LXL04_011930 | RubberDandelionOmics

Gene overview

LXL04_011930

Reference: OH-1004 Chr: Chr03 Coordinates: 2970358-2971595 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

789 bp · LXL04_011930|LXL04_011930|OH1004|cDNA

ATGAGTAGCCAGATAGAAGTGCAAAATCATCTAAATGGCAGTTTCCCAGCTGATATTCCCGACGATTTGAAAAACTTTTTGTCAGAAGTAGACGGCGTTAGTTTTGAAGAAGCTATCTTGCAACAGGCAAGCGCTTATCAATCATATCAAGAATCTGAGAGGAACAGGGTTGCGGTTACAGATGATGAGCATAGCGGTGACGCTAGCTGTTCTTCAGAGGAtgaggaagaagatgaagatgaagatgatggcGAATCCTC...

CDS

Download CDS FASTA

789 bp · LXL04_011930|LXL04_011930|OH1004|CDS

ATGAGTAGCCAGATAGAAGTGCAAAATCATCTAAATGGCAGTTTCCCAGCTGATATTCCCGACGATTTGAAAAACTTTTTGTCAGAAGTAGACGGCGTTAGTTTTGAAGAAGCTATCTTGCAACAGGCAAGCGCTTATCAATCATATCAAGAATCTGAGAGGAACAGGGTTGCGGTTACAGATGATGAGCATAGCGGTGACGCTAGCTGTTCTTCAGAGGATGAGGAAGAAGATGAAGATGAAGATGATGGCGAATCCTC...

Protein

Download Protein FASTA

262 aa · LXL04_011930|LXL04_011930|OH1004|PROTEIN

MSSQIEVQNHLNGSFPADIPDDLKNFLSEVDGVSFEEAILQQASAYQSYQESERNRVAVTDDEHSGDASCSSEDEEEDEDEDDGESSRHEIDDSQEAMDEALARTLQELGEEYDEYFIREFNGRASGPTESPISTPSISSPDSSQEDPDPDNMRYEELLNLGETVGVENVGLSPAQIARLPNSIYTSGMFSKNNEENCAICQENFTLWKPMTTLPCSHQYHRKCIIKWLKLKKLKLLGLFSELPYLSKRGGLKPFEARKE...

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_011930`
TK1151 ID	TkA02G602800
OH-1004 ID	LXL04_011930
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 95.885 / OH-1004 88.931 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_011930

Location Chr03:2970358-2971595 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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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
`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

Reference gene ID	Possible function	Papers / DOI
`Os01g0667700`	Probable E3 ubiquitin-protein ligase.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011930 · 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:AT3G19910

ath:AT3G63530

ath:AT4G34040

ath:AT5G42940

dosa:Os01g0667700

osa:4326322

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.

Cytoplasm0.555

Rank 1 · LXL04_011930 · OH-1004

Nucleus0.486

Rank 2 · LXL04_011930 · OH-1004

Cell membrane0.076

Rank 3 · LXL04_011930 · OH-1004

Endoplasmic reticulum0.061

Rank 4 · LXL04_011930 · OH-1004

Mitochondrion0.057

Rank 5 · LXL04_011930 · 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.

PF17123.12zf-RING_11197-225 aa

PF13639.13zf-RING_2197-232 aa

PF13923.13zf-C3HC4_2197-233 aa

PF13445.13zf-RING_UBOX198-231 aa

PF00097.32zf-C3HC4198-230 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011930	`PF17123.12`	zf-RING_11	197	225	4.4e-10	39.8
LXL04_011930	`PF13639.13`	zf-RING_2	197	232	5.7e-09	36.8
LXL04_011930	`PF13923.13`	zf-C3HC4_2	197	233	2.3e-07	31.2
LXL04_011930	`PF13445.13`	zf-RING_UBOX	198	231	1.2e-07	32.4
LXL04_011930	`PF00097.32`	zf-C3HC4	198	230	1.1e-06	29.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LT17`	Arabidopsis thaliana	E3 ubiquitin ligase BIG BROTHER-related	39.241%	Swiss-Prot	moderate database homology
`Q8L649`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BIG BROTHER	47.872%	Swiss-Prot	weak database homology
`Q9FMM4`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHG1A	43.678%	Swiss-Prot	weak database homology
`O49500`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR2	39.773%	Swiss-Prot	weak database homology
`Q5QLR5`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase ZFP1	40.000%	Swiss-Prot	weak database homology

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