LXL04_000789 | RubberDandelionOmics

Gene overview

LXL04_000789

Reference: OH-1004 Chr: Chr01 Coordinates: 14412027-14413517 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1491 bp · LXL04_000789|LXL04_000789|OH1004|cDNA

ATGGCGAAAAGCGGGGTGTTTGAAAGGGATCCCACCGCCGCAACGAAGGTGGCCACCGACAACTTGAAGAAGGAATTACAGCGACTTGTTAATTCGATTGTGGAGGGATCTTCACCAGATGAAGAAAACGGATTTGGATTTACGGATTGTATTGATAGAGCTACTCAAACTTTACAGAGTTTGAAGGATTTGAAACATCGATCATTAGATAATACGAGTTTTGATTCGTGCCCTAAAGAATTCAACTGCCCCCTTTCGAA...

CDS

Download CDS FASTA

1491 bp · LXL04_000789|LXL04_000789|OH1004|CDS

ATGGCGAAAAGCGGGGTGTTTGAAAGGGATCCCACCGCCGCAACGAAGGTGGCCACCGACAACTTGAAGAAGGAATTACAGCGACTTGTTAATTCGATTGTGGAGGGATCTTCACCAGATGAAGAAAACGGATTTGGATTTACGGATTGTATTGATAGAGCTACTCAAACTTTACAGAGTTTGAAGGATTTGAAACATCGATCATTAGATAATACGAGTTTTGATTCGTGCCCTAAAGAATTCAACTGCCCCCTTTCGAA...

Protein

Download Protein FASTA

496 aa · LXL04_000789|LXL04_000789|OH1004|PROTEIN

MAKSGVFERDPTAATKVATDNLKKELQRLVNSIVEGSSPDEENGFGFTDCIDRATQTLQSLKDLKHRSLDNTSFDSCPKEFNCPLSKEIMRDPVIISSGEVISLLNSSIILCVFFCDRFSNMFTVNDTLTFCNLQTYDRASIQKWLKAGNRSCPKTKQVLSHTILTPNQLVRDMITQWCKNRGVRLPGPLHYSDQNPATEPNHSVFLSLLNKLSSTLSDQKEAASSLRSLTKRVPSFRAYFGESNDAIPQLLAPLSGIKT...

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_000789`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_000789

Location Chr01:14412027-14413517 (-)

Description Similar to PUB9: U-box domain-containing protein 9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g07360`	Functions as an E3 ubiquitin ligase (By similarity).	Interactions between the S-domain receptor kinases and AtPUB-ARM E3 ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis.2008 · DOI: 10.1104/pp.108.123380
`At5g18320`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g46510`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At2g28830`	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_000789 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007166 cell surface receptor signaling pathway Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042631 cellular response to water deprivation Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0048527 lateral root development Biological Process

GO:0050777 negative regulation of immune response Biological Process

GO:0071215 cellular response to abscisic acid stimulus Biological Process

GO:2000028 regulation of photoperiodism, flowering Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT2G28830

ath:AT3G07360

ath:AT3G46510

ath:AT5G18320

dosa:Os06g0102700

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.

Cytoplasm0.532

Rank 1 · LXL04_000789 · OH-1004

Nucleus0.459

Rank 2 · LXL04_000789 · OH-1004

Cell membrane0.095

Rank 3 · LXL04_000789 · OH-1004

Endoplasmic reticulum0.057

Rank 4 · LXL04_000789 · OH-1004

Mitochondrion0.049

Rank 5 · LXL04_000789 · 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-box78-102 aa

PF04564.22U-box135-181 aa

PF25598.2ARM_PUB209-382 aa

PF00514.30Arm326-363 aa

PF25598.2ARM_PUB390-459 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000789	`PF04564.22`	U-box	78	102	1.3e-16	61.3
LXL04_000789	`PF04564.22`	U-box	135	181	1.3e-16	61.3
LXL04_000789	`PF25598.2`	ARM_PUB	209	382	1.4e-15	58.2
LXL04_000789	`PF00514.30`	Arm	326	363	9.8e-10	38.8
LXL04_000789	`PF25598.2`	ARM_PUB	390	459	1.4e-15	58.2

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
`Q9SRT0`	Arabidopsis thaliana	U-box domain-containing protein 9	52.071%	Swiss-Prot	strong database homology
`Q3E9F7`	Arabidopsis thaliana	Putative U-box domain-containing protein 46	40.204%	Swiss-Prot	moderate database homology
`Q9SNC6`	Arabidopsis thaliana	U-box domain-containing protein 13	38.756%	Swiss-Prot	moderate database homology
`Q9ZV31`	Arabidopsis thaliana	U-box domain-containing protein 12	38.588%	Swiss-Prot	moderate database homology
`Q5VRH9`	Oryza sativa subsp. japonica	U-box domain-containing protein 12	36.382%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card