LXL04_029337 | RubberDandelionOmics

Gene overview

LXL04_029337

Reference: OH-1004 Chr: Chr06 Coordinates: 87862468-87863382 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

915 bp · LXL04_029337|LXL04_029337|OH1004|cDNA

ATGTCTGCTTCAGGACCTTCTGTTGATTCTTCAATAAACAATCAATGGAGACTTGATGGGGAACAAGAAGACTCCTCCAAAAACTACGCTCTCAGCGGCAAAATTATGCTTTCTTCAATAGTTGTCCTCTTCGTCGTCGTCGTTTTCTTGGTTCTTCTCCACCTGTACGCAAGATGGTATCTTCTACGCCTCCGCCGCCGTAACGACAACCGACGTGGTAATCGCCGCAACCGTTCCACCCGTGTTGTCTTCTACGTCGA...

CDS

Download CDS FASTA

915 bp · LXL04_029337|LXL04_029337|OH1004|CDS

ATGTCTGCTTCAGGACCTTCTGTTGATTCTTCAATAAACAATCAATGGAGACTTGATGGGGAACAAGAAGACTCCTCCAAAAACTACGCTCTCAGCGGCAAAATTATGCTTTCTTCAATAGTTGTCCTCTTCGTCGTCGTCGTTTTCTTGGTTCTTCTCCACCTGTACGCAAGATGGTATCTTCTACGCCTCCGCCGCCGTAACGACAACCGACGTGGTAATCGCCGCAACCGTTCCACCCGTGTTGTCTTCTACGTCGA...

Protein

Download Protein FASTA

304 aa · LXL04_029337|LXL04_029337|OH1004|PROTEIN

MSASGPSVDSSINNQWRLDGEQEDSSKNYALSGKIMLSSIVVLFVVVVFLVLLHLYARWYLLRLRRRNDNRRGNRRNRSTRVVFYVDSNNNLAVPTGGLDASVLKGLPLFVYSSETHGNMTECAVCLSEFEEGEKGRILPKCKHSFHTECIDMWFHSNSTCPLCRSPVELAQSEMTISVEQETVFEPGSSTSLSLPAQVDENHTEAPSLADRRKGIDVRIDVPSRNEFAAENEFRLPSPSQAFRSPGSRLLALKRIISMS...

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_029337`
TK1151 ID	TkA07G304990
OH-1004 ID	LXL04_029337
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	92.800
Protein coverage (%)	TK1151 85.000 / OH-1004 50.329 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_029337

Location Chr06:87862468-87863382 (-)

Description Similar to ATL2: RING-H2 finger protein ATL2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g16720`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At3g62690`	RING-H2 finger protein ATL5.	No verified direct reference in this release
`At2g47560`	RING-H2 finger protein ATL64.	No verified direct reference in this release
`At4g15975`	May be involved in the early steps of the plant defense signaling pathway.	No verified direct reference in this release
`At1g72310`	RING-H2 finger protein ATL3.	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_029337 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0065003 protein-containing complex assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0016020 membrane Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

GO:0061659 ubiquitin-like protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G72310

ath:AT2G47560

ath:AT3G16720

ath:AT3G62690

ath:AT4G15975

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.

Endoplasmic reticulum0.271

Rank 1 · LXL04_029337 · OH-1004

Cytoplasm0.264

Rank 2 · LXL04_029337 · OH-1004

Cell membrane0.234

Rank 3 · LXL04_029337 · OH-1004

Golgi apparatus0.195

Rank 4 · LXL04_029337 · OH-1004

Nucleus0.193

Rank 5 · LXL04_029337 · 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_2122-165 aa

PF17123.12zf-RING_11122-151 aa

PF13923.13zf-C3HC4_2122-164 aa

PF14634.13zf-RING_5122-165 aa

PF00097.32zf-C3HC4123-164 aa

PF12678.14zf-rbx1135-165 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029337	`PF13639.13`	zf-RING_2	122	165	4e-14	53.3
LXL04_029337	`PF17123.12`	zf-RING_11	122	151	9.8e-11	41.9
LXL04_029337	`PF13923.13`	zf-C3HC4_2	122	164	5.4e-08	33.2
LXL04_029337	`PF14634.13`	zf-RING_5	122	165	9.5e-06	26.2
LXL04_029337	`PF00097.32`	zf-C3HC4	123	164	7.9e-07	29.6
LXL04_029337	`PF12678.14`	zf-rbx1	135	165	2.4e-08	34.8

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
`Q8L9T5`	Arabidopsis thaliana	RING-H2 finger protein ATL2	47.883%	Swiss-Prot	moderate database homology
`Q9LZJ6`	Arabidopsis thaliana	RING-H2 finger protein ATL5	46.154%	Swiss-Prot	moderate database homology
`O22255`	Arabidopsis thaliana	RING-H2 finger protein ATL64	40.161%	Swiss-Prot	moderate database homology
`Q8LF65`	Arabidopsis thaliana	RING-H2 finger protein ATL17	39.000%	Swiss-Prot	moderate database homology
`Q9XF63`	Arabidopsis thaliana	RING-H2 finger protein ATL3	36.471%	Swiss-Prot	weak database homology

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