LXL04_026133 | RubberDandelionOmics

Gene overview

LXL04_026133

Reference: OH-1004 Chr: Chr05 Coordinates: 121372292-121373670 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1023 bp · LXL04_026133|LXL04_026133|OH1004|cDNA

ATGTCGACAAACCCCACACATGCCGCACCACCTACGATACCATACGCATCTCCTCCTATTACCGTCATCCTCACCATTATTCTCCTCCTGTGCTTCATGCAAAACCTATTTTACACGTGGCATCACCGGCAAAGTCCGTCGTCTAGGGCACCTACTGTTCCCGGAACGGATAACGCCACCCTTGGACTCGACCCTTCCATCATCAAAACTTTTCCGACGTTCACATACTCAGAAGTCAAAGAATATCGAGGGAAAAACTA...

CDS

Download CDS FASTA

1023 bp · LXL04_026133|LXL04_026133|OH1004|CDS

ATGTCGACAAACCCCACACATGCCGCACCACCTACGATACCATACGCATCTCCTCCTATTACCGTCATCCTCACCATTATTCTCCTCCTGTGCTTCATGCAAAACCTATTTTACACGTGGCATCACCGGCAAAGTCCGTCGTCTAGGGCACCTACTGTTCCCGGAACGGATAACGCCACCCTTGGACTCGACCCTTCCATCATCAAAACTTTTCCGACGTTCACATACTCAGAAGTCAAAGAATATCGAGGGAAAAACTA...

Protein

Download Protein FASTA

340 aa · LXL04_026133|LXL04_026133|OH1004|PROTEIN

MSTNPTHAAPPTIPYASPPITVILTIILLLCFMQNLFYTWHHRQSPSSRAPTVPGTDNATLGLDPSIIKTFPTFTYSEVKEYRGKNYGLECAICLCEFKDENMLRLLTKCCHIFHQECIDLWLGSHKSCPWCRSSLDTPINSPEKSPVSVASTGGMHEVQENGSHGDRSVSIDIRDNNENGDKEESKMEKHVSIKVDDDRGREGGHKSTDGFMRSKSTGHSIIRNAKRCENDERYTLRLPQDVQAKLIPRHNWTRSCTEF...

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_026133`
TK1151 ID	TkA06G026580
OH-1004 ID	LXL04_026133
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 98.625 / OH-1004 84.412 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_026133

Location Chr05:121372292-121373670 (+)

Description Similar to ATL30: RING-H2 finger protein ATL30

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g46650`	RING-H2 finger protein ATL30.	No verified direct reference in this release
`At4g17920`	RING-H2 finger protein ATL29.	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
`At2g35000`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 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_026133 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010200 response to chitin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm 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

KEGG gene cross-reference

ath:AT1G72200

ath:AT2G35000

ath:AT3G05200

ath:AT4G17920

ath:AT5G46650

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.

Cell membrane0.377

Rank 1 · LXL04_026133 · OH-1004

Cytoplasm0.278

Rank 2 · LXL04_026133 · OH-1004

Nucleus0.252

Rank 3 · LXL04_026133 · OH-1004

Endoplasmic reticulum0.132

Rank 4 · LXL04_026133 · OH-1004

Lysosome / Vacuole0.101

Rank 5 · LXL04_026133 · 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_290-133 aa

PF17123.12zf-RING_1190-119 aa

PF13923.13zf-C3HC4_290-132 aa

PF13445.13zf-RING_UBOX91-130 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026133	`PF13639.13`	zf-RING_2	90	133	3.8e-12	47.0
LXL04_026133	`PF17123.12`	zf-RING_11	90	119	2.7e-08	34.1
LXL04_026133	`PF13923.13`	zf-C3HC4_2	90	132	1.3e-06	28.8
LXL04_026133	`PF13445.13`	zf-RING_UBOX	91	130	9e-06	26.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FIR0`	Arabidopsis thaliana	RING-H2 finger protein ATL30	37.954%	Swiss-Prot	moderate database homology
`O49691`	Arabidopsis thaliana	RING-H2 finger protein ATL29	37.755%	Swiss-Prot	moderate database homology
`Q84W40`	Arabidopsis thaliana	RING-H2 finger protein ATL11	33.871%	Swiss-Prot	moderate database homology
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	31.923%	Swiss-Prot	moderate database homology
`O64763`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL9	34.646%	Swiss-Prot	moderate database homology

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