LXL04_005546 | RubberDandelionOmics

Gene overview

LXL04_005546

Reference: OH-1004 Chr: Chr01 Coordinates: 168072529-168073715 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

501 bp · LXL04_005546|LXL04_005546|OH1004|cDNA

ATGGGATTTCCAGTTGGATACACCGACCTCTTCCTCCCCAAACTCCTCCTCCACATCCTAACCGTTCTGGGTTTCATCCGAAAGCTCATTTCCTTCGTTTTCCGATTTGTTGGCCTCGGAGAGTTTCTCGAACCCGATTTCTCATCGGACCCGACCCGGAACGAACCGGTGATGCAGTTCCATTCCGTTTCTGCGGTCCTCATCCGTGAGCTTCTCCCGGTGGTGAAGTTCTCAGAGCTAGTGGATCCGCCGGAGAGTTG...

CDS

Download CDS FASTA

501 bp · LXL04_005546|LXL04_005546|OH1004|CDS

ATGGGATTTCCAGTTGGATACACCGACCTCTTCCTCCCCAAACTCCTCCTCCACATCCTAACCGTTCTGGGTTTCATCCGAAAGCTCATTTCCTTCGTTTTCCGATTTGTTGGCCTCGGAGAGTTTCTCGAACCCGATTTCTCATCGGACCCGACCCGGAACGAACCGGTGATGCAGTTCCATTCCGTTTCTGCGGTCCTCATCCGTGAGCTTCTCCCGGTGGTGAAGTTCTCAGAGCTAGTGGATCCGCCGGAGAGTTG...

Protein

Download Protein FASTA

166 aa · LXL04_005546|LXL04_005546|OH1004|PROTEIN

MGFPVGYTDLFLPKLLLHILTVLGFIRKLISFVFRFVGLGEFLEPDFSSDPTRNEPVMQFHSVSAVLIRELLPVVKFSELVDPPESCAVCLYEFDAGDEIRRLTNCRHIFHRCCLDRWMDHDQKTCPLCRTPFIPDDLQDSFNERLWAASGIADYYGDSSLKGHSS

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_005546`
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_005546

Location Chr01:168072529-168073715 (-)

Description Similar to BRH1: Brassinosteroid-responsive RING protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g61460`	May be involved in the brassinosteroids (BRs) signaling pathway and regulate the growth and development of rosette leaves.	Characterisation of BRH1, a brassinosteroid-responsive RING-H2 gene from Arabidopsis thaliana.2002 · DOI: 10.1007/s00425-001-0723-z Overexpressed BRH1, a RING finger gene, alters rosette leaf shape in Arabidopsis thaliana.2018 · DOI: 10.1007/s11427-017-9133-8
`At4g11360`	Possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro.	No verified direct reference in this release
`At4g11370`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At2g01150`	E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid (ABA) signaling and responses to salt and osmotic stresses during seed germination and early seedling development.	The Arabidopsis RING finger E3 ligase RHA2b acts additively with RHA2a in regulating abscisic acid signaling and drought response.2011 · DOI: 10.1104/pp.111.176214

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005546 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009742 brassinosteroid mediated signaling pathway Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010200 response to chitin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0047484 regulation of response to osmotic stress Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:1901371 regulation of leaf morphogenesis Biological Process

GO:1905421 regulation of plant organ morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G01150

ath:AT3G61460

ath:AT4G11360

ath:AT4G11370

spo:2541304

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.

Endoplasmic reticulum0.307

Rank 1 · LXL04_005546 · OH-1004

Cytoplasm0.248

Rank 2 · LXL04_005546 · OH-1004

Golgi apparatus0.217

Rank 3 · LXL04_005546 · OH-1004

Lysosome / Vacuole0.198

Rank 4 · LXL04_005546 · OH-1004

Nucleus0.188

Rank 5 · LXL04_005546 · 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.

PF13639.13zf-RING_286-130 aa

PF17123.12zf-RING_1187-115 aa

PF00097.32zf-C3HC487-129 aa

PF13923.13zf-C3HC4_287-129 aa

PF14634.13zf-RING_587-131 aa

PF12678.14zf-rbx1101-130 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005546	`PF13639.13`	zf-RING_2	86	130	4.4e-13	50.0
LXL04_005546	`PF17123.12`	zf-RING_11	87	115	4.7e-07	30.1
LXL04_005546	`PF00097.32`	zf-C3HC4	87	129	1.3e-06	28.9
LXL04_005546	`PF13923.13`	zf-C3HC4_2	87	129	2.2e-06	28.1
LXL04_005546	`PF14634.13`	zf-RING_5	87	131	7.2e-06	26.6
LXL04_005546	`PF12678.14`	zf-rbx1	101	130	8.7e-07	29.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9XF92`	Arabidopsis thaliana	Brassinosteroid-responsive RING protein 1	61.818%	Swiss-Prot	strong database homology
`Q9SUS5`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA1B	39.375%	Swiss-Prot	moderate database homology
`Q9SUS4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHA1A	37.267%	Swiss-Prot	moderate database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	43.103%	Swiss-Prot	weak database homology

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