LXL04_029437 | RubberDandelionOmics

Gene overview

LXL04_029437

Reference: OH-1004 Chr: Chr06 Coordinates: 90624022-90624537 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

516 bp · LXL04_029437|LXL04_029437|OH1004|cDNA

ATGGGGTTTTGGTATCTAGCAATCAAGATTCCGCAAGCACTCACCATGACAGTCTTCGCAAACTTAGCATCTCATCTCGTATCACTCCTACTAGCAGCACTTTCTCATGTGGGCCTTTTCAAATCGCCGCCCGATCCCGACGATTACACCTCCTCCTCCGCCAACTACGTCCTCATCTTAGACGGCTCCTCCCCTTCCCTCCTCCCTGTCCCCGTCCACGTCGTGACGGCCTCCATTAAAGCTAAAGTGCCAATCATACC...

CDS

Download CDS FASTA

516 bp · LXL04_029437|LXL04_029437|OH1004|CDS

ATGGGGTTTTGGTATCTAGCAATCAAGATTCCGCAAGCACTCACCATGACAGTCTTCGCAAACTTAGCATCTCATCTCGTATCACTCCTACTAGCAGCACTTTCTCATGTGGGCCTTTTCAAATCGCCGCCCGATCCCGACGATTACACCTCCTCCTCCGCCAACTACGTCCTCATCTTAGACGGCTCCTCCCCTTCCCTCCTCCCTGTCCCCGTCCACGTCGTGACGGCCTCCATTAAAGCTAAAGTGCCAATCATACC...

Protein

Download Protein FASTA

171 aa · LXL04_029437|LXL04_029437|OH1004|PROTEIN

MGFWYLAIKIPQALTMTVFANLASHLVSLLLAALSHVGLFKSPPDPDDYTSSSANYVLILDGSSPSLLPVPVHVVTASIKAKVPIIPYSDFVYSHGGSETAACSVCLECIDATHLIRELLNCKHVFHRECLDRWVDEGQVTCPLCRSMLLPPKKLLPSSSALVTSTAADCH

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_029437`
TK1151 ID	TkA07G317470
OH-1004 ID	LXL04_029437
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_029437

Location Chr06:90624022-90624537 (+)

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
`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
`At1g22500`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029437 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009416 response to light stimulus 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:0033591 response to L-ascorbic acid 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

KEGG gene cross-reference

ath:AT1G22500

ath:AT2G01150

ath:AT3G61460

ath:AT4G11360

ath:AT4G11370

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.

Endoplasmic reticulum0.282

Rank 1 · LXL04_029437 · OH-1004

Nucleus0.265

Rank 2 · LXL04_029437 · OH-1004

Cytoplasm0.249

Rank 3 · LXL04_029437 · OH-1004

Cell membrane0.206

Rank 4 · LXL04_029437 · OH-1004

Lysosome / Vacuole0.170

Rank 5 · LXL04_029437 · 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.

PF13639.13zf-RING_2102-146 aa

PF00097.32zf-C3HC4103-145 aa

PF13923.13zf-C3HC4_2103-145 aa

PF13445.13zf-RING_UBOX103-143 aa

PF12678.14zf-rbx1104-146 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029437	`PF13639.13`	zf-RING_2	102	146	3.2e-10	40.8
LXL04_029437	`PF00097.32`	zf-C3HC4	103	145	4.3e-08	33.6
LXL04_029437	`PF13923.13`	zf-C3HC4_2	103	145	1.3e-07	32.0
LXL04_029437	`PF13445.13`	zf-RING_UBOX	103	143	3.4e-07	30.8
LXL04_029437	`PF12678.14`	zf-rbx1	104	146	4e-08	34.1

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	43.836%	Swiss-Prot	weak database homology
`Q9SUS5`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA1B	40.789%	Swiss-Prot	weak database homology
`Q9ZU51`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RHA2B	36.585%	Swiss-Prot	weak database homology
`Q9SK92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL15	32.692%	Swiss-Prot	moderate database homology
`Q9SUS4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHA1A	29.496%	Swiss-Prot	weak database homology

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