LXL04_004217 | RubberDandelionOmics

Gene overview

LXL04_004217

Reference: OH-1004 Chr: Chr01 Coordinates: 129734929-129737500 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1506 bp · LXL04_004217|LXL04_004217|OH1004|cDNA

ATGGCAATTGTGGAGCCTCCATGCAAAGGTTATGGTGCTTCGAGAATAGGTTGTGGTGTGTCTTTGATTTCTACTTTTCTCCCTCACCCATTTTCCAATCATTTTTACCTCCCGAGCTACAAAATTCCCATTTCCACTTCCTTCCACCAAACACAAACCCCTCAATTTCACCAAAGAGAAAGAGGGGAAATCTGTTTGAGAAAAGGACATCCCAAGAACAACCCCACAAATAGTTCAACAAATTCTCCACCAAAACAACT...

CDS

Download CDS FASTA

1506 bp · LXL04_004217|LXL04_004217|OH1004|CDS

ATGGCAATTGTGGAGCCTCCATGCAAAGGTTATGGTGCTTCGAGAATAGGTTGTGGTGTGTCTTTGATTTCTACTTTTCTCCCTCACCCATTTTCCAATCATTTTTACCTCCCGAGCTACAAAATTCCCATTTCCACTTCCTTCCACCAAACACAAACCCCTCAATTTCACCAAAGAGAAAGAGGGGAAATCTGTTTGAGAAAAGGACATCCCAAGAACAACCCCACAAATAGTTCAACAAATTCTCCACCAAAACAACT...

Protein

Download Protein FASTA

501 aa · LXL04_004217|LXL04_004217|OH1004|PROTEIN

MAIVEPPCKGYGASRIGCGVSLISTFLPHPFSNHFYLPSYKIPISTSFHQTQTPQFHQRERGEICLRKGHPKNNPTNSSTNSPPKQLLSHCPLRFLGGFQMEEGSEPTTYWCHGCSRVVETFTEAEMIKCSLCQDGFVEEYDSARSDHHNHQHAGDPESDSALSLWAPIFFGMMSDPRRRRRIRQIEHGENDENEDSEERYRRYQREGGESELDRELESIMTRRRRSSATIVQLLRTGLRTQSENIPDREGGENNRERDR...

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_004217`
TK1151 ID	TkA01G182930
OH-1004 ID	LXL04_004217
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.600
Protein coverage (%)	TK1151 95.859 / OH-1004 92.415 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004217

Location Chr01:129734929-129737500 (+)

Description Similar to SIRP1: E3 ubiquitin-protein ligase SIRP1

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
`At3g56580`	E3 ubiquitin-protein ligase that promotes osmotic stress and abscisic acid (ABA) responses.	The atrzf1 mutation of the novel RING-type E3 ubiquitin ligase increases proline contents and enhances drought tolerance in Arabidopsis.2013 · DOI: 10.1016/j.plantsci.2012.12.007 PCA22 acts as a suppressor of atrzf1 to mediate proline accumulation in response to abiotic stress in Arabidopsis.2017 · DOI: 10.1093/jxb/erx069
`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_004217 · 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:0006970 response to osmotic stress Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0047484 regulation of response to osmotic stress 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

KEGG gene cross-reference

ath:AT1G26800

ath:AT3G19950

ath:AT3G56580

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.

Cytoplasm0.555

Rank 1 · LXL04_004217 · OH-1004

Nucleus0.440

Rank 2 · LXL04_004217 · OH-1004

Cell membrane0.111

Rank 3 · LXL04_004217 · OH-1004

Endoplasmic reticulum0.084

Rank 4 · LXL04_004217 · OH-1004

Mitochondrion0.055

Rank 5 · LXL04_004217 · 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.

PF14369.12Zn_ribbon_19108-141 aa

PF13639.13zf-RING_2348-390 aa

PF17123.12zf-RING_11348-376 aa

PF13923.13zf-C3HC4_2348-389 aa

PF00097.32zf-C3HC4349-389 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004217	`PF14369.12`	Zn_ribbon_19	108	141	3.3e-08	34.2
LXL04_004217	`PF13639.13`	zf-RING_2	348	390	7.1e-14	52.5
LXL04_004217	`PF17123.12`	zf-RING_11	348	376	7.6e-10	39.0
LXL04_004217	`PF13923.13`	zf-C3HC4_2	348	389	1.7e-08	34.8
LXL04_004217	`PF00097.32`	zf-C3HC4	349	389	1.3e-06	28.9

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
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	48.077%	Swiss-Prot	weak database homology
`Q94AK4`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RZF1	32.192%	Swiss-Prot	moderate database homology
`Q9LQX2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MPSR1	39.073%	Swiss-Prot	weak database homology
`Q6AVN2`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase SIRP1	40.339%	Swiss-Prot	moderate database homology

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