LXL04_033098 | RubberDandelionOmics

Gene overview

LXL04_033098

Reference: OH-1004 Chr: Chr07 Coordinates: 35897459-35898956 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

765 bp · LXL04_033098|LXL04_033098|OH1004|cDNA

ATGAACTGGTTCCTGCAAACTGAAGATCCGCGTATAAGTACTGGAATACAGTATCAATCGAGTAAAAGCTATATGGATTTTCTAGAAGAGCTTACCTACGAGCATGTCAATTTCATATTTTCCGATGCTATATATCCTCAGGAGAGCGCAAACTCTACAATCAATACCTACGCTTATAAATTTGGGCATTCAGAAGCTGGGACGTTCTCATACTATGATTACTGTGATGATTATCCGATCTATAATCAGACAATGGGGAA...

CDS

Download CDS FASTA

765 bp · LXL04_033098|LXL04_033098|OH1004|CDS

ATGAACTGGTTCCTGCAAACTGAAGATCCGCGTATAAGTACTGGAATACAGTATCAATCGAGTAAAAGCTATATGGATTTTCTAGAAGAGCTTACCTACGAGCATGTCAATTTCATATTTTCCGATGCTATATATCCTCAGGAGAGCGCAAACTCTACAATCAATACCTACGCTTATAAATTTGGGCATTCAGAAGCTGGGACGTTCTCATACTATGATTACTGTGATGATTATCCGATCTATAATCAGACAATGGGGAA...

Protein

Download Protein FASTA

254 aa · LXL04_033098|LXL04_033098|OH1004|PROTEIN

MNWFLQTEDPRISTGIQYQSSKSYMDFLEELTYEHVNFIFSDAIYPQESANSTINTYAYKFGHSEAGTFSYYDYCDDYPIYNQTMGNNEYIRQLDVNQRTTSEHRQQNEQLSSSFRANPPECLEINHDGGESLHVWEDNVDLDNMTYEELIELGEIVGSQSRGLSQEAISLLPISKFKRGFFWRNFWKKKSRDERCVICQMEYKRGDRQITLPCKHAYHAACGNRWLTINKACPVCYKDVHVNVCPSKREERFR

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_033098`
TK1151 ID	TkA08G230350
OH-1004 ID	LXL04_033098
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.800
Protein coverage (%)	TK1151 93.727 / 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_033098

Location Chr07:35897459-35898956 (+)

Description Similar to BB: E3 ubiquitin-protein ligase BIG BROTHER

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At3g19910`	E3 ubiquitin-ligase probably involved in organ size regulation.	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
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0648800`	Probable E3 ubiquitin-protein ligase that functions downstream of HAL3 and is required for HAL3-regulated plant growth.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033098 · 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

dosa:Os04g0648800

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.

Cytoplasm0.499

Rank 1 · LXL04_033098 · OH-1004

Nucleus0.482

Rank 2 · LXL04_033098 · OH-1004

Cell membrane0.110

Rank 3 · LXL04_033098 · OH-1004

Endoplasmic reticulum0.064

Rank 4 · LXL04_033098 · OH-1004

Lysosome / Vacuole0.061

Rank 5 · LXL04_033098 · 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-rbx1191-236 aa

PF13639.13zf-RING_2195-236 aa

PF13923.13zf-C3HC4_2195-236 aa

PF17123.12zf-RING_11196-222 aa

PF00097.32zf-C3HC4196-236 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033098	`PF12678.14`	zf-rbx1	191	236	9.1e-08	32.9
LXL04_033098	`PF13639.13`	zf-RING_2	195	236	5.8e-13	49.6
LXL04_033098	`PF13923.13`	zf-C3HC4_2	195	236	3e-08	34.0
LXL04_033098	`PF17123.12`	zf-RING_11	196	222	5.6e-07	29.9
LXL04_033098	`PF00097.32`	zf-C3HC4	196	236	3e-06	27.7

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
`Q8L649`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BIG BROTHER	39.565%	Swiss-Prot	moderate database homology
`Q9LT17`	Arabidopsis thaliana	E3 ubiquitin ligase BIG BROTHER-related	45.872%	Swiss-Prot	weak database homology
`O49500`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR2	40.206%	Swiss-Prot	weak database homology
`Q9ZQF9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase MBR1	39.423%	Swiss-Prot	weak database homology
`Q7XTV7`	Oryza sativa subsp. japonica	Probable E3 ubiquitin-protein ligase HIP1	42.857%	Swiss-Prot	weak database homology

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