LXL04_026490 | RubberDandelionOmics

Gene overview

LXL04_026490

Reference: OH-1004 Chr: Chr05 Coordinates: 127243757-127244383 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

627 bp · LXL04_026490|LXL04_026490|OH1004|cDNA

ATGACACCTGGATCCGAGAACAACGAAGAGGCAACCGGAAACAGAGACAGCACCCAGGAACACGTTATTCTGATCAATCCTTTCAACCGGTCTATCATTGTCCATGGCGGCAATGGTGGCGGCAACCCCTTCGATACTGGCAACCTCTCGCCCAACAACCCTTTTGGATCTTTCGGCGATTATTTCATCGGCCCTGGTTTAGAGCAACTTTTACAGCATCTATCCGAAAACGACCCGAACAAATACGGAACCCCACCCGC...

CDS

Download CDS FASTA

627 bp · LXL04_026490|LXL04_026490|OH1004|CDS

ATGACACCTGGATCCGAGAACAACGAAGAGGCAACCGGAAACAGAGACAGCACCCAGGAACACGTTATTCTGATCAATCCTTTCAACCGGTCTATCATTGTCCATGGCGGCAATGGTGGCGGCAACCCCTTCGATACTGGCAACCTCTCGCCCAACAACCCTTTTGGATCTTTCGGCGATTATTTCATCGGCCCTGGTTTAGAGCAACTTTTACAGCATCTATCCGAAAACGACCCGAACAAATACGGAACCCCACCCGC...

Protein

Download Protein FASTA

208 aa · LXL04_026490|LXL04_026490|OH1004|PROTEIN

MTPGSENNEEATGNRDSTQEHVILINPFNRSIIVHGGNGGGNPFDTGNLSPNNPFGSFGDYFIGPGLEQLLQHLSENDPNKYGTPPAQKEAIEAMPKVKIEQDSIQCSVCLEEFEIGNEAREMPCKHMFHGDCILPWLELHSSCPVCRYQMPADESKIDREREGSGGIVGNSSGVNGESGNRNSEERRFSVSLPWPLSLLSSPRANTK

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_026490`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_026490

Location Chr05:127243757-127244383 (+)

Description Similar to RING1: E3 ubiquitin-protein ligase RING1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At2g40830`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At1g26800`	E3 ubiquitin-protein ligase involved in protein quality control (PQC) under proteotoxic stress.	MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana.2017 · DOI: 10.1073/pnas.1713574114

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

View annotation sources

Functional annotation source: OH1004 · LXL04_026490 · 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:0009651 response to salt stress Biological Process

GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0061635 regulation of protein complex stability Biological Process

GO:0071218 cellular response to misfolded protein Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system Biological Process

GO:0090378 seed trichome elongation Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G26800

ath:AT2G40830

ath:AT3G19950

dosa:Os05g0488800

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.

Cytoplasm0.694

Rank 1 · LXL04_026490 · OH-1004

Nucleus0.446

Rank 2 · LXL04_026490 · OH-1004

Endoplasmic reticulum0.071

Rank 3 · LXL04_026490 · OH-1004

Cell membrane0.059

Rank 4 · LXL04_026490 · OH-1004

Golgi apparatus0.049

Rank 5 · LXL04_026490 · 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.

PF12678.14zf-rbx1100-148 aa

PF13639.13zf-RING_2106-148 aa

PF17123.12zf-RING_11106-134 aa

PF13923.13zf-C3HC4_2106-147 aa

PF00097.32zf-C3HC4107-147 aa

PF13445.13zf-RING_UBOX107-145 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026490	`PF12678.14`	zf-rbx1	100	148	2.3e-06	28.5
LXL04_026490	`PF13639.13`	zf-RING_2	106	148	5.4e-15	56.1
LXL04_026490	`PF17123.12`	zf-RING_11	106	134	1.1e-10	41.7
LXL04_026490	`PF13923.13`	zf-C3HC4_2	106	147	4.6e-10	39.9
LXL04_026490	`PF00097.32`	zf-C3HC4	107	147	2.9e-07	31.0
LXL04_026490	`PF13445.13`	zf-RING_UBOX	107	145	1.9e-06	28.5

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
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	51.553%	Swiss-Prot	strong database homology
`O22197`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHC1A	50.485%	Swiss-Prot	weak database homology
`Q9LQX2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MPSR1	38.889%	Swiss-Prot	moderate database homology
`Q6AVN2`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase SIRP1	42.500%	Swiss-Prot	moderate database homology

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