LXL04_009905 | RubberDandelionOmics

Gene overview

LXL04_009905

Reference: OH-1004 Chr: Chr02 Coordinates: 135699162-135700973 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

918 bp · LXL04_009905|LXL04_009905|OH1004|cDNA

ATGGACAACTCCAAAGACCAAGGCAGCAAGATCGCCGATACCGATGAAAACCCTAGCAACAATACTCAATCTCCCGTTGATTCTTCCCTTCTTCCTCCTGTCGAGGTAGAAAATGGCAACCAAAATCGACCTTCTGCGGCTCCTAGAACCCCCTTTACCAATCTAAGTCAGGTCGATGCTGATCTTGCCTTGGCTCGTACACTACAAGACCAGGAAAGGGCATATATGATGTTGAGGATGAATGGCGATGTTAGTGACCA...

CDS

Download CDS FASTA

918 bp · LXL04_009905|LXL04_009905|OH1004|CDS

ATGGACAACTCCAAAGACCAAGGCAGCAAGATCGCCGATACCGATGAAAACCCTAGCAACAATACTCAATCTCCCGTTGATTCTTCCCTTCTTCCTCCTGTCGAGGTAGAAAATGGCAACCAAAATCGACCTTCTGCGGCTCCTAGAACCCCCTTTACCAATCTAAGTCAGGTCGATGCTGATCTTGCCTTGGCTCGTACACTACAAGACCAGGAAAGGGCATATATGATGTTGAGGATGAATGGCGATGTTAGTGACCA...

Protein

Download Protein FASTA

305 aa · LXL04_009905|LXL04_009905|OH1004|PROTEIN

MDNSKDQGSKIADTDENPSNNTQSPVDSSLLPPVEVENGNQNRPSAAPRTPFTNLSQVDADLALARTLQDQERAYMMLRMNGDVSDHESWETGSYVHDDDDEFDHHNSEYDGSEANEEEEDAFDVHAHLDLGSGDENRSNRGVELDPASFPNDEAYARALQDAEDQEMAARLLALTGIHEMVTEEDDDDIDDHGGNSQGTWDDVDPDELSYEELLALGEVVGTESRGLSADSISSLRSIVYNIKNNQNGSSDTCVICRLD...

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_009905`
TK1151 ID	TkA03G481500
OH-1004 ID	LXL04_009905
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

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_009905

Location Chr02:135699162-135700973 (-)

Description Similar to BBR: E3 ubiquitin ligase BIG BROTHER-related

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19910`	E3 ubiquitin-ligase probably involved in organ size regulation.	No verified direct reference in this release
`At3g63530`	E3 ubiquitin-protein ligase that limits organ size, and possibly seed size, in a dose-dependent manner.	Forever Young: The Role of Ubiquitin Receptor DA1 and E3 Ligase BIG BROTHER in Controlling Leaf Growth and Development.2017 · DOI: 10.1104/pp.16.01410
`At2g15530`	E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.	Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500
`At5g42940`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At4g34040`	E3 ubiquitin-protein ligase that functions as a regulator of MED25 stability by targeting MED25 for degradation in a RING-H2- dependent way.	Proteasome-mediated turnover of Arabidopsis MED25 is coupled to the activation of FLOWERING LOCUS T transcription.2012 · DOI: 10.1104/pp.112.205500

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009905 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009845 seed germination Biological Process

GO:0009908 flower development Biological Process

GO:0010218 response to far red light Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0046621 negative regulation of organ growth Biological Process

GO:0048437 floral organ development Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:1900057 positive regulation of leaf senescence Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G15530

ath:AT3G19910

ath:AT3G63530

ath:AT4G34040

ath:AT5G42940

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.

Cytoplasm0.617

Rank 1 · LXL04_009905 · OH-1004

Nucleus0.510

Rank 2 · LXL04_009905 · OH-1004

Cell membrane0.063

Rank 3 · LXL04_009905 · OH-1004

Lysosome / Vacuole0.055

Rank 4 · LXL04_009905 · OH-1004

Endoplasmic reticulum0.049

Rank 5 · LXL04_009905 · 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.

PF12678.14zf-rbx1251-294 aa

PF13639.13zf-RING_2252-294 aa

PF13923.13zf-C3HC4_2254-294 aa

PF00097.32zf-C3HC4254-294 aa

PF17123.12zf-RING_11254-281 aa

PF14634.13zf-RING_5254-295 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009905	`PF12678.14`	zf-rbx1	251	294	2.4e-09	38.0
LXL04_009905	`PF13639.13`	zf-RING_2	252	294	3e-13	50.5
LXL04_009905	`PF13923.13`	zf-C3HC4_2	254	294	6.7e-08	32.9
LXL04_009905	`PF00097.32`	zf-C3HC4	254	294	1.1e-07	32.3
LXL04_009905	`PF17123.12`	zf-RING_11	254	281	2.2e-07	31.2
LXL04_009905	`PF14634.13`	zf-RING_5	254	295	3.1e-07	31.0

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
`Q9LT17`	Arabidopsis thaliana	E3 ubiquitin ligase BIG BROTHER-related	52.147%	Swiss-Prot	strong database homology
`Q8L649`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BIG BROTHER	53.846%	Swiss-Prot	weak database homology
`Q9ZQF9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR1	40.196%	Swiss-Prot	weak database homology
`Q9FMM4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHG1A	37.234%	Swiss-Prot	weak database homology
`O49500`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR2	36.634%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card