LXL04_035767 | RubberDandelionOmics

Gene overview

LXL04_035767

Reference: OH-1004 Chr: Chr08 Coordinates: 28538905-28541692 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2430 bp · LXL04_035767|LXL04_035767|OH1004|cDNA

ATGTCGGTAAGCCGGAATGGAAGTCGTGACCTTGGTAGCCAATCAGACGACAGCTTCCAATACGAAAGACCACACGTAGAGCCAATTTACGACACATTCATCTGCCCTCTTTCAAAACAAATCATGAGAAACCCAGTCACGATTGAAAACGGGCAAACATTTGAGCGAGAAGCCATTGAGAAATGGTTCAATGAATGCAAGGAGAACGGAAGAAAGCTGACGTGTCCCTTAACATTAAAAGAACTAAAAACAACAGACAT...

CDS

Download CDS FASTA

2430 bp · LXL04_035767|LXL04_035767|OH1004|CDS

ATGTCGGTAAGCCGGAATGGAAGTCGTGACCTTGGTAGCCAATCAGACGACAGCTTCCAATACGAAAGACCACACGTAGAGCCAATTTACGACACATTCATCTGCCCTCTTTCAAAACAAATCATGAGAAACCCAGTCACGATTGAAAACGGGCAAACATTTGAGCGAGAAGCCATTGAGAAATGGTTCAATGAATGCAAGGAGAACGGAAGAAAGCTGACGTGTCCCTTAACATTAAAAGAACTAAAAACAACAGACAT...

Protein

Download Protein FASTA

809 aa · LXL04_035767|LXL04_035767|OH1004|PROTEIN

MSVSRNGSRDLGSQSDDSFQYERPHVEPIYDTFICPLSKQIMRNPVTIENGQTFEREAIEKWFNECKENGRKLTCPLTLKELKTTDMNPSIALRNTIEEWSARNEAVQLDMASKSLSPGSSESDSLHALKFIQQLCTKNLSSKNIIRNADLIPMIVEMLKSTSRKVRCIAFETLRVVVEDDDDNKEIMAEGDKVRTIVKFLNHEQSQEREEAVSLLYELSKSEALCEKIGSVNGAILILVGMTSSKSENLLIVEKAEKVL...

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_035767`
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_035767

Location Chr08:28538905-28541692 (+)

Description Similar to PUB43: U-box domain-containing protein 43

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76390`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`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
`At1g68940`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g42340`	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_035767 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006970 response to osmotic stress Biological Process

GO:0007166 cell surface receptor signaling pathway 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:0090359 negative regulation of abscisic acid biosynthetic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G20780

ath:AT1G76390

ath:AT5G42340

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.

Cytoplasm0.501

Rank 1 · LXL04_035767 · OH-1004

Nucleus0.366

Rank 2 · LXL04_035767 · OH-1004

Cell membrane0.201

Rank 3 · LXL04_035767 · OH-1004

Golgi apparatus0.057

Rank 4 · LXL04_035767 · OH-1004

Endoplasmic reticulum0.056

Rank 5 · LXL04_035767 · 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.

PF04564.22U-box31-105 aa

PF24768.2ARM_ARMC5117-288 aa

PF25598.2ARM_PUB117-224 aa

PF25598.2ARM_PUB236-391 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035767	`PF04564.22`	U-box	31	105	3.4e-14	53.5
LXL04_035767	`PF24768.2`	ARM_ARMC5	117	288	4e-13	50.1
LXL04_035767	`PF25598.2`	ARM_PUB	117	224	2.7e-08	34.3
LXL04_035767	`PF25598.2`	ARM_PUB	236	391	2.7e-08	34.3

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
`Q9SFX2`	Arabidopsis thaliana	U-box domain-containing protein 43	61.586%	Swiss-Prot	strong database homology
`Q9LM76`	Arabidopsis thaliana	U-box domain-containing protein 44	60.936%	Swiss-Prot	strong database homology
`Q9CAA7`	Arabidopsis thaliana	Putative U-box domain-containing protein 42	34.430%	Swiss-Prot	moderate database homology
`Q681N2`	Arabidopsis thaliana	U-box domain-containing protein 15	24.773%	Swiss-Prot	weak database homology
`Q10FT0`	Oryza sativa subsp. japonica	U-box domain-containing protein 24	50.925%	Swiss-Prot	strong database homology

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