LXL04_005738 | RubberDandelionOmics

Gene overview

LXL04_005738

Reference: OH-1004 Chr: Chr01 Coordinates: 172466273-172467521 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

675 bp · LXL04_005738|LXL04_005738|OH1004|cDNA

ATGGGGTACCTTCAAACTTCAAGTACAAGTGGTGATGTTAGCTCTCACTTGTATTCTCAAGCACTTCAAATGAAGTTATACCAAGCATTCATATTTTCCATTCCAATACTCTTCTCCATAATACTTTTTCTCCTGTTTTACTTGTTCTACCTCAAAAGAACTTTTAGCAACACCAATTCTTCATCTTCTGCATCTATTCTCCATCTAAGAACCTCAAGGAATCAAGATTCTTCAACTCTTCATCAATATATCGATACGGG...

CDS

Download CDS FASTA

675 bp · LXL04_005738|LXL04_005738|OH1004|CDS

ATGGGGTACCTTCAAACTTCAAGTACAAGTGGTGATGTTAGCTCTCACTTGTATTCTCAAGCACTTCAAATGAAGTTATACCAAGCATTCATATTTTCCATTCCAATACTCTTCTCCATAATACTTTTTCTCCTGTTTTACTTGTTCTACCTCAAAAGAACTTTTAGCAACACCAATTCTTCATCTTCTGCATCTATTCTCCATCTAAGAACCTCAAGGAATCAAGATTCTTCAACTCTTCATCAATATATCGATACGGG...

Protein

Download Protein FASTA

224 aa · LXL04_005738|LXL04_005738|OH1004|PROTEIN

MGYLQTSSTSGDVSSHLYSQALQMKLYQAFIFSIPILFSIILFLLFYLFYLKRTFSNTNSSSSASILHLRTSRNQDSSTLHQYIDTGSKINLEDKLSVILFDEDLYTKDSMCCVCLGEFEMDEKLHQIPSCQHMFHGDCIRNWLHSNFTCPLCRCSVVVSAAKDSHHEPPVVPEPATMTNMSSSSQGVPLEHSVIIFDEGSSSSSMDNKLSHPNQESVVISVYP

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_005738`
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_005738

Location Chr01:172466273-172467521 (+)

Description Similar to RHA4A: Probable E3 ubiquitin-protein ligase RHA4A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g24015`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At4g10150`	RING-H2 finger protein ATL7.	No verified direct reference in this release
`At1g33480`	RING-H2 finger protein ATL58.	No verified direct reference in this release
`At4g10160`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, and UBC34 in vitro.	No verified direct reference in this release
`At1g23980`	RING-H2 finger protein ATL47.	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_005738 · 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: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:AT1G23980

ath:AT1G33480

ath:AT4G10150

ath:AT4G10160

ath:AT4G24015

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 / Vacuole0.257

Rank 1 · LXL04_005738 · OH-1004

Cytoplasm0.247

Rank 2 · LXL04_005738 · OH-1004

Cell membrane0.235

Rank 3 · LXL04_005738 · OH-1004

Endoplasmic reticulum0.220

Rank 4 · LXL04_005738 · OH-1004

Nucleus0.215

Rank 5 · LXL04_005738 · 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_2111-154 aa

PF13923.13zf-C3HC4_2111-153 aa

PF17123.12zf-RING_11112-140 aa

PF12678.14zf-rbx1124-154 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005738	`PF13639.13`	zf-RING_2	111	154	2.2e-12	47.7
LXL04_005738	`PF13923.13`	zf-C3HC4_2	111	153	3.1e-06	27.6
LXL04_005738	`PF17123.12`	zf-RING_11	112	140	6.5e-07	29.6
LXL04_005738	`PF12678.14`	zf-rbx1	124	154	5.3e-07	30.5

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
`Q84TF5`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHA4A	60.131%	Swiss-Prot	moderate database homology
`Q9SN28`	Arabidopsis thaliana	RING-H2 finger protein ATL7	38.000%	Swiss-Prot	moderate database homology
`Q570X5`	Arabidopsis thaliana	RING-H2 finger protein ATL58	37.374%	Swiss-Prot	moderate database homology
`Q9SN27`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL59	32.911%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	40.000%	Swiss-Prot	moderate database homology

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