LXL04_026642 | RubberDandelionOmics

Gene overview

LXL04_026642

Reference: OH-1004 Chr: Chr06 Coordinates: 796205-800990 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2715 bp · LXL04_026642|LXL04_026642|OH1004|cDNA

ATGGAATGGGAGGCAGACGATGGGAGGGAGGCGGTGGTGGTAAGGTTGATAGAGAAGGCTACCAACTCAACTAAACCTGACTTGGATCCGCGAATCCTCAAATCAATCAAATCGGTTGTCCGTCACTCTGATTTGGAGCTCCGTCTCGCGGTCGAAAACCTAATGAGTCTCATGAAACAAGGCCACTCTCAGATACGGTACCTGGCACTAACCATAATCCATGAACTATTCATGCGATCAAAGCTTTTCAGAAGCCTTAT...

CDS

Download CDS FASTA

2715 bp · LXL04_026642|LXL04_026642|OH1004|CDS

ATGGAATGGGAGGCAGACGATGGGAGGGAGGCGGTGGTGGTAAGGTTGATAGAGAAGGCTACCAACTCAACTAAACCTGACTTGGATCCGCGAATCCTCAAATCAATCAAATCGGTTGTCCGTCACTCTGATTTGGAGCTCCGTCTCGCGGTCGAAAACCTAATGAGTCTCATGAAACAAGGCCACTCTCAGATACGGTACCTGGCACTAACCATAATCCATGAACTATTCATGCGATCAAAGCTTTTCAGAAGCCTTAT...

Protein

Download Protein FASTA

904 aa · LXL04_026642|LXL04_026642|OH1004|PROTEIN

MEWEADDGREAVVVRLIEKATNSTKPDLDPRILKSIKSVVRHSDLELRLAVENLMSLMKQGHSQIRYLALTIIHELFMRSKLFRSLIVGNLEQLLTLSVGFRRNQPLPAPPAIASKLRLKAIEFLERWNTTFGVHYRQLRLGHDYLKNTLRFQFPNLQANAARVQQERRERELRTKEILIKKYEQLKSNLPSIKDEVKSIVDEITECLDILESSKEKNLPLSPIDEEDFVEFRSIELQQIRANSLLEADKVEENSENKVV...

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_026642`
TK1151 ID	TkAUNG081130
OH-1004 ID	LXL04_026642
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.500
Protein coverage (%)	TK1151 91.297 / OH-1004 63.938 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_026642

Location Chr06:796205-800990 (+)

Description Similar to At3g61800: UV-stimulated scaffold protein A homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g61800`	UV-stimulated scaffold protein A homolog.	No verified direct reference in this release
`At4g27880`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267
`At5g53360`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals.2002 · DOI: 10.1038/nature00998 SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants.2020 · DOI: 10.1111/jipb.13005
`At3g61790`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0356414`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	The SINA E3 ligase OsDIS1 negatively regulates drought response in rice.2011 · DOI: 10.1104/pp.111.180893

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026642 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006283 transcription-coupled nucleotide-excision repair Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009411 response to UV Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0080148 negative regulation of response to water deprivation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005694 chromosome Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005776 autophagosome Cellular Component

GO:0005886 plasma membrane Cellular Component

KEGG gene cross-reference

ath:AT3G61790

ath:AT3G61800

ath:AT4G27880

ath:AT5G53360

dosa:Os03g0356414

osa:9266295

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.

Nucleus0.799

Rank 1 · LXL04_026642 · OH-1004

Cytoplasm0.249

Rank 2 · LXL04_026642 · OH-1004

Cell membrane0.033

Rank 3 · LXL04_026642 · OH-1004

Mitochondrion0.024

Rank 4 · LXL04_026642 · OH-1004

Endoplasmic reticulum0.022

Rank 5 · LXL04_026642 · 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.

PF20867.4UVSSA_N14-149 aa

PF09740.15DUF2043387-488 aa

PF21362.4Sina_RING644-679 aa

PF21361.4Sina_ZnF693-768 aa

PF03145.23Sina_TRAF788-885 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026642	`PF20867.4`	UVSSA_N	14	149	9.6e-36	123.2
LXL04_026642	`PF09740.15`	DUF2043	387	488	1.7e-31	109.8
LXL04_026642	`PF21362.4`	Sina_RING	644	679	1.8e-12	47.9
LXL04_026642	`PF21361.4`	Sina_ZnF	693	768	8.4e-29	100.5
LXL04_026642	`PF03145.23`	Sina_TRAF	788	885	8.6e-35	119.9

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
`Q9M358`	Arabidopsis thaliana	UV-stimulated scaffold protein A homolog	49.689%	Swiss-Prot	moderate database homology
`Q9STN8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT4	80.000%	Swiss-Prot	weak database homology
`Q8S3N1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT5	82.253%	Swiss-Prot	weak database homology
`Q84JL3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT3	86.738%	Swiss-Prot	weak database homology
`Q10L91`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase DIS1	81.712%	Swiss-Prot	weak database homology

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