LXL04_002346 | RubberDandelionOmics

Gene overview

LXL04_002346

Reference: OH-1004 Chr: Chr01 Coordinates: 46734620-46735141 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

522 bp · LXL04_002346|LXL04_002346|OH1004|cDNA

ATGGGAGGCTATCTAAATGTTTACAGACCTATAGACAcctcaccaccaccaccaccgtcACCGTCGTCACTTCAGCCGCAAAAGCCAAATATCCCCATGTTATACTACGGCCTCGTGGTGGTAGCCACCGCAGCCATCATCCTAGCTTTCTACAACCTGATAATCATCCGATGGTGCACCATCCAGTACCAACGTCGCTTACAACAAGAAAATCAGCTCGCTCGCCGCCGGCAAAATCCTACCAGCACCACGTCTCCACC...

CDS

Download CDS FASTA

522 bp · LXL04_002346|LXL04_002346|OH1004|CDS

ATGGGAGGCTATCTAAATGTTTACAGACCTATAGACACCTCACCACCACCACCACCGTCACCGTCGTCACTTCAGCCGCAAAAGCCAAATATCCCCATGTTATACTACGGCCTCGTGGTGGTAGCCACCGCAGCCATCATCCTAGCTTTCTACAACCTGATAATCATCCGATGGTGCACCATCCAGTACCAACGTCGCTTACAACAAGAAAATCAGCTCGCTCGCCGCCGGCAAAATCCTACCAGCACCACGTCTCCACC...

Protein

Download Protein FASTA

173 aa · LXL04_002346|LXL04_002346|OH1004|PROTEIN

MGGYLNVYRPIDTSPPPPPSPSSLQPQKPNIPMLYYGLVVVATAAIILAFYNLIIIRWCTIQYQRRLQQENQLARRRQNPTSTTSPPLSRGGSGVCLVSSFKYKKGGEGNKNQLDSDSECSVCLSIFEEGEEVRKLPTCDHCFHAYCIDMWLYSHIDCPLCRAPVVELPPPPG

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_002346`
TK1151 ID	TkA01G453260
OH-1004 ID	LXL04_002346
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	84.300
Protein coverage (%)	TK1151 100.000 / OH-1004 99.422 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

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Basic Information and Functional Annotation

Gene ID LXL04_002346

Location Chr01:46734620-46735141 (+)

Description Similar to ATL52: RING-H2 finger protein ATL52

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g17600`	RING-H2 finger protein ATL52.	No verified direct reference in this release
`At1g04360`	RING-H2 finger protein ATL1.	No verified direct reference in this release
`At5g43420`	RING-H2 finger protein ATL16.	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
`At4g17905`	Putative RING-H2 finger protein ATL53.	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_002346 · 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:AT1G04360

ath:AT4G17905

ath:AT5G10380

ath:AT5G17600

ath:AT5G43420

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 membrane0.383

Rank 1 · LXL04_002346 · OH-1004

Lysosome / Vacuole0.256

Rank 2 · LXL04_002346 · OH-1004

Endoplasmic reticulum0.219

Rank 3 · LXL04_002346 · OH-1004

Cytoplasm0.154

Rank 4 · LXL04_002346 · OH-1004

Nucleus0.116

Rank 5 · LXL04_002346 · 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_2119-162 aa

PF17123.12zf-RING_11119-148 aa

PF13923.13zf-C3HC4_2119-161 aa

PF12678.14zf-rbx1123-162 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002346	`PF13639.13`	zf-RING_2	119	162	2.4e-12	47.6
LXL04_002346	`PF17123.12`	zf-RING_11	119	148	8.9e-09	35.6
LXL04_002346	`PF13923.13`	zf-C3HC4_2	119	161	6.8e-06	26.5
LXL04_002346	`PF12678.14`	zf-rbx1	123	162	1.1e-06	29.5

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
`Q9LF64`	Arabidopsis thaliana	RING-H2 finger protein ATL52	37.410%	Swiss-Prot	moderate database homology
`P93823`	Arabidopsis thaliana	RING-H2 finger protein ATL1	35.862%	Swiss-Prot	moderate database homology
`Q9LSW9`	Arabidopsis thaliana	RING-H2 finger protein ATL16	31.788%	Swiss-Prot	moderate database homology
`Q9LX93`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1	47.126%	Swiss-Prot	moderate database homology
`P0C041`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL53	31.176%	Swiss-Prot	moderate database homology

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