LXL04_038327 | RubberDandelionOmics

Gene overview

LXL04_038327

Reference: OH-1004 Chr: Chr09 Coordinates: 37343449-37344633 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1185 bp · LXL04_038327|LXL04_038327|OH1004|cDNA

ATGATCACCGTCTCGCCGGCACCTTCACCGAATGATAATCTTCATCGTCAAGCTCCAGCTTCAGCTCCGGCTTCATGGCTTCCTAATTCCTCGTCAAAACCGCCTGTTCGATTCAGCCCGCCTTTGATAGCTATGGTTGTGATCATCGCCACTGCTTTTATCACAATCACATACTCCCGAGCCATTTCCCGACGATTCCTCCGTTTACGACGGAGCTGGCGACAGTGGCGGAGACGGCGACGCCTTCTCCGTTCATACGT...

CDS

Download CDS FASTA

1185 bp · LXL04_038327|LXL04_038327|OH1004|CDS

ATGATCACCGTCTCGCCGGCACCTTCACCGAATGATAATCTTCATCGTCAAGCTCCAGCTTCAGCTCCGGCTTCATGGCTTCCTAATTCCTCGTCAAAACCGCCTGTTCGATTCAGCCCGCCTTTGATAGCTATGGTTGTGATCATCGCCACTGCTTTTATCACAATCACATACTCCCGAGCCATTTCCCGACGATTCCTCCGTTTACGACGGAGCTGGCGACAGTGGCGGAGACGGCGACGCCTTCTCCGTTCATACGT...

Protein

Download Protein FASTA

394 aa · LXL04_038327|LXL04_038327|OH1004|PROTEIN

MITVSPAPSPNDNLHRQAPASAPASWLPNSSSKPPVRFSPPLIAMVVIIATAFITITYSRAISRRFLRLRRSWRQWRRRRRLLRSYVPSSVGNGDIESPVYTGEESYDPTYGYQMFSPYGLDDAVIKTIPLSVHSRKSSVHECAVCLLEFEDNDYVRTLPVCYHAFHVECIDVWLRCHANCPLCRASVFRPESPFIPVMSARIRPNFEDVMIESPIIEPSPVPEHDQQVDSAVSVSEITQETSPIRIPSEDRFSRRDFLL...

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_038327`
TK1151 ID	TkA04G418130
OH-1004 ID	LXL04_038327
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.700
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_038327

Location Chr09:37343449-37344633 (+)

Description Similar to ATL65: RING-H2 finger protein ATL65

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18930`	RING-H2 finger protein ATL65.	No verified direct reference in this release
`At1g23980`	RING-H2 finger protein ATL47.	No verified direct reference in this release
`At1g04360`	RING-H2 finger protein ATL1.	No verified direct reference in this release
`At4g17905`	Putative RING-H2 finger protein ATL53.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0590900`	Possesses E3 ubiquitin-protein ligase in vitro.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038327 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0031982 vesicle 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:AT1G04360

ath:AT1G23980

ath:AT3G18930

ath:AT4G17905

dosa:Os04g0590900

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 membrane0.336

Rank 1 · LXL04_038327 · OH-1004

Nucleus0.325

Rank 2 · LXL04_038327 · OH-1004

Cytoplasm0.249

Rank 3 · LXL04_038327 · OH-1004

Endoplasmic reticulum0.140

Rank 4 · LXL04_038327 · OH-1004

Lysosome / Vacuole0.090

Rank 5 · LXL04_038327 · 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-rbx1140-185 aa

PF13639.13zf-RING_2142-185 aa

PF17123.12zf-RING_11142-171 aa

PF13923.13zf-C3HC4_2142-184 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038327	`PF12678.14`	zf-rbx1	140	185	4.4e-08	33.9
LXL04_038327	`PF13639.13`	zf-RING_2	142	185	4.2e-12	46.9
LXL04_038327	`PF17123.12`	zf-RING_11	142	171	4.4e-09	36.6
LXL04_038327	`PF13923.13`	zf-C3HC4_2	142	184	2.8e-06	27.7

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q67YI6`	Arabidopsis thaliana	RING-H2 finger protein ATL65	46.682%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	30.570%	Swiss-Prot	weak database homology
`P93823`	Arabidopsis thaliana	RING-H2 finger protein ATL1	31.818%	Swiss-Prot	weak database homology
`P0C041`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL53	33.742%	Swiss-Prot	weak database homology
`Q7XLY8`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase Os04g0590900	35.625%	Swiss-Prot	weak database homology

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