LXL04_009102 | RubberDandelionOmics

Gene overview

LXL04_009102

Reference: OH-1004 Chr: Chr02 Coordinates: 117959989-117960864 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

876 bp · LXL04_009102|LXL04_009102|OH1004|cDNA

ATGAGCAGTTACCATGATTCGAATGTGATagagctcgccggaaaaatctTGATTGTGTCTATCGTAGTATTGTCCGTGGTTTTgatatttgttttttttgttcacCTCTACTCCAAGTGGTTCTGGCAGCGCCGTGAAGAAAACCAGAACGGCTCCACCACCCTCCGTCGCCGTCGTCGGGGAGATTTTACAGCGGGTCACCAGGAACAACAGTCCGGCGTCACCGTTCTCCGGCGTGGGCTAAACCCCTCATTCCTGAA...

CDS

Download CDS FASTA

876 bp · LXL04_009102|LXL04_009102|OH1004|CDS

ATGAGCAGTTACCATGATTCGAATGTGATAGAGCTCGCCGGAAAAATCTTGATTGTGTCTATCGTAGTATTGTCCGTGGTTTTGATATTTGTTTTTTTTGTTCACCTCTACTCCAAGTGGTTCTGGCAGCGCCGTGAAGAAAACCAGAACGGCTCCACCACCCTCCGTCGCCGTCGTCGGGGAGATTTTACAGCGGGTCACCAGGAACAACAGTCCGGCGTCACCGTTCTCCGGCGTGGGCTAAACCCCTCATTCCTGAA...

Protein

Download Protein FASTA

291 aa · LXL04_009102|LXL04_009102|OH1004|PROTEIN

MSSYHDSNVIELAGKILIVSIVVLSVVLIFVFFVHLYSKWFWQRREENQNGSTTLRRRRRGDFTAGHQEQQSGVTVLRRGLNPSFLKTIPVLPFDRKDFKDGLECAVCLSELDEGEKTRILPKCSHGFHVECIDMWFHSHSTCPICRSSVSDQIEISVEDLLEIRQTQEESPENGDSHIFPTNILFWGDETEVSTLTSQLEEANNHHQTPVSASEPSSSSSSTSSHAINDQSRPDLVIDVPRQIDDDEDQKSPVSYRMRS...

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_009102`
TK1151 ID	TkA03G398490
OH-1004 ID	LXL04_009102
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.400
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009102

Location Chr02:117959989-117960864 (-)

Description Similar to ATL3: RING-H2 finger protein ATL3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g72310`	RING-H2 finger protein ATL3.	No verified direct reference in this release
`At1g53820`	RING-H2 finger protein ATL60.	No verified direct reference in this release
`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
`At3g14320`	Putative RING-H2 finger protein ATL61.	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_009102 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0042631 cellular response to water deprivation Biological Process

GO:0065003 protein-containing complex assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm 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:AT1G53820

ath:AT1G72310

ath:AT3G14320

ath:AT3G16720

ath:AT3G62690

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 membrane0.309

Rank 1 · LXL04_009102 · OH-1004

Cytoplasm0.276

Rank 2 · LXL04_009102 · OH-1004

Nucleus0.233

Rank 3 · LXL04_009102 · OH-1004

Endoplasmic reticulum0.172

Rank 4 · LXL04_009102 · OH-1004

Lysosome / Vacuole0.164

Rank 5 · LXL04_009102 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13639.13zf-RING_2104-147 aa

PF17123.12zf-RING_11104-133 aa

PF13923.13zf-C3HC4_2104-146 aa

PF12678.14zf-rbx1105-147 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009102	`PF13639.13`	zf-RING_2	104	147	2.4e-14	54.0
LXL04_009102	`PF17123.12`	zf-RING_11	104	133	5.9e-11	42.6
LXL04_009102	`PF13923.13`	zf-C3HC4_2	104	146	2.7e-07	31.0
LXL04_009102	`PF12678.14`	zf-rbx1	105	147	9.8e-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
`Q9XF63`	Arabidopsis thaliana	RING-H2 finger protein ATL3	32.911%	Swiss-Prot	moderate database homology
`P0C035`	Arabidopsis thaliana	RING-H2 finger protein ATL60	36.986%	Swiss-Prot	moderate database homology
`Q8L9T5`	Arabidopsis thaliana	RING-H2 finger protein ATL2	34.448%	Swiss-Prot	moderate database homology
`Q9LZJ6`	Arabidopsis thaliana	RING-H2 finger protein ATL5	36.735%	Swiss-Prot	moderate database homology
`Q9LUL6`	Arabidopsis thaliana	Putative RING-H2 finger protein ATL61	59.459%	Swiss-Prot	weak database homology

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