LXL04_018386 | RubberDandelionOmics

Gene overview

LXL04_018386

Reference: OH-1004 Chr: Chr04 Coordinates: 12370561-12371658 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1098 bp · LXL04_018386|LXL04_018386|OH1004|cDNA

ATGGGTGACGAAACACCACAGAACGTAATGAATCTCGACCTAAATTTAGGACCGGTCGTTCATCACTCCCGTGAAAACGAACCCGGCGGTTTAAACCTAGAAGATTGGTTAGATGGGCCCGTAAGAGAAGTAATCAACCACCGAACAATAGCAAGACAAAGATGGCGGTCAATTTGGAGACCCGTTCTTTTCCCAATGGAAACCACAAACATGGCTCTTGAATTAATAACCGGAAGTAACCCAAGTGGTTCAGAAACCGG...

CDS

Download CDS FASTA

1098 bp · LXL04_018386|LXL04_018386|OH1004|CDS

ATGGGTGACGAAACACCACAGAACGTAATGAATCTCGACCTAAATTTAGGACCGGTCGTTCATCACTCCCGTGAAAACGAACCCGGCGGTTTAAACCTAGAAGATTGGTTAGATGGGCCCGTAAGAGAAGTAATCAACCACCGAACAATAGCAAGACAAAGATGGCGGTCAATTTGGAGACCCGTTCTTTTCCCAATGGAAACCACAAACATGGCTCTTGAATTAATAACCGGAAGTAACCCAAGTGGTTCAGAAACCGG...

Protein

Download Protein FASTA

365 aa · LXL04_018386|LXL04_018386|OH1004|PROTEIN

MGDETPQNVMNLDLNLGPVVHHSRENEPGGLNLEDWLDGPVREVINHRTIARQRWRSIWRPVLFPMETTNMALELITGSNPSGSETGEGSVAAAGRPPAKAACDTTYPENEIQEEKQDIAKKSNENEGGFFDCNICLDMASDPVVTCCGHLFCWPCLYRWLHVHEKECPICKGEMSIKSVTPIYGRGNPTRVVVEEDSGLKIPHRPQAKRVESWRQTIQRNAFTMPMEEMIRRLGSRFDLTRDLVPGQPDNPREITNNSL...

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_018386`
TK1151 ID	TkA08G058140
OH-1004 ID	LXL04_018386
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_018386

Location Chr04:12370561-12371658 (-)

Description Similar to RMA3: E3 ubiquitin-protein ligase RMA3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g27470`	E3 ubiquitin-protein ligase.	Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.2009 · DOI: 10.1007/s00299-009-0680-8

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018386 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006914 autophagy Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009409 response to cold Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009611 response to wounding Biological Process

GO:0009723 response to ethylene Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0018996 molting cycle, collagen and cuticulin-based cuticle Biological Process

GO:0036503 ERAD pathway Biological Process

GO:0040039 inductive cell migration Biological Process

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

KEGG gene cross-reference

ath:AT4G27470

cann:107855034

cel:CELE_C16C10.7

gga:416965

mmu:193670

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.

Nucleus0.876

Rank 1 · LXL04_018386 · OH-1004

Cytoplasm0.247

Rank 2 · LXL04_018386 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_018386 · OH-1004

Mitochondrion0.020

Rank 4 · LXL04_018386 · OH-1004

Endoplasmic reticulum0.019

Rank 5 · LXL04_018386 · 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.

PF13639.13zf-RING_2132-172 aa

PF14634.13zf-RING_5132-172 aa

PF13923.13zf-C3HC4_2133-171 aa

PF13445.13zf-RING_UBOX133-161 aa

PF00097.32zf-C3HC4133-171 aa

PF13920.13zf-C3HC4_3133-174 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018386	`PF13639.13`	zf-RING_2	132	172	7.3e-08	33.3
LXL04_018386	`PF14634.13`	zf-RING_5	132	172	3.6e-07	30.7
LXL04_018386	`PF13923.13`	zf-C3HC4_2	133	171	1.8e-09	38.0
LXL04_018386	`PF13445.13`	zf-RING_UBOX	133	161	2.5e-08	34.5
LXL04_018386	`PF00097.32`	zf-C3HC4	133	171	2.7e-08	34.3
LXL04_018386	`PF13920.13`	zf-C3HC4_3	133	174	7.9e-07	29.5

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
`Q8GUK7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RMA3	60.563%	Swiss-Prot	weak database homology

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