LXL04_005658 | RubberDandelionOmics

Gene overview

LXL04_005658

Reference: OH-1004 Chr: Chr01 Coordinates: 170265173-170267581 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1260 bp · LXL04_005658|LXL04_005658|OH1004|cDNA

ATGGGTGTTCCTAAACCAGGACTACATCGTAAAATCCAAACAAGCAAGGCGCCATTACTAATGGAGAGAACAGAAACCAATACCGATTGTGAACATGTGATTAATATACCAACAAGTAGCAATGAAGCTTCATCATCTACCTCAACTCTCTCTACACCTTCAACAAGTTCACAACCTCCAGTCTTGCAACATTCTTTTTCTACTACAAACACAAGGAATACATCATTTTCAAGACGAGGGAATGGGAATGGGAATGGGAA...

CDS

Download CDS FASTA

1260 bp · LXL04_005658|LXL04_005658|OH1004|CDS

ATGGGTGTTCCTAAACCAGGACTACATCGTAAAATCCAAACAAGCAAGGCGCCATTACTAATGGAGAGAACAGAAACCAATACCGATTGTGAACATGTGATTAATATACCAACAAGTAGCAATGAAGCTTCATCATCTACCTCAACTCTCTCTACACCTTCAACAAGTTCACAACCTCCAGTCTTGCAACATTCTTTTTCTACTACAAACACAAGGAATACATCATTTTCAAGACGAGGGAATGGGAATGGGAATGGGAA...

Protein

Download Protein FASTA

419 aa · LXL04_005658|LXL04_005658|OH1004|PROTEIN

MGVPKPGLHRKIQTSKAPLLMERTETNTDCEHVINIPTSSNEASSSTSTLSTPSTSSQPPVLQHSFSTTNTRNTSFSRRGNGNGNGNGRRRSPLNSGYWISVELVITVSQIIAAIVVLSLSRDEHPHAPLFTWVIGYASGCVVTLPLLFWRFYNRNASNQEVSQGRQNSTPGSLSAVASSFTSSSNGRIFEGDNRNTAGTSTRRMAMGALSARVKVLVEYFKMGLDCFFAVWFVVGNVWIFGGHTSSSVAPNLYRLCIVF...

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_005658`
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_005658

Location Chr01:170265173-170267581 (+)

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
`At1g63170`	Mediates E2-dependent protein ubiquitination.	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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005658 · 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:0046330 positive regulation of JNK cascade Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005637 nuclear inner membrane Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005765 lysosomal membrane Cellular Component

GO:0005768 endosome Cellular Component

KEGG gene cross-reference

ath:AT1G12760

ath:AT1G63170

ath:AT2G01735

ath:AT4G11680

mmu:24017

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.

Lysosome / Vacuole0.383

Rank 1 · LXL04_005658 · OH-1004

Cell membrane0.263

Rank 2 · LXL04_005658 · OH-1004

Endoplasmic reticulum0.199

Rank 3 · LXL04_005658 · OH-1004

Cytoplasm0.190

Rank 4 · LXL04_005658 · OH-1004

Golgi apparatus0.140

Rank 5 · LXL04_005658 · 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.

PF13639.13zf-RING_2354-395 aa

PF17123.12zf-RING_11354-381 aa

PF00097.32zf-C3HC4354-394 aa

PF12678.14zf-rbx1366-395 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005658	`PF13639.13`	zf-RING_2	354	395	1.7e-14	54.5
LXL04_005658	`PF17123.12`	zf-RING_11	354	381	2.6e-09	37.3
LXL04_005658	`PF00097.32`	zf-C3HC4	354	394	5.6e-06	26.8
LXL04_005658	`PF12678.14`	zf-rbx1	366	395	4.2e-08	34.0

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
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	30.321%	Swiss-Prot	moderate database homology
`Q9LN71`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g12760	32.680%	Swiss-Prot	moderate database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	35.640%	Swiss-Prot	moderate database homology
`Q8GUU2`	Arabidopsis thaliana	E3 ubiquitin protein ligase RIE1	25.987%	Swiss-Prot	weak database homology

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