LXL04_005694 | RubberDandelionOmics

Gene overview

LXL04_005694

Reference: OH-1004 Chr: Chr01 Coordinates: 170965896-170966897 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1002 bp · LXL04_005694|LXL04_005694|OH1004|cDNA

ATGTTAGGTTACAGTTACATCTCAATTGCTGAAGAAAATCGTTCTGATCGAAGTTTGGGGGTTGTTGAAGGAAATGAAGATGTCAATTCGAATGAATTCGAGGTGGATTTCGTGTCGGAATTAGGTTTTCATGTAGAAAATCAGGATAACCATAACCTTAATGGTGTCGATGGTGATTATTCTGGGTTTACGATTGCGGAGACTGGGGATGAGTTCCTTGTGTCCAGACGGAGAATGGATCGCCATGCTGCTCGATCTGA...

CDS

Download CDS FASTA

1002 bp · LXL04_005694|LXL04_005694|OH1004|CDS

ATGTTAGGTTACAGTTACATCTCAATTGCTGAAGAAAATCGTTCTGATCGAAGTTTGGGGGTTGTTGAAGGAAATGAAGATGTCAATTCGAATGAATTCGAGGTGGATTTCGTGTCGGAATTAGGTTTTCATGTAGAAAATCAGGATAACCATAACCTTAATGGTGTCGATGGTGATTATTCTGGGTTTACGATTGCGGAGACTGGGGATGAGTTCCTTGTGTCCAGACGGAGAATGGATCGCCATGCTGCTCGATCTGA...

Protein

Download Protein FASTA

333 aa · LXL04_005694|LXL04_005694|OH1004|PROTEIN

MLGYSYISIAEENRSDRSLGVVEGNEDVNSNEFEVDFVSELGFHVENQDNHNLNGVDGDYSGFTIAETGDEFLVSRRRMDRHAARSESSRSSIDSGAPGFFMGGLAVTDMAEDGPAMDRDCDDETSLHLCWDAFHLDDDNTTPNTNSNVNGDFDWEEVDERIDGRELSMFFGAEADDDASVLPGIPPVNQEPVEAEDRDGLEWEVLLNVQNFEPNPDLSGEYDDYNYTEYEMFFGQFADSDLSSMGRPPASKTTIENLSI...

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_005694`
TK1151 ID	TkA01G023520
OH-1004 ID	LXL04_005694
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.100
Protein coverage (%)	TK1151 94.017 / OH-1004 66.066 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_005694

Location Chr01:170965896-170966897 (-)

Description Similar to RING1: E3 ubiquitin-protein ligase RING1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19950`	E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.	No verified direct reference in this release
`At5g64920`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein.1999 · DOI: 10.1074/jbc.274.39.27674 Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8).2002 · DOI: 10.1046/j.1365-313x.2002.01298.x
`At5g20910`	E3 ubiquitin-protein ligase that acts as a negative regulator of abscisic acid (ABA) signaling.	No verified direct reference in this release
`At2g40830`	Probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro.	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_005694 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009938 negative regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0090378 seed trichome elongation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009505 plant-type cell wall Cellular Component

KEGG gene cross-reference

ath:AT2G40830

ath:AT3G19950

ath:AT5G20910

ath:AT5G64920

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.

Cytoplasm0.546

Rank 1 · LXL04_005694 · OH-1004

Nucleus0.490

Rank 2 · LXL04_005694 · OH-1004

Cell membrane0.077

Rank 3 · LXL04_005694 · OH-1004

Endoplasmic reticulum0.063

Rank 4 · LXL04_005694 · OH-1004

Lysosome / Vacuole0.053

Rank 5 · LXL04_005694 · 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_2274-316 aa

PF13923.13zf-C3HC4_2275-315 aa

PF12678.14zf-rbx1292-316 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005694	`PF13639.13`	zf-RING_2	274	316	8.2e-10	39.5
LXL04_005694	`PF13923.13`	zf-C3HC4_2	275	315	4.4e-07	30.3
LXL04_005694	`PF12678.14`	zf-rbx1	292	316	2.3e-06	28.4

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
`Q8LPN7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RING1-like	39.695%	Swiss-Prot	weak database homology
`Q9SPL2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase CIP8	54.217%	Swiss-Prot	weak database homology
`Q8RXD3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase AIP2	45.122%	Swiss-Prot	weak database homology
`O22197`	Arabidopsis thaliana	Probable E3 ubiquitin-protein ligase RHC1A	40.777%	Swiss-Prot	weak database homology

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