LXL04_025922 | RubberDandelionOmics

Gene overview

LXL04_025922

Reference: OH-1004 Chr: Chr05 Coordinates: 118602107-118603744 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1278 bp · LXL04_025922|LXL04_025922|OH1004|cDNA

ATGGGCGTTTGTGTATTGCGACTACATTGTAAAGTTCAAACAACGAAGGTACCACAAGTAATGGATCGATCGGAAACCCGTGAGGATAATGACCACAGGCATGTGATTGATATAACAAGCGAACCTTCATCTTCATCTACCTCAACACAAGACAGACAAACCAACAGGTCAAATCCAAACCTCCCTTCAACTAGTGTAACCGATCTTTTCGAACATCCTTTCTCAACCACAAACGCAACAACAAACACACGAACTGCACC...

CDS

Download CDS FASTA

1278 bp · LXL04_025922|LXL04_025922|OH1004|CDS

ATGGGCGTTTGTGTATTGCGACTACATTGTAAAGTTCAAACAACGAAGGTACCACAAGTAATGGATCGATCGGAAACCCGTGAGGATAATGACCACAGGCATGTGATTGATATAACAAGCGAACCTTCATCTTCATCTACCTCAACACAAGACAGACAAACCAACAGGTCAAATCCAAACCTCCCTTCAACTAGTGTAACCGATCTTTTCGAACATCCTTTCTCAACCACAAACGCAACAACAAACACACGAACTGCACC...

Protein

Download Protein FASTA

425 aa · LXL04_025922|LXL04_025922|OH1004|PROTEIN

MGVCVLRLHCKVQTTKVPQVMDRSETREDNDHRHVIDITSEPSSSSTSTQDRQTNRSNPNLPSTSVTDLFEHPFSTTNATTNTRTAPFARRSNGTTNGRRRSPLNSGYWISFELVITISQIIAAIVVLSMSRHEHPRAPLFTWVIGYASGCVATLPLLFWRFYFRNDTDQDPAQPRQNSSPTFLSAMATSLTSSNTRTSVGDTNNPTGTPATRPVRVLLNARVKVLVEYFKMGLDCFFAVWFVVGNVWIFGGHSSASDAP...

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_025922`
TK1151 ID	TkA06G036190
OH-1004 ID	LXL04_025922
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025922

Location Chr05:118602107-118603744 (+)

Description Similar to At4g11680: E3 ubiquitin-protein ligase At4g11680

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g11680`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g12760`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At2g01735`	Probable E3 ubiquitin-protein ligase required for embryo development.	A RING-H2 zinc-finger protein gene RIE1 is essential for seed development in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000009256.01620.a6
`At1g63170`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025922 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane 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:AT1G12760

ath:AT1G63170

ath:AT2G01735

ath:AT4G11680

dre:767686

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.

Lysosome / Vacuole0.350

Rank 1 · LXL04_025922 · OH-1004

Cell membrane0.241

Rank 2 · LXL04_025922 · OH-1004

Cytoplasm0.239

Rank 3 · LXL04_025922 · OH-1004

Endoplasmic reticulum0.200

Rank 4 · LXL04_025922 · OH-1004

Golgi apparatus0.173

Rank 5 · LXL04_025922 · OH-1004

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.

PF13639.13zf-RING_2363-404 aa

PF17123.12zf-RING_11363-390 aa

PF12678.14zf-rbx1364-404 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025922	`PF13639.13`	zf-RING_2	363	404	2.8e-13	50.6
LXL04_025922	`PF17123.12`	zf-RING_11	363	390	1.7e-08	34.7
LXL04_025922	`PF12678.14`	zf-rbx1	364	404	1.2e-07	32.6

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
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	28.990%	Swiss-Prot	weak database homology
`Q9LN71`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g12760	32.362%	Swiss-Prot	moderate database homology
`Q8GUU2`	Arabidopsis thaliana	E3 ubiquitin protein ligase RIE1	27.393%	Swiss-Prot	weak database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	40.761%	Swiss-Prot	weak database homology

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