LXL04_030323 | RubberDandelionOmics

Gene overview

LXL04_030323

Reference: OH-1004 Chr: Chr06 Coordinates: 114320688-114321879 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

618 bp · LXL04_030323|LXL04_030323|OH1004|cDNA

ATGGCTGGTTCCGCGGACGGATCGTCATCACCATCAGGCGGTACAGAAGGTTGCAGTAATTGCTGGAATTGGAGGAAGGCACTATCAGCTGAAGTAAAGCTGTTCCGAGGGTTTGCGTTTGCTTTTACCCTCGTCTTCACCTTACTCCTGTTTTTGTCCTTCTATCTCTTCTACCTTCGCCTCCGTCGTCTCCGTCGCCGTACACCGCATTGGTCGGAAGCCTCATCTGCCAACAATGCGGTATCCACGGAGCAAGCCGA...

CDS

Download CDS FASTA

618 bp · LXL04_030323|LXL04_030323|OH1004|CDS

ATGGCTGGTTCCGCGGACGGATCGTCATCACCATCAGGCGGTACAGAAGGTTGCAGTAATTGCTGGAATTGGAGGAAGGCACTATCAGCTGAAGTAAAGCTGTTCCGAGGGTTTGCGTTTGCTTTTACCCTCGTCTTCACCTTACTCCTGTTTTTGTCCTTCTATCTCTTCTACCTTCGCCTCCGTCGTCTCCGTCGCCGTACACCGCATTGGTCGGAAGCCTCATCTGCCAACAATGCGGTATCCACGGAGCAAGCCGA...

Protein

Download Protein FASTA

205 aa · LXL04_030323|LXL04_030323|OH1004|PROTEIN

MAGSADGSSSPSGGTEGCSNCWNWRKALSAEVKLFRGFAFAFTLVFTLLLFLSFYLFYLRLRRLRRRTPHWSEASSANNAVSTEQAELGLKKELREMLPIIVFKESFSVTDTICSVCLGDYEADDRLQQIPACKHAFHVECIDHWLSTHTTCPLCRLSLLSSSSSPPSLPETANATATSSTTTTDASLHIENCGQSSSNMELITQ

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_030323`
TK1151 ID	TkA07G397520
OH-1004 ID	LXL04_030323
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_030323

Location Chr06:114320688-114321879 (+)

Description Similar to ATL58: RING-H2 finger protein ATL58

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g33480`	RING-H2 finger protein ATL58.	No verified direct reference in this release
`At4g10150`	RING-H2 finger protein ATL7.	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
`At4g24015`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	No verified direct reference in this release
`At3g10910`	RING-H2 finger protein ATL72.	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_030323 · 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:0048481 plant ovule development Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast 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:AT1G33480

ath:AT3G10910

ath:AT4G10150

ath:AT4G10160

ath:AT4G24015

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 membrane0.402

Rank 1 · LXL04_030323 · OH-1004

Endoplasmic reticulum0.238

Rank 2 · LXL04_030323 · OH-1004

Cytoplasm0.194

Rank 3 · LXL04_030323 · OH-1004

Lysosome / Vacuole0.194

Rank 4 · LXL04_030323 · OH-1004

Nucleus0.169

Rank 5 · LXL04_030323 · 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_2113-156 aa

PF17123.12zf-RING_11114-142 aa

PF00097.32zf-C3HC4114-155 aa

PF13923.13zf-C3HC4_2114-155 aa

PF12678.14zf-rbx1127-156 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030323	`PF13639.13`	zf-RING_2	113	156	1.3e-13	51.7
LXL04_030323	`PF17123.12`	zf-RING_11	114	142	5.2e-08	33.2
LXL04_030323	`PF00097.32`	zf-C3HC4	114	155	9.3e-07	29.3
LXL04_030323	`PF13923.13`	zf-C3HC4_2	114	155	1.3e-06	28.8
LXL04_030323	`PF12678.14`	zf-rbx1	127	156	5.4e-10	40.1

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
`Q570X5`	Arabidopsis thaliana	RING-H2 finger protein ATL58	53.061%	Swiss-Prot	strong database homology
`Q9SN28`	Arabidopsis thaliana	RING-H2 finger protein ATL7	48.951%	Swiss-Prot	moderate database homology
`Q9SN27`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL59	43.529%	Swiss-Prot	moderate database homology
`Q84TF5`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHA4A	39.286%	Swiss-Prot	moderate database homology
`Q9SG96`	Arabidopsis thaliana	RING-H2 finger protein ATL72	37.273%	Swiss-Prot	moderate database homology

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