGTTCGTTTCTGATTTGGGAGATGAAAGAAAATGTGATCACAACATGACTCCATCCATCTATCTAAACTTAACCAAACTTCACTATTTGGGTTCAATTTATCCCAAAACCGACCCGAACGGCTCACCACTTGAGTCTCTGGACCGTAGAAAACGTAGCCTAAAATATCACTGTACACCCGACCGTAAGATACGTCCCGTTCCTTCCAAGCGTAACGGCGCTGCAATGAA...

CDS

Download CDS FASTA

1326 bp · LXL04_033262|LXL04_033262|OH1004|CDS

ATGGCTTTTGATATCAAATTTTGCAACTTAAAGTTCGTTTCTGATTTGGGAGATGAAAGAAAATGTGATCACAACATGACTCCATCCATCTATCTAAACTTAACCAAACTTCACTATTTGGGTTCAATTTATCCCAAAACCGACCCGAACGGCTCACCACTTGAGTCTCTGGACCGTAGAAAACGTAGCCTAAAATATCACTGTACACCCGACCGTAAGATACGTCCCGTTCCTTCCAAGCGTAACGGCGCTGCAATGAA...

Protein

Download Protein FASTA

441 aa · LXL04_033262|LXL04_033262|OH1004|PROTEIN

MAFDIKFCNLKFVSDLGDERKCDHNMTPSIYLNLTKLHYLGSIYPKTDPNGSPLESLDRRKRSLKYHCTPDRKIRPVPSKRNGAAMNRIENDPAGGGCDNAGNDELEEFSDEFKCCVCLDLIYKPVVLACGHISCFWCVFEAMDYWHESHCPVCRHSYNHFPTICWLLHSVLLKLYPKDYQRRERQVSADEKTNGTSSPQFENPTNPTISNDKTTKNVAVGDLLCTVCKQLIYRPVVLNCGHVFCETCIVDSCDGPCRCP...

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_033262`
TK1151 ID	TkA08G246910
OH-1004 ID	LXL04_033262
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
Protein coverage (%)	TK1151 100.000 / OH-1004 80.726 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_033262

Location Chr07:39599663-39602849 (-)

Description Similar to PRT1: E3 ubiquitin-protein ligase PRT1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g24800`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues.2003 · DOI: 10.1104/pp.103.029272 PRT1 of Arabidopsis thaliana encodes a component of the plant N-end rule pathway.1998 · DOI: 10.1073/pnas.95.14.7904

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033262 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway Biological Process

GO:0000151 ubiquitin ligase complex Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT3G24800

hsa:79836

mcf:102135813

mmu:74365

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.

Nucleus0.718

Rank 1 · LXL04_033262 · OH-1004

Cytoplasm0.318

Rank 2 · LXL04_033262 · OH-1004

Cell membrane0.061

Rank 3 · LXL04_033262 · OH-1004

Endoplasmic reticulum0.034

Rank 4 · LXL04_033262 · OH-1004

Lysosome / Vacuole0.022

Rank 5 · LXL04_033262 · 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.

PF13920.13zf-C3HC4_3112-159 aa

PF13923.13zf-C3HC4_2114-154 aa

PF15227.13zf-C3HC4_4115-154 aa

PF13920.13zf-C3HC4_3223-264 aa

PF13923.13zf-C3HC4_2225-262 aa

PF13445.13zf-RING_UBOX225-260 aa

PF00097.32zf-C3HC4225-262 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033262	`PF13920.13`	zf-C3HC4_3	112	159	2.2e-10	40.9
LXL04_033262	`PF13923.13`	zf-C3HC4_2	114	154	2.1e-09	37.7
LXL04_033262	`PF15227.13`	zf-C3HC4_4	115	154	4.7e-08	33.7
LXL04_033262	`PF13920.13`	zf-C3HC4_3	223	264	2.2e-10	40.9
LXL04_033262	`PF13923.13`	zf-C3HC4_2	225	262	2.1e-09	37.7
LXL04_033262	`PF13445.13`	zf-RING_UBOX	225	260	1.3e-06	29.0
LXL04_033262	`PF00097.32`	zf-C3HC4	225	262	9.7e-06	26.1

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
`Q8LBL5`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PRT1	40.278%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card