LXL04_012853 | RubberDandelionOmics

Gene overview

LXL04_012853

Reference: OH-1004 Chr: Chr03 Coordinates: 19818342-19820219 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

603 bp · LXL04_012853|LXL04_012853|OH1004|cDNA

ATGTCTCCTGGGATTAATTTGGTGATGACTGTAATCGGATTCACGGTTAGTACTATGTTCATCGTCTTCGTGTGTACAAGACTCATCTGTGCTCGTATTCATTACATATCTTCAAGACGATCATTTCGTATGTCTTCTAGATCTGATCTCAACGTTTTAGAGCGTGGCATACGTGGTGCTGAACCTTTTGTTGCAGCGAGCTTCCCTACAAAGAAGTACAGTGATCCATTCTTTTCGTGCGCAAAAGATGCTCAATGCAT...

CDS

Download CDS FASTA

603 bp · LXL04_012853|LXL04_012853|OH1004|CDS

ATGTCTCCTGGGATTAATTTGGTGATGACTGTAATCGGATTCACGGTTAGTACTATGTTCATCGTCTTCGTGTGTACAAGACTCATCTGTGCTCGTATTCATTACATATCTTCAAGACGATCATTTCGTATGTCTTCTAGATCTGATCTCAACGTTTTAGAGCGTGGCATACGTGGTGCTGAACCTTTTGTTGCAGCGAGCTTCCCTACAAAGAAGTACAGTGATCCATTCTTTTCGTGCGCAAAAGATGCTCAATGCAT...

Protein

Download Protein FASTA

200 aa · LXL04_012853|LXL04_012853|OH1004|PROTEIN

MSPGINLVMTVIGFTVSTMFIVFVCTRLICARIHYISSRRSFRMSSRSDLNVLERGIRGAEPFVAASFPTKKYSDPFFSCAKDAQCIVCLSEYHADDTLRILPFCGHFFHSSCIDIWLQQHCTCPVCRVSLREMCDRRYAMQPLSSSAIRFSSRDDDNRRIDITTDGQLRSNVHEEETEPSNSNMNENSGNKQSGSRSDV

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_012853`
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_012853

Location Chr03:19818342-19820219 (+)

Description Similar to ATL10: RING-H2 finger protein ATL10

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g05200`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.	No verified direct reference in this release
`At1g49220`	RING-H2 finger protein ATL10.	No verified direct reference in this release
`At4g40070`	RING-H2 finger protein ATL32.	No verified direct reference in this release
`At1g49200`	RING-H2 finger protein ATL75.	No verified direct reference in this release
`At4g10160`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8, UBC10, UBC11, and UBC34 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_012853 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0016567 protein ubiquitination 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:0005634 nucleus 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:AT1G49200

ath:AT1G49220

ath:AT3G05200

ath:AT4G10160

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.

Lysosome / Vacuole0.295

Rank 1 · LXL04_012853 · OH-1004

Cytoplasm0.291

Rank 2 · LXL04_012853 · OH-1004

Endoplasmic reticulum0.225

Rank 3 · LXL04_012853 · OH-1004

Golgi apparatus0.203

Rank 4 · LXL04_012853 · OH-1004

Cell membrane0.202

Rank 5 · LXL04_012853 · 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-rbx184-128 aa

PF13639.13zf-RING_285-128 aa

PF17123.12zf-RING_1185-114 aa

PF13923.13zf-C3HC4_285-127 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012853	`PF12678.14`	zf-rbx1	84	128	1.7e-06	28.9
LXL04_012853	`PF13639.13`	zf-RING_2	85	128	8.2e-14	52.3
LXL04_012853	`PF17123.12`	zf-RING_11	85	114	1.1e-07	32.1
LXL04_012853	`PF13923.13`	zf-C3HC4_2	85	127	7.3e-06	26.4

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
`Q8RXX9`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL6	41.000%	Swiss-Prot	weak database homology
`P0C034`	Arabidopsis thaliana	RING-H2 finger protein ATL10	36.434%	Swiss-Prot	moderate database homology
`Q8W571`	Arabidopsis thaliana	RING-H2 finger protein ATL32	40.476%	Swiss-Prot	moderate database homology
`Q94BY6`	Arabidopsis thaliana	RING-H2 finger protein ATL75	30.435%	Swiss-Prot	moderate database homology
`Q9SN27`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL59	37.607%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card