LXL04_006664 | RubberDandelionOmics

Gene overview

LXL04_006664

Reference: OH-1004 Chr: Chr02 Coordinates: 21690417-21691790 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1290 bp · LXL04_006664|LXL04_006664|OH1004|cDNA

ATGTTTGTGGAAATGCCTGTGTTTTCGACGAGGAGATGTGGGGCTGGCGGGCAGGTTTTAGATCTAGAGACTGCTGTAAGAGATGGAGTGTTgggcggcggcggtggtggaggAGTTGGTTTCGGTGGTGGGTTTTCTGAGAAACTGGATCTGAGAAAGATGATTAGAGAGTTGGATTTGCCGGAGATTCCGTCGGTGTTCATTTGCCCGATTTCACTTGAACCGATGGAAGACCCAGTCACCCTGTGCACCGGCCAAAC...

CDS

Download CDS FASTA

1290 bp · LXL04_006664|LXL04_006664|OH1004|CDS

ATGTTTGTGGAAATGCCTGTGTTTTCGACGAGGAGATGTGGGGCTGGCGGGCAGGTTTTAGATCTAGAGACTGCTGTAAGAGATGGAGTGTTGGGCGGCGGCGGTGGTGGAGGAGTTGGTTTCGGTGGTGGGTTTTCTGAGAAACTGGATCTGAGAAAGATGATTAGAGAGTTGGATTTGCCGGAGATTCCGTCGGTGTTCATTTGCCCGATTTCACTTGAACCGATGGAAGACCCAGTCACCCTGTGCACCGGCCAAAC...

Protein

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429 aa · LXL04_006664|LXL04_006664|OH1004|PROTEIN

MFVEMPVFSTRRCGAGGQVLDLETAVRDGVLGGGGGGGVGFGGGFSEKLDLRKMIRELDLPEIPSVFICPISLEPMEDPVTLCTGQTYERSNILKWFAIGHFTCPTTMQELWDDSVTPNNTLHRLIHTWFSQKYFQKKKKSEDVQGLTSEILDTLKQIKGQARIQSLKELRQVVTAHVIARKTVVDKGGVSLLSSLLGPYTSHAIGSEVISILVHLNLDSSSKSNLTQPAKISLMVDMLNEGSIETKINCTQLLKLLIGD...

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_006664`
TK1151 ID	TkA03G055660
OH-1004 ID	LXL04_006664
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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

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Basic Information and Functional Annotation

Gene ID LXL04_006664

Location Chr02:21690417-21691790 (-)

Description Similar to PUB31: U-box domain-containing protein 31

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g65920`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g49810`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g35930`	E3 ubiquitin-protein ligase that negatively regulates water stress response.	Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress.2008 · DOI: 10.1105/tpc.108.060699 Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085
`At3g19380`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0232600`	E3 ubiquitin ligase that may function as positive regulator of brassinosteroid (BR) signaling.	The U-box E3 ubiquitin ligase TUD1 functions with a heterotrimeric G α subunit to regulate Brassinosteroid-mediated growth in rice.2013 · DOI: 10.1371/journal.pgen.1003391 An E3 ubiquitin ligase, ERECT LEAF1, functions in brassinosteroid signaling of rice.2013 · DOI: 10.4161/psb.27117

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006664 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002679 respiratory burst involved in defense response Biological Process

GO:0006952 defense response Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0071472 cellular response to salt stress Biological Process

GO:0098542 defense response to other organism Biological Process

GO:1900457 regulation of brassinosteroid mediated signaling pathway Biological Process

GO:1901001 negative regulation of response to salt stress Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT2G35930

ath:AT3G19380

ath:AT3G49810

ath:AT5G65920

dosa:Os03g0232600

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.

Nucleus0.548

Rank 1 · LXL04_006664 · OH-1004

Cytoplasm0.478

Rank 2 · LXL04_006664 · OH-1004

Cell membrane0.071

Rank 3 · LXL04_006664 · OH-1004

Endoplasmic reticulum0.041

Rank 4 · LXL04_006664 · OH-1004

Mitochondrion0.033

Rank 5 · LXL04_006664 · 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.

PF04564.22U-box63-133 aa

PF25598.2ARM_PUB150-371 aa

PF25598.2ARM_PUB377-428 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006664	`PF04564.22`	U-box	63	133	4.2e-15	56.4
LXL04_006664	`PF25598.2`	ARM_PUB	150	371	7.7e-56	190.5
LXL04_006664	`PF25598.2`	ARM_PUB	377	428	7.7e-56	190.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FHN9`	Arabidopsis thaliana	U-box domain-containing protein 31	59.912%	Swiss-Prot	strong database homology
`Q058P4`	Arabidopsis thaliana	U-box domain-containing protein 30	61.937%	Swiss-Prot	strong database homology
`Q84TG3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase PUB23	25.679%	Swiss-Prot	weak database homology
`Q9LT79`	Arabidopsis thaliana	U-box domain-containing protein 25	28.462%	Swiss-Prot	weak database homology
`Q10PI9`	Oryza sativa subsp. japonica	U-box domain-containing protein 75	49.362%	Swiss-Prot	moderate database homology

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