LXL04_026998 | RubberDandelionOmics

Gene overview

LXL04_026998

Reference: OH-1004 Chr: Chr06 Coordinates: 6693596-6695111 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1419 bp · LXL04_026998|LXL04_026998|OH1004|cDNA

ATGGTGTCTTTAGAAGAAACTCATCGTTCTAGGTCCTCCATAGCTCGACCTTACCCTTACTACACCCCaccttcatcttcttcttcacctTCCAGAAGCAAGCATATGGGTCGCTCCATGAGAACGATTCGTTCAAACTTTTACCAGTCCGATTACAGCAACGCGTGTTCCTTCACATCCACTGATGTCCCTGTAAACGATGAAAACTTAAGCGATTCTGTCATTGATGTTCGTTTGCAGGAGCTTGCTACAGCTACGTG...

CDS

Download CDS FASTA

1419 bp · LXL04_026998|LXL04_026998|OH1004|CDS

ATGGTGTCTTTAGAAGAAACTCATCGTTCTAGGTCCTCCATAGCTCGACCTTACCCTTACTACACCCCACCTTCATCTTCTTCTTCACCTTCCAGAAGCAAGCATATGGGTCGCTCCATGAGAACGATTCGTTCAAACTTTTACCAGTCCGATTACAGCAACGCGTGTTCCTTCACATCCACTGATGTCCCTGTAAACGATGAAAACTTAAGCGATTCTGTCATTGATGTTCGTTTGCAGGAGCTTGCTACAGCTACGTG...

Protein

Download Protein FASTA

472 aa · LXL04_026998|LXL04_026998|OH1004|PROTEIN

MVSLEETHRSRSSIARPYPYYTPPSSSSSPSRSKHMGRSMRTIRSNFYQSDYSNACSFTSTDVPVNDENLSDSVIDVRLQELATATCGSNRKSLNSASSTMSSDDFLEISQAFSDFSAYSSDISGELQRLACFPEELKEGDSDKNREEKSELEPCEGFLQRESFSTEIIEIISPEDLQPTVKICVDSLRSSSVAMKRSAAAKLRLLAKNRSDNRALIGESGAIPELITLLRCTDPWTQEHAVTAILNLSLLDANKPLIAN...

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_026998`
TK1151 ID	TkA07G023670
OH-1004 ID	LXL04_026998
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_026998

Location Chr06:6693596-6695111 (-)

Description Similar to PUB4: U-box domain-containing protein 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g23140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g67340`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g54790`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g23030`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0102700`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026998 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G23140

ath:AT3G54790

ath:AT5G67340

dosa:Os06g0102700

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.

Cytoplasm0.486

Rank 1 · LXL04_026998 · OH-1004

Nucleus0.383

Rank 2 · LXL04_026998 · OH-1004

Cell membrane0.230

Rank 3 · LXL04_026998 · OH-1004

Endoplasmic reticulum0.050

Rank 4 · LXL04_026998 · OH-1004

Golgi apparatus0.037

Rank 5 · LXL04_026998 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF24768.2ARM_ARMC5182-312 aa

PF25598.2ARM_PUB196-465 aa

PF00514.30Arm211-249 aa

PF24768.2ARM_ARMC5245-423 aa

PF00514.30Arm293-332 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026998	`PF24768.2`	ARM_ARMC5	182	312	1.7e-19	71.0
LXL04_026998	`PF25598.2`	ARM_PUB	196	465	4.6e-24	86.1
LXL04_026998	`PF00514.30`	Arm	211	249	1.1e-25	89.4
LXL04_026998	`PF24768.2`	ARM_ARMC5	245	423	1.7e-19	71.0
LXL04_026998	`PF00514.30`	Arm	293	332	1.1e-25	89.4

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
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	43.878%	Swiss-Prot	moderate database homology
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	47.931%	Swiss-Prot	moderate database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	46.503%	Swiss-Prot	moderate database homology
`Q8GUG9`	Arabidopsis thaliana	U-box domain-containing protein 11	41.993%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	46.753%	Swiss-Prot	weak database homology

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