LXL04_012217 | RubberDandelionOmics

Gene overview

LXL04_012217

Reference: OH-1004 Chr: Chr03 Coordinates: 8525578-8526057 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

480 bp · LXL04_012217|LXL04_012217|OH1004|cDNA

ATGACAACTCAAGACTCTCAGTCCTTTCACTGGCGTTACGACGAGCTCGACGATAAAAACTTTCAAATCCGAGGCCGTACTCTCTTCTTCATCATCGTACTCTTCTCCGTCATCTTCTTGATAACACTACTCTTCCTCTACGCTCGCTGGATCTGCCGGTCGTCCTCCTCTTCCGCGGCTGTTTCTGACACCACCACCTTGTCCCCGCACGTGCAGCCCTGTTCACGGCCTCAAGGCCTAGATTCGATCGTGATCGATAG...

CDS

Download CDS FASTA

480 bp · LXL04_012217|LXL04_012217|OH1004|CDS

ATGACAACTCAAGACTCTCAGTCCTTTCACTGGCGTTACGACGAGCTCGACGATAAAAACTTTCAAATCCGAGGCCGTACTCTCTTCTTCATCATCGTACTCTTCTCCGTCATCTTCTTGATAACACTACTCTTCCTCTACGCTCGCTGGATCTGCCGGTCGTCCTCCTCTTCCGCGGCTGTTTCTGACACCACCACCTTGTCCCCGCACGTGCAGCCCTGTTCACGGCCTCAAGGCCTAGATTCGATCGTGATCGATAG...

Protein

Download Protein FASTA

159 aa · LXL04_012217|LXL04_012217|OH1004|PROTEIN

MTTQDSQSFHWRYDELDDKNFQIRGRTLFFIIVLFSVIFLITLLFLYARWICRSSSSSAAVSDTTTLSPHVQPCSRPQGLDSIVIDSLPITLHHRPSTASETAGESECCICIGEFDEGEKVKVLPNCCHTYHCECVDKWLTTHSSCPICRASLLVDSPV

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_012217`
TK1151 ID	TkA02G580850
OH-1004 ID	LXL04_012217
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	93.700
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_012217

Location Chr03:8525578-8526057 (+)

Description Similar to ATL66: RING-H2 finger protein ATL66

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g11110`	RING-H2 finger protein ATL66.	No verified direct reference in this release
`At1g23980`	RING-H2 finger protein ATL47.	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
`At2g35000`	E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 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_012217 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006952 defense response Biological Process

GO:0010200 response to chitin Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0048481 plant ovule development Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0005576 extracellular region Cellular Component

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:AT1G23980

ath:AT2G35000

ath:AT3G10910

ath:AT3G11110

ath:AT3G16720

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.

Lysosome / Vacuole0.269

Rank 1 · LXL04_012217 · OH-1004

Endoplasmic reticulum0.267

Rank 2 · LXL04_012217 · OH-1004

Cell membrane0.262

Rank 3 · LXL04_012217 · OH-1004

Cytoplasm0.220

Rank 4 · LXL04_012217 · OH-1004

Nucleus0.185

Rank 5 · LXL04_012217 · 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_2107-150 aa

PF17123.12zf-RING_11107-136 aa

PF12678.14zf-rbx1107-150 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012217	`PF13639.13`	zf-RING_2	107	150	1.8e-13	51.2
LXL04_012217	`PF17123.12`	zf-RING_11	107	136	7.3e-08	32.7
LXL04_012217	`PF12678.14`	zf-rbx1	107	150	8.7e-07	29.8

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
`Q9SRM0`	Arabidopsis thaliana	RING-H2 finger protein ATL66	46.795%	Swiss-Prot	moderate database homology
`Q8GW38`	Arabidopsis thaliana	RING-H2 finger protein ATL47	34.752%	Swiss-Prot	moderate database homology
`Q8L9T5`	Arabidopsis thaliana	RING-H2 finger protein ATL2	32.370%	Swiss-Prot	moderate database homology
`O64763`	Arabidopsis thaliana	E3 ubiquitin-protein ligase ATL9	30.827%	Swiss-Prot	moderate database homology
`Q9SG96`	Arabidopsis thaliana	RING-H2 finger protein ATL72	36.111%	Swiss-Prot	moderate database homology

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