LXL04_004310 | RubberDandelionOmics

Gene overview

LXL04_004310

Reference: OH-1004 Chr: Chr01 Coordinates: 132016466-132021172 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2664 bp · LXL04_004310|LXL04_004310|OH1004|cDNA

ATGGAAACTTCTGATTCAGATGAGCCAGAGAAAAAGCGGCCTCATCTGAACAATTCCGACATGGCACGTCACCCTAACCCTTCTCCGGAAAATGGCACCGTTGATGCAACAGTGCTGCAGTATCAAAATCAGAAACTTGTCCAGCAGTTAGATGTCCAGAAACAGGAGTTACATGATCTTGAAGATAAAATTAAAGAATTAAGACAGGAGCAAACTTCTTACGATGACTTTTTGATCAAAATTAACCAACTATGGAGTCA...

CDS

Download CDS FASTA

2664 bp · LXL04_004310|LXL04_004310|OH1004|CDS

ATGGAAACTTCTGATTCAGATGAGCCAGAGAAAAAGCGGCCTCATCTGAACAATTCCGACATGGCACGTCACCCTAACCCTTCTCCGGAAAATGGCACCGTTGATGCAACAGTGCTGCAGTATCAAAATCAGAAACTTGTCCAGCAGTTAGATGTCCAGAAACAGGAGTTACATGATCTTGAAGATAAAATTAAAGAATTAAGACAGGAGCAAACTTCTTACGATGACTTTTTGATCAAAATTAACCAACTATGGAGTCA...

Protein

Download Protein FASTA

887 aa · LXL04_004310|LXL04_004310|OH1004|PROTEIN

METSDSDEPEKKRPHLNNSDMARHPNPSPENGTVDATVLQYQNQKLVQQLDVQKQELHDLEDKIKELRQEQTSYDDFLIKINQLWSQLDDDLILLGSRAGTGQSALEALQHADSSRGSIPSCPAEDIFICRLLQSDSIGKNGSEEERIIYIKEALALRHSSTSQLMKLIEDTIQVLMVKIETIDQSFHEKDKSSEEDAIIQLNKIDELMKEEVKHLQIVIEALHVKHKEYADMIQSYSLSHSTDQSEIKRVAGDLEDSMA...

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_004310`
TK1151 ID	TkA01G174100
OH-1004 ID	LXL04_004310
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004310

Location Chr01:132016466-132021172 (-)

Description Similar to HUB2: E3 ubiquitin-protein ligase BRE1-like 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q9C895`	E3 ubiquitin-protein ligase that monoubiquitinates H2B to form H2BK143ub1.	No verified direct reference in this release
`UniProt: Q8RXD6`	E3 ubiquitin-protein ligase that monoubiquitinates H2B to form H2BK143ub1.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0565600`	E3 ubiquitin-protein ligase that monoubiquitinates H2B to form H2BK143ub1.	Histone H2B Monoubiquitination Mediated by HISTONE MONOUBIQUITINATION1 and HISTONE MONOUBIQUITINATION2 Is Involved in Anther Development by Regulating Tapetum Degradation-Related Genes in Rice.2015 · DOI: 10.1104/pp.114.256578 Flowering-Related RING Protein 1 (FRRP1) Regulates Flowering Time and Yield Potential by Affecting Histone H2B Monoubiquitination in Rice (Oryza Sativa).2016 · DOI: 10.1371/journal.pone.0150458
`UniProt: A2ZAC2`	E3 ubiquitin-protein ligase that monoubiquitinates H2B to form H2BK143ub1.	No verified direct reference in this release
`Os04g0550400`	E3 ubiquitin-protein ligase that monoubiquitinates H2B to form H2BK143ub1.	Histone H2B Monoubiquitination Mediated by HISTONE MONOUBIQUITINATION1 and HISTONE MONOUBIQUITINATION2 Is Involved in Anther Development by Regulating Tapetum Degradation-Related Genes in Rice.2015 · DOI: 10.1104/pp.114.256578

Functional annotation source

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Functional annotation source: OH1004 · LXL04_004310 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006513 protein monoubiquitination Biological Process

GO:0009908 flower development Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010162 seed dormancy process Biological Process

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

GO:0010389 regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0045087 innate immune response Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0051301 cell division Biological Process

GO:0051781 positive regulation of cell division Biological Process

KEGG gene cross-reference

ath:AT1G55250

ath:AT2G44950

dosa:Os04g0550400

dosa:Os10g0565600

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.

Nucleus0.795

Rank 1 · LXL04_004310 · OH-1004

Cytoplasm0.232

Rank 2 · LXL04_004310 · OH-1004

Golgi apparatus0.024

Rank 3 · LXL04_004310 · OH-1004

Mitochondrion0.022

Rank 4 · LXL04_004310 · OH-1004

Cell membrane0.021

Rank 5 · LXL04_004310 · 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.

PF13920.13zf-C3HC4_3833-875 aa

PF13923.13zf-C3HC4_2834-873 aa

PF00097.32zf-C3HC4835-873 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004310	`PF13920.13`	zf-C3HC4_3	833	875	9.9e-08	32.4
LXL04_004310	`PF13923.13`	zf-C3HC4_2	834	873	1.5e-07	31.8
LXL04_004310	`PF00097.32`	zf-C3HC4	835	873	6.4e-09	36.3

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
`Q9C895`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BRE1-like 2	55.750%	Swiss-Prot	strong database homology
`Q8RXD6`	Arabidopsis thaliana	E3 ubiquitin-protein ligase BRE1-like 1	32.376%	Swiss-Prot	moderate database homology
`Q336R3`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase BRE1-like 2	53.044%	Swiss-Prot	strong database homology
`A2ZAC2`	Oryza sativa subsp. indica	E3 ubiquitin-protein ligase BRE1-like 2	53.044%	Swiss-Prot	strong database homology
`Q7XU27`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase BRE1-like 1	31.159%	Swiss-Prot	moderate database homology

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