LXL04_003131 | RubberDandelionOmics

Gene overview

LXL04_003131

Reference: OH-1004 Chr: Chr01 Coordinates: 68825391-68826534 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

915 bp · LXL04_003131|LXL04_003131|OH1004|cDNA

ATGCCTCAGAGACATTCCAAGAACAACAACGATCTAGCGTTCTTCACGTATGACGAGAAGAGGAAGCTAGGTTACGGTACTCAAAAGGAGAGGCTTGGTAAAGACTCCATCAAACCCTTCGATGCTTGCTCGCTCTGCTTGAAACCCTTCATCGATCCGTTGTGCTGTCAAAAAGGCCACGTCTTCTGTAAAGAGTGCATCCTCGAATGCTTATTGTCCCAAAAGAAAGACATCCAAAGGAAGCTGACTGCGCACACTAC...

CDS

Download CDS FASTA

915 bp · LXL04_003131|LXL04_003131|OH1004|CDS

ATGCCTCAGAGACATTCCAAGAACAACAACGATCTAGCGTTCTTCACGTATGACGAGAAGAGGAAGCTAGGTTACGGTACTCAAAAGGAGAGGCTTGGTAAAGACTCCATCAAACCCTTCGATGCTTGCTCGCTCTGCTTGAAACCCTTCATCGATCCGTTGTGCTGTCAAAAAGGCCACGTCTTCTGTAAAGAGTGCATCCTCGAATGCTTATTGTCCCAAAAGAAAGACATCCAAAGGAAGCTGACTGCGCACACTAC...

Protein

Download Protein FASTA

304 aa · LXL04_003131|LXL04_003131|OH1004|PROTEIN

MPQRHSKNNNDLAFFTYDEKRKLGYGTQKERLGKDSIKPFDACSLCLKPFIDPLCCQKGHVFCKECILECLLSQKKDIQRKLTAHTTQQKQQKEDETEKLALQKARELDAFDQQNHGAVPQYTDKNLTHNQNNFHGANSVKTTSYEAEALRTMKAFWLPSATPEAPVKITAPSTTTTCPEGSEKLKMKSLFPIIFTEEPNDEKTNSPLDKTYVCPSCKVTLTNTLGLVALSSCGHVFCKKCAEKFMAVDKVCLVCNRGCK...

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_003131`
TK1151 ID	TkAUNG042140
OH-1004 ID	LXL04_003131
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_003131

Location Chr01:68825391-68826534 (-)

Description Similar to CSU1: E3 ubiquitin-protein ligase CSU1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g61620`	RING-finger E3 ubiquitin-protein ligase that plays an major role in maintaining COP1 homeostasis in darkness.	The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings.2014 · DOI: 10.1105/tpc.114.124024

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003131 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009640 photomorphogenesis Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031648 protein destabilization Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G61620

dre:492793

mcf:102130453

xla:414557

xtr:394625

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.

Nucleus0.877

Rank 1 · LXL04_003131 · OH-1004

Cytoplasm0.188

Rank 2 · LXL04_003131 · OH-1004

Mitochondrion0.025

Rank 3 · LXL04_003131 · OH-1004

Cell membrane0.018

Rank 4 · LXL04_003131 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_003131 · 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.

PF15906.11zf-NOSIP5-75 aa

PF13445.13zf-RING_UBOX43-72 aa

PF04641.19Rtf2186-268 aa

PF13445.13zf-RING_UBOX214-250 aa

PF13639.13zf-RING_2214-256 aa

PF14634.13zf-RING_5214-257 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003131	`PF15906.11`	zf-NOSIP	5	75	1.2e-17	64.4
LXL04_003131	`PF13445.13`	zf-RING_UBOX	43	72	1.4e-09	38.5
LXL04_003131	`PF04641.19`	Rtf2	186	268	1.2e-07	32.1
LXL04_003131	`PF13445.13`	zf-RING_UBOX	214	250	1.4e-09	38.5
LXL04_003131	`PF13639.13`	zf-RING_2	214	256	5.5e-07	30.4
LXL04_003131	`PF14634.13`	zf-RING_5	214	257	7.8e-07	29.7

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
`Q9SY88`	Arabidopsis thaliana	E3 ubiquitin-protein ligase CSU1	74.026%	Swiss-Prot	strong database homology

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