LXL04_022299 | RubberDandelionOmics

Gene overview

LXL04_022299

Reference: OH-1004 Chr: Chr04 Coordinates: 147796150-147796536 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

387 bp · LXL04_022299|LXL04_022299|OH1004|cDNA

ATGCTGCTCTCAGTATTTCTCGCCCTCTTCCTCCCCTGTGCCGGCATGAGCGCTGTCTTCCTCATCTACATTTGCTTGCTCTGCTACGCCGCCCGCCACTACCATCCTGATGATCCGGTAAAACCCGCCACCGAAGAAGGTCTATCTTCCAACCAGCTCGCCAGATTGCCGACCACCATGGGGAAGGACCTGGTATTGGGGACGGAATGCGCCGTCTGCCTTGACGATATCGAGCCGGAGCAACGTGCTCGGATGTTTCC...

CDS

Download CDS FASTA

387 bp · LXL04_022299|LXL04_022299|OH1004|CDS

ATGCTGCTCTCAGTATTTCTCGCCCTCTTCCTCCCCTGTGCCGGCATGAGCGCTGTCTTCCTCATCTACATTTGCTTGCTCTGCTACGCCGCCCGCCACTACCATCCTGATGATCCGGTAAAACCCGCCACCGAAGAAGGTCTATCTTCCAACCAGCTCGCCAGATTGCCGACCACCATGGGGAAGGACCTGGTATTGGGGACGGAATGCGCCGTCTGCCTTGACGATATCGAGCCGGAGCAACGTGCTCGGATGTTTCC...

Protein

Download Protein FASTA

128 aa · LXL04_022299|LXL04_022299|OH1004|PROTEIN

MLLSVFLALFLPCAGMSAVFLIYICLLCYAARHYHPDDPVKPATEEGLSSNQLARLPTTMGKDLVLGTECAVCLDDIEPEQRARMFPGCNHGFHVQCADTWLSKNPVCPVCRNKLDADFFVPPEANPC

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_022299`
TK1151 ID	TkA05G468300
OH-1004 ID	LXL04_022299
Relationship / confidence	Rbh Sequence Supported / Probable
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_022299

Location Chr04:147796150-147796536 (-)

Description Similar to ATL23: E3 ubiquitin-protein ligase ATL23

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g42200`	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
`At2g42350`	RING-H2 finger protein ATL40.	No verified direct reference in this release
`At5g05810`	RING-H2 finger protein ATL43.	No verified direct reference in this release
`At3g10910`	RING-H2 finger protein ATL72.	No verified direct reference in this release
`At1g72220`	RING-H2 finger protein ATL54.	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_022299 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0048481 plant ovule development Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0005634 nucleus 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:AT1G72220

ath:AT2G42350

ath:AT3G10910

ath:AT5G05810

ath:AT5G42200

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.

Lysosome / Vacuole0.258

Rank 1 · LXL04_022299 · OH-1004

Endoplasmic reticulum0.250

Rank 2 · LXL04_022299 · OH-1004

Cell membrane0.245

Rank 3 · LXL04_022299 · OH-1004

Golgi apparatus0.239

Rank 4 · LXL04_022299 · OH-1004

Cytoplasm0.217

Rank 5 · LXL04_022299 · 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_269-112 aa

PF17123.12zf-RING_1169-97 aa

PF13923.13zf-C3HC4_269-111 aa

PF00097.32zf-C3HC470-111 aa

PF12678.14zf-rbx184-112 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022299	`PF13639.13`	zf-RING_2	69	112	1.4e-13	51.5
LXL04_022299	`PF17123.12`	zf-RING_11	69	97	7.1e-11	42.3
LXL04_022299	`PF13923.13`	zf-C3HC4_2	69	111	8e-08	32.7
LXL04_022299	`PF00097.32`	zf-C3HC4	70	111	5.6e-07	30.0
LXL04_022299	`PF12678.14`	zf-rbx1	84	112	4.5e-08	33.9

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
`Q8L9W3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL23	50.794%	Swiss-Prot	strong database homology
`Q9SLC4`	Arabidopsis thaliana	RING-H2 finger protein ATL40	52.778%	Swiss-Prot	moderate database homology
`Q5EAE9`	Arabidopsis thaliana	RING-H2 finger protein ATL43	50.000%	Swiss-Prot	weak database homology
`Q9SG96`	Arabidopsis thaliana	RING-H2 finger protein ATL72	36.735%	Swiss-Prot	moderate database homology
`Q8LFY8`	Arabidopsis thaliana	RING-H2 finger protein ATL54	48.077%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card