LXL04_002771 | RubberDandelionOmics

Gene overview

LXL04_002771

Reference: OH-1004 Chr: Chr01 Coordinates: 57984346-57989723 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

555 bp · LXL04_002771|LXL04_002771|OH1004|cDNA

ATGGCTGGTAAGATACCTGGAGTCGAAATCGCTCGGCGGAGGAGGTTCGGTGGGTGGTCTGATAATCCGTCGTTTCTCATCAACTCTGCTTTTGGGTCTGCACGAAGCAGAGTTTTTTACCATAGCCATCTCACCTCCACTTCTTTCTCGCAAAGAAGATCAGATGAAGATGAGAAGCTTGGAGGTGTAGCCAGAAAAGCCAAACATAGACTTGATGAGAAGCTCAGAGGCCACTGTAAATCAGAAATCGACAGCCAAGA...

CDS

Download CDS FASTA

555 bp · LXL04_002771|LXL04_002771|OH1004|CDS

ATGGCTGGTAAGATACCTGGAGTCGAAATCGCTCGGCGGAGGAGGTTCGGTGGGTGGTCTGATAATCCGTCGTTTCTCATCAACTCTGCTTTTGGGTCTGCACGAAGCAGAGTTTTTTACCATAGCCATCTCACCTCCACTTCTTTCTCGCAAAGAAGATCAGATGAAGATGAGAAGCTTGGAGGTGTAGCCAGAAAAGCCAAACATAGACTTGATGAGAAGCTCAGAGGCCACTGTAAATCAGAAATCGACAGCCAAGA...

Protein

Download Protein FASTA

184 aa · LXL04_002771|LXL04_002771|OH1004|PROTEIN

MAGKIPGVEIARRRRFGGWSDNPSFLINSAFGSARSRVFYHSHLTSTSFSQRRSDEDEKLGGVARKAKHRLDEKLRGHCKSEIDSQERSEIGTKSSACMVVGDRQMEVFGLKKNGSKRFSWGRLWLNWKSSNQEECAVCLEKFKFSEKVTRMPCAHKFHSICLLPWLKSHAHCPCCRTSVLGST

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_002771`
TK1151 ID	TkA01G422060
OH-1004 ID	LXL04_002771
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.400
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_002771

Location Chr01:57984346-57989723 (-)

Description Similar to RHY1A: Probable E3 ubiquitin-protein ligase RHY1A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g49850`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At3g19950`	E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0488800`	Possesses E3 ubiqutin-protein ligase activity in vitro.	Molecular dissection of Oryza sativa salt-induced RING Finger Protein 1 (OsSIRP1): possible involvement in the sensitivity response to salinity stress.2016 · DOI: 10.1111/ppl.12459

Functional annotation source

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Functional annotation source: OH1004 · LXL04_002771 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0006893 Golgi to plasma membrane transport Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0034122 negative regulation of toll-like receptor signaling pathway Biological Process

GO:0034123 positive regulation of toll-like receptor signaling pathway Biological Process

GO:0034142 toll-like receptor 4 signaling pathway Biological Process

GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway Biological Process

GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0070534 protein K63-linked ubiquitination Biological Process

KEGG gene cross-reference

ath:AT1G49850

ath:AT3G19950

dme:Dmel_CG11982

dosa:Os05g0488800

mmu:67845

osa:4339152

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.

Nucleus0.591

Rank 1 · LXL04_002771 · OH-1004

Cytoplasm0.315

Rank 2 · LXL04_002771 · OH-1004

Cell membrane0.122

Rank 3 · LXL04_002771 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_002771 · OH-1004

Mitochondrion0.045

Rank 5 · LXL04_002771 · 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_2135-177 aa

PF17123.12zf-RING_11135-163 aa

PF13923.13zf-C3HC4_2135-176 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002771	`PF13639.13`	zf-RING_2	135	177	2.7e-12	47.5
LXL04_002771	`PF17123.12`	zf-RING_11	135	163	2.4e-09	37.4
LXL04_002771	`PF13923.13`	zf-C3HC4_2	135	176	8.2e-08	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
`Q852U6`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHY1A	31.884%	Swiss-Prot	moderate database homology
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	51.064%	Swiss-Prot	weak database homology
`Q6AVN2`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase SIRP1	52.381%	Swiss-Prot	weak database homology

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