LXL04_009109 | RubberDandelionOmics

Gene overview

LXL04_009109

Reference: OH-1004 Chr: Chr02 Coordinates: 118032782-118033240 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

459 bp · LXL04_009109|LXL04_009109|OH1004|cDNA

atgatgatgatgatgattatgATAGCGGGATTCGTGGACTCCATAACGACGCCCATCAAGTCTTGGTTAGACACGGTGGCAAACACCCAGGACCACCACAAGACCACCAGCGTCGTGGTGACGGAGCTTGGTGGTGGAAGCCCTCGAGTTGACTGCATCGTGTGCTTATCTGAGGTGGCGATCGGAGAAAAGTTGGCGAGGTTAGAAAGGTGCCGACATGGATTTCATGTTGAGTGCGTTGAAGCATGGTTGAAAGACCA...

CDS

Download CDS FASTA

459 bp · LXL04_009109|LXL04_009109|OH1004|CDS

ATGATGATGATGATGATTATGATAGCGGGATTCGTGGACTCCATAACGACGCCCATCAAGTCTTGGTTAGACACGGTGGCAAACACCCAGGACCACCACAAGACCACCAGCGTCGTGGTGACGGAGCTTGGTGGTGGAAGCCCTCGAGTTGACTGCATCGTGTGCTTATCTGAGGTGGCGATCGGAGAAAAGTTGGCGAGGTTAGAAAGGTGCCGACATGGATTTCATGTTGAGTGCGTTGAAGCATGGTTGAAAGACCA...

Protein

Download Protein FASTA

152 aa · LXL04_009109|LXL04_009109|OH1004|PROTEIN

MMMMMIMIAGFVDSITTPIKSWLDTVANTQDHHKTTSVVVTELGGGSPRVDCIVCLSEVAIGEKLARLERCRHGFHVECVEAWLKDHRNCPLCRTPLSGGDEDRHKSGVYLKKLYEIMCCYGFRVLETMAGWLTSSFSQGLHSSLSESCSYL

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_009109`
TK1151 ID	TkA03G398780
OH-1004 ID	LXL04_009109
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	88.800
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_009109

Location Chr02:118032782-118033240 (-)

Description Similar to ATL79: RING-H2 finger protein ATL79

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g47610`	RING-H2 finger protein ATL79.	No verified direct reference in this release
`At2g37580`	RING-H2 finger protein ATL33.	No verified direct reference in this release
`At3g03550`	RING-H2 finger protein ATL51.	No verified direct reference in this release
`At5g05280`	RING-H2 finger protein ATL73.	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_009109 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009555 pollen development Biological Process

GO:0009901 anther dehiscence Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0048443 stamen development Biological Process

GO:0080141 regulation of jasmonic acid biosynthetic process Biological Process

GO:0005634 nucleus 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:AT2G37580

ath:AT3G03550

ath:AT5G05280

ath:AT5G47610

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.

Cytoplasm0.376

Rank 1 · LXL04_009109 · OH-1004

Nucleus0.350

Rank 2 · LXL04_009109 · OH-1004

Cell membrane0.182

Rank 3 · LXL04_009109 · OH-1004

Endoplasmic reticulum0.147

Rank 4 · LXL04_009109 · OH-1004

Golgi apparatus0.105

Rank 5 · LXL04_009109 · 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_251-94 aa

PF17123.12zf-RING_1151-80 aa

PF13923.13zf-C3HC4_252-93 aa

PF00097.32zf-C3HC452-93 aa

PF12678.14zf-rbx169-94 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009109	`PF13639.13`	zf-RING_2	51	94	1.2e-12	48.6
LXL04_009109	`PF17123.12`	zf-RING_11	51	80	4.7e-08	33.3
LXL04_009109	`PF13923.13`	zf-C3HC4_2	52	93	5.8e-07	29.9
LXL04_009109	`PF00097.32`	zf-C3HC4	52	93	8.4e-07	29.5
LXL04_009109	`PF12678.14`	zf-rbx1	69	94	9.9e-08	32.8

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
`Q9FGJ6`	Arabidopsis thaliana	RING-H2 finger protein ATL79	32.432%	Swiss-Prot	moderate database homology
`O80927`	Arabidopsis thaliana	RING-H2 finger protein ATL33	41.667%	Swiss-Prot	weak database homology
`Q9SRQ8`	Arabidopsis thaliana	RING-H2 finger protein ATL51	59.091%	Swiss-Prot	weak database homology
`Q9FLC6`	Arabidopsis thaliana	RING-H2 finger protein ATL73	36.047%	Swiss-Prot	moderate database homology
`Q7XLY8`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase Os04g0590900	53.061%	Swiss-Prot	weak database homology

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