LXL04_004595 | RubberDandelionOmics

Gene overview

LXL04_004595

Reference: OH-1004 Chr: Chr01 Coordinates: 141182847-141183434 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

588 bp · LXL04_004595|LXL04_004595|OH1004|cDNA

ATGGAGCAGCATCAGTCTGAACATGGCGACGAGCACCTCCGCCTCTTCCCCTTTGATCCTTATCAACACCATCATTCTTCTCTCATCAACATGAACTTCCTTTCCTACCGCCGGAGTTTACTACAAGATGAAGAGACCTCCAGAGCTATCGGATCGCCGACGCCATCCTTCACCACCAACTCACCTTTCGACTCTTCACTAGCCCTCACGATCCTCGTCCTTCTCACCGTTCTCTTCTTCATGGCCTTCTTCTCTCTCTA...

CDS

Download CDS FASTA

588 bp · LXL04_004595|LXL04_004595|OH1004|CDS

ATGGAGCAGCATCAGTCTGAACATGGCGACGAGCACCTCCGCCTCTTCCCCTTTGATCCTTATCAACACCATCATTCTTCTCTCATCAACATGAACTTCCTTTCCTACCGCCGGAGTTTACTACAAGATGAAGAGACCTCCAGAGCTATCGGATCGCCGACGCCATCCTTCACCACCAACTCACCTTTCGACTCTTCACTAGCCCTCACGATCCTCGTCCTTCTCACCGTTCTCTTCTTCATGGCCTTCTTCTCTCTCTA...

Protein

Download Protein FASTA

195 aa · LXL04_004595|LXL04_004595|OH1004|PROTEIN

MEQHQSEHGDEHLRLFPFDPYQHHHSSLINMNFLSYRRSLLQDEETSRAIGSPTPSFTTNSPFDSSLALTILVLLTVLFFMAFFSLYIRRFSSVSNSDDSLSGRRRSAPHLRRDKHGGLDASTVRSLPVVPYSADSKIWGECSICLSEFQERETVKVIPYCNHGFHPLCIDTWLSSHVSCPLCRSTELFPAGDEA

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_004595`
TK1151 ID	TkA01G131780
OH-1004 ID	LXL04_004595
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

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_004595

Location Chr01:141182847-141183434 (-)

Description Similar to ATL57: RING-H2 finger protein ATL57

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g27940`	RING-H2 finger protein ATL57.	No verified direct reference in this release
`At1g72200`	RING-H2 finger protein ATL11.	No verified direct reference in this release
`At3g05200`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	No verified direct reference in this release
`At1g22500`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, UBC28 and UBC29 in vitro.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004595 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009416 response to light stimulus Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0033591 response to L-ascorbic acid Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G22500

ath:AT1G72200

ath:AT2G27940

ath:AT3G05200

ath:AT4G40070

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.

Endoplasmic reticulum0.303

Rank 1 · LXL04_004595 · OH-1004

Cell membrane0.269

Rank 2 · LXL04_004595 · OH-1004

Lysosome / Vacuole0.233

Rank 3 · LXL04_004595 · OH-1004

Nucleus0.195

Rank 4 · LXL04_004595 · OH-1004

Cytoplasm0.163

Rank 5 · LXL04_004595 · 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-rbx1138-184 aa

PF13639.13zf-RING_2141-184 aa

PF17123.12zf-RING_11141-170 aa

PF13923.13zf-C3HC4_2141-183 aa

PF00097.32zf-C3HC4142-183 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004595	`PF12678.14`	zf-rbx1	138	184	6.6e-09	36.6
LXL04_004595	`PF13639.13`	zf-RING_2	141	184	2.9e-13	50.6
LXL04_004595	`PF17123.12`	zf-RING_11	141	170	4.8e-10	39.7
LXL04_004595	`PF13923.13`	zf-C3HC4_2	141	183	9.1e-08	32.5
LXL04_004595	`PF00097.32`	zf-C3HC4	142	183	6.2e-07	29.9

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
`Q9SJJ7`	Arabidopsis thaliana	RING-H2 finger protein ATL57	47.945%	Swiss-Prot	moderate database homology
`Q84W40`	Arabidopsis thaliana	RING-H2 finger protein ATL11	41.844%	Swiss-Prot	moderate database homology
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	39.855%	Swiss-Prot	moderate database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	46.218%	Swiss-Prot	moderate database homology
`Q9SK92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL15	38.406%	Swiss-Prot	moderate database homology

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