LXL04_039113 | RubberDandelionOmics

Gene overview

LXL04_039113

Reference: OH-1004 Chr: Chr09 Coordinates: 59481771-59482834 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1041 bp · LXL04_039113|LXL04_039113|OH1004|cDNA

ATGGAATATTATCACCGGAAACTGTTGCCGGAACCAGATTCCAGCCAAACTGGAGACTGTTCCGACTGTGGTTCAACCTGCCAATACGACTGCGACTACGTATCAATCTATTGGCCGCCGGAGCGACCACAATTACCGCCATCACCAACAACCAATACGGACAGCTCCACCACACATATTTCTCCTCTTATCATCGTCATGGTCGCCTTGATTGCCAGTGCAGTTCTGTTTATCAGCTACTACGTTATCATGAAAAGATA...

CDS

Download CDS FASTA

1041 bp · LXL04_039113|LXL04_039113|OH1004|CDS

ATGGAATATTATCACCGGAAACTGTTGCCGGAACCAGATTCCAGCCAAACTGGAGACTGTTCCGACTGTGGTTCAACCTGCCAATACGACTGCGACTACGTATCAATCTATTGGCCGCCGGAGCGACCACAATTACCGCCATCACCAACAACCAATACGGACAGCTCCACCACACATATTTCTCCTCTTATCATCGTCATGGTCGCCTTGATTGCCAGTGCAGTTCTGTTTATCAGCTACTACGTTATCATGAAAAGATA...

Protein

Download Protein FASTA

346 aa · LXL04_039113|LXL04_039113|OH1004|PROTEIN

MEYYHRKLLPEPDSSQTGDCSDCGSTCQYDCDYVSIYWPPERPQLPPSPTTNTDSSTTHISPLIIVMVALIASAVLFISYYVIMKRYCARFRQPFATQVNEESQDFVNEDHQPEIDHPIWYINTIGLQPAVIRSITVVKFKKGENVIDVTDCSVCLSQFEDDESLRLLPKCKHAFHITCIDTWLRSHTNCPLCRAAVLSNNSNTNSQSNDQNRNHVFGLNQNTQRENAENNGELRSNRVQEIGIRENRRETGNGVEVEED...

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_039113`
TK1151 ID	TkA04G505010
OH-1004 ID	LXL04_039113
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
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_039113

Location Chr09:59481771-59482834 (+)

Description Similar to ATL54: RING-H2 finger protein ATL54

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g72220`	RING-H2 finger protein ATL54.	No verified direct reference in this release
`At5g17600`	RING-H2 finger protein ATL52.	No verified direct reference in this release
`At3g03550`	RING-H2 finger protein ATL51.	No verified direct reference in this release
`At5g10380`	E3 ubiquitin-protein ligase that may be involved in positive regulation of programmed cell death (PCD) by facilitating degradation of negative regulators of PCD.	RING1 E3 ligase localizes to plasma membrane lipid rafts to trigger FB1-induced programmed cell death in Arabidopsis.2008 · DOI: 10.1111/j.1365-313x.2008.03625.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0590900`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_039113 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002238 response to molecule of fungal origin Biological Process

GO:0006952 defense response Biological Process

GO:0009617 response to bacterium Biological Process

GO:0012501 programmed cell death Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0043068 positive regulation of programmed cell death Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT1G72220

ath:AT3G03550

ath:AT5G10380

ath:AT5G17600

dosa:Os04g0590900

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.

Cell membrane0.326

Rank 1 · LXL04_039113 · OH-1004

Cytoplasm0.238

Rank 2 · LXL04_039113 · OH-1004

Endoplasmic reticulum0.207

Rank 3 · LXL04_039113 · OH-1004

Lysosome / Vacuole0.196

Rank 4 · LXL04_039113 · OH-1004

Nucleus0.195

Rank 5 · LXL04_039113 · 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_2151-194 aa

PF17123.12zf-RING_11151-180 aa

PF13923.13zf-C3HC4_2152-193 aa

PF00097.32zf-C3HC4152-193 aa

PF12678.14zf-rbx1154-194 aa

PF12861.14zf-ANAPC11159-196 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039113	`PF13639.13`	zf-RING_2	151	194	6e-14	52.7
LXL04_039113	`PF17123.12`	zf-RING_11	151	180	1.7e-10	41.1
LXL04_039113	`PF13923.13`	zf-C3HC4_2	152	193	1.3e-07	32.0
LXL04_039113	`PF00097.32`	zf-C3HC4	152	193	1.7e-07	31.7
LXL04_039113	`PF12678.14`	zf-rbx1	154	194	6.4e-10	39.8
LXL04_039113	`PF12861.14`	zf-ANAPC11	159	196	5.1e-06	27.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8LFY8`	Arabidopsis thaliana	RING-H2 finger protein ATL54	41.333%	Swiss-Prot	moderate database homology
`Q9LF64`	Arabidopsis thaliana	RING-H2 finger protein ATL52	33.750%	Swiss-Prot	moderate database homology
`Q9SRQ8`	Arabidopsis thaliana	RING-H2 finger protein ATL51	42.105%	Swiss-Prot	weak database homology
`Q9LX93`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1	54.545%	Swiss-Prot	weak database homology
`Q7XLY8`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase Os04g0590900	41.772%	Swiss-Prot	weak database homology

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