LXL04_010928 | RubberDandelionOmics

Gene overview

LXL04_010928

Reference: OH-1004 Chr: Chr02 Coordinates: 155250491-155254221 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2868 bp · LXL04_010928|LXL04_010928|OH1004|cDNA

ATGATTGCAAGTCCGCAATCATGGTTCGAGTCCACTCCATCGTTGGTTGTTACCAACCACGATTTAAATAATCCCGGCCACCTACGGCATCAGCCGCCGTCCCCCCCAATTCCATACGCCACTTCGAagtttttgttgtttcttgtttgtCTTTCCCTCGACCCTCCGGTCACGTCATTTGGAAGTTTCTCCTCACTCTTTCTTTATGCCTTTTGCTTTCATCTTCAACGCAACAAGTTGGAAAATGAACCCCGAAGACG...

CDS

Download CDS FASTA

2868 bp · LXL04_010928|LXL04_010928|OH1004|CDS

ATGATTGCAAGTCCGCAATCATGGTTCGAGTCCACTCCATCGTTGGTTGTTACCAACCACGATTTAAATAATCCCGGCCACCTACGGCATCAGCCGCCGTCCCCCCCAATTCCATACGCCACTTCGAAGTTTTTGTTGTTTCTTGTTTGTCTTTCCCTCGACCCTCCGGTCACGTCATTTGGAAGTTTCTCCTCACTCTTTCTTTATGCCTTTTGCTTTCATCTTCAACGCAACAAGTTGGAAAATGAACCCCGAAGACG...

Protein

Download Protein FASTA

955 aa · LXL04_010928|LXL04_010928|OH1004|PROTEIN

MIASPQSWFESTPSLVVTNHDLNNPGHLRHQPPSPPIPYATSKFLLFLVCLSLDPPVTSFGSFSSLFLYAFCFHLQRNKLENEPRRRSQPPYLLPSFNPLTVFRHLGFIFQMEGSNHSVIASDSDETTNSVSKDSETLSDFTHSTRKLGVILTEFKENKIMETSPIRKAVDSLETELQRAKALVASPLYSSSPKNRIEDITENLGRSIGLVLFASHDVSLTGKEKLETLRREMMSVAQFSAASSDSKSDFLDDVYTEQND...

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_010928`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_010928

Location Chr02:155250491-155254221 (-)

Description Similar to PUB44: U-box domain-containing protein 44

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20780`	Functions as an E3 ubiquitin-protein ligase.	Identification of a novel E3 ubiquitin ligase that is required for suppression of premature senescence in Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2009.03846.x
`At1g76390`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At1g68940`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g23140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0657100`	E3 ubiquitin-protein ligase that functions as a negative regulator of brassinosteroid (BR) signaling.	OsBZR1 turnover mediated by OsSK22-regulated U-box E3 ligase OsPUB24 in rice BR response.2019 · DOI: 10.1111/tpj.14332

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010928 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006970 response to osmotic stress Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0010115 regulation of abscisic acid biosynthetic process Biological Process

GO:0010150 leaf senescence Biological Process

GO:0010271 regulation of chlorophyll catabolic process Biological Process

GO:0010380 regulation of chlorophyll biosynthetic process Biological Process

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:0090359 negative regulation of abscisic acid biosynthetic process Biological Process

GO:1904821 chloroplast disassembly Biological Process

KEGG gene cross-reference

ath:AT1G20780

ath:AT1G76390

ath:AT2G23140

dosa:Os03g0657100

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Cytoplasm0.428

Rank 1 · LXL04_010928 · OH-1004

Nucleus0.410

Rank 2 · LXL04_010928 · OH-1004

Cell membrane0.200

Rank 3 · LXL04_010928 · OH-1004

Endoplasmic reticulum0.070

Rank 4 · LXL04_010928 · OH-1004

Golgi apparatus0.043

Rank 5 · LXL04_010928 · 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.

PF24768.2ARM_ARMC5329-481 aa

PF25598.2ARM_PUB381-577 aa

PF24768.2ARM_ARMC5574-782 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010928	`PF24768.2`	ARM_ARMC5	329	481	6.5e-18	65.8
LXL04_010928	`PF25598.2`	ARM_PUB	381	577	2e-11	44.6
LXL04_010928	`PF24768.2`	ARM_ARMC5	574	782	6.5e-18	65.8

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
`Q9LM76`	Arabidopsis thaliana	U-box domain-containing protein 44	26.736%	Swiss-Prot	weak database homology
`Q9SFX2`	Arabidopsis thaliana	U-box domain-containing protein 43	26.284%	Swiss-Prot	weak database homology
`Q9CAA7`	Arabidopsis thaliana	Putative U-box domain-containing protein 42	25.371%	Swiss-Prot	weak database homology
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	27.848%	Swiss-Prot	weak database homology
`Q10FT0`	Oryza sativa subsp. japonica	U-box domain-containing protein 24	25.105%	Swiss-Prot	weak database homology

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