LXL04_037042 | RubberDandelionOmics

Gene overview

LXL04_037042

Reference: OH-1004 Chr: Chr08 Coordinates: 52155121-52156903 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

804 bp · LXL04_037042|LXL04_037042|OH1004|cDNA

ATGCAAACGCCAGACACTCCCCTCGAAACCTCACCCATGGCGGACGACGATACTCCTTCACTTCAAACCAACCCTCAAGATTTTCAAAAATCGCTTCACGGGTGCAATCATTACAGGAGACGATGCAAAATTCGTGCTCCGTGTTGTAATCAGATATTTTTCTGCCGCCATTGTCACAACGAAGCCACGAGCGCGTTGGCAAACCCAAAGGAACGCCATGAAATTGTTCGGCACGATATTAAACAAGTTATATGTGCAAT...

CDS

Download CDS FASTA

804 bp · LXL04_037042|LXL04_037042|OH1004|CDS

ATGCAAACGCCAGACACTCCCCTCGAAACCTCACCCATGGCGGACGACGATACTCCTTCACTTCAAACCAACCCTCAAGATTTTCAAAAATCGCTTCACGGGTGCAATCATTACAGGAGACGATGCAAAATTCGTGCTCCGTGTTGTAATCAGATATTTTTCTGCCGCCATTGTCACAACGAAGCCACGAGCGCGTTGGCAAACCCAAAGGAACGCCATGAAATTGTTCGGCACGATATTAAACAAGTTATATGTGCAAT...

Protein

Download Protein FASTA

267 aa · LXL04_037042|LXL04_037042|OH1004|PROTEIN

MQTPDTPLETSPMADDDTPSLQTNPQDFQKSLHGCNHYRRRCKIRAPCCNQIFFCRHCHNEATSALANPKERHEIVRHDIKQVICAICNTEQQVAHICINCGVKMGEYFCGICKFYDDDVNTKHHLSFILFYSIENKRFQKNSFIAMTVGYVELEALRNSSIAKSVVWRSCYDVSLRDIHACLENSTKNHCPICYEFIFDSTKGATIIKCGHTMHLDCYEEMIIKNQYRCPICSKSMCNMSRTWQRLDQEIEATAMPEEY...

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_037042`
TK1151 ID	TkA04G008750
OH-1004 ID	LXL04_037042
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	80.900
Protein coverage (%)	TK1151 86.268 / OH-1004 99.625 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

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Basic Information and Functional Annotation

Gene ID LXL04_037042

Location Chr08:52155121-52156903 (+)

Description Similar to MIEL1: E3 ubiquitin-protein ligase MIEL1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g18650`	E3 ubiquitin-protein ligase that acts as a regulator of cell death and defense.	Arabidopsis ubiquitin ligase MIEL1 mediates degradation of the transcription factor MYB30 weakening plant defence.2013 · DOI: 10.1038/ncomms2479
`At5g22920`	Possesses E3 ubiquitin-protein ligase activity in vitro.	Expression of a gene encoding a rice RING zinc-finger protein, OsRZFP34, enhances stomata opening.2014 · DOI: 10.1007/s11103-014-0217-6 Arabidopsis RZFP34/CHYR1, a Ubiquitin E3 Ligase, Regulates Stomatal Movement and Drought Tolerance via SnRK2.6-Mediated Phosphorylation.2015 · DOI: 10.1105/tpc.15.00321

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0348900`	Possesses E3 ubiquitin-protein ligase activity in vitro.	Knock-down of stress inducible OsSRFP1 encoding an E3 ubiquitin ligase with transcriptional activation activity confers abiotic stress tolerance through enhancing antioxidant protection in rice.2015 · DOI: 10.1007/s11103-015-0294-1
`Os01g0719100`	Possesses transactivation activity in yeast cells (Ref.1).	Expression of a gene encoding a rice RING zinc-finger protein, OsRZFP34, enhances stomata opening.2014 · DOI: 10.1007/s11103-014-0217-6

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037042 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006952 defense response Biological Process

GO:0010255 glucose mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031398 positive regulation of protein ubiquitination Biological Process

GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0072344 rescue of stalled cytosolic ribosome Biological Process

GO:1900425 negative regulation of defense response to bacterium Biological Process

GO:1902456 regulation of stomatal opening Biological Process

GO:0000151 ubiquitin ligase complex Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT5G18650

ath:AT5G22920

dosa:Os01g0719100

dosa:Os03g0348900

mmu:68098

osa:4324695

osa:4332833

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.

Cytoplasm0.543

Rank 1 · LXL04_037042 · OH-1004

Nucleus0.479

Rank 2 · LXL04_037042 · OH-1004

Mitochondrion0.071

Rank 3 · LXL04_037042 · OH-1004

Cell membrane0.054

Rank 4 · LXL04_037042 · OH-1004

Endoplasmic reticulum0.047

Rank 5 · LXL04_037042 · 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.

PF05495.18zf-CHY35-108 aa

PF13639.13zf-RING_2189-233 aa

PF14634.13zf-RING_5190-235 aa

PF00097.32zf-C3HC4191-233 aa

PF13923.13zf-C3HC4_2191-233 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037042	`PF05495.18`	zf-CHY	35	108	4.3e-19	69.4
LXL04_037042	`PF13639.13`	zf-RING_2	189	233	9.9e-08	32.8
LXL04_037042	`PF14634.13`	zf-RING_5	190	235	5.2e-07	30.2
LXL04_037042	`PF00097.32`	zf-C3HC4	191	233	1.3e-06	28.9
LXL04_037042	`PF13923.13`	zf-C3HC4_2	191	233	2.4e-06	27.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8VZK0`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MIEL1	51.639%	Swiss-Prot	strong database homology
`Q9FFB6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RZFP34	43.515%	Swiss-Prot	moderate database homology
`Q10LI1`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase SRFP1	46.352%	Swiss-Prot	moderate database homology
`Q5JL96`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase RZFP34	41.270%	Swiss-Prot	moderate database homology

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