LXL04_013687 | RubberDandelionOmics

Gene overview

LXL04_013687

Reference: OH-1004 Chr: Chr03 Coordinates: 34140037-34147250 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3315 bp · LXL04_013687|LXL04_013687|OH1004|cDNA

ATGACGGGAAGGAAGATGACGGTGGTTGAGGTCCAATTCGATTTCAAAACCTTAGCATACAGGGGTGCTATCGATGGTGAATATATACCTGAAATTTTCCGATTGAGGTTTAGTGATCAGTTTTCAGAGCTTAACAAAGGAAAGTGGAGAATCAGTCTCGACGAGGATAGGAGGGGAATGGTAGGACCGGTGATTGGGGCAACTTGGGGAATAAATCGTGAGACAGAGAGAATGGCAAATTGGAATCTCAAATCAATGGC...

CDS

Download CDS FASTA

3315 bp · LXL04_013687|LXL04_013687|OH1004|CDS

ATGACGGGAAGGAAGATGACGGTGGTTGAGGTCCAATTCGATTTCAAAACCTTAGCATACAGGGGTGCTATCGATGGTGAATATATACCTGAAATTTTCCGATTGAGGTTTAGTGATCAGTTTTCAGAGCTTAACAAAGGAAAGTGGAGAATCAGTCTCGACGAGGATAGGAGGGGAATGGTAGGACCGGTGATTGGGGCAACTTGGGGAATAAATCGTGAGACAGAGAGAATGGCAAATTGGAATCTCAAATCAATGGC...

Protein

Download Protein FASTA

1104 aa · LXL04_013687|LXL04_013687|OH1004|PROTEIN

MTGRKMTVVEVQFDFKTLAYRGAIDGEYIPEIFRLRFSDQFSELNKGKWRISLDEDRRGMVGPVIGATWGINRETERMANWNLKSMAGRSQKIGRKRQASASMTSAGSQDEAEIPVFNRVHHILPHFAESASELQTVQPARGARRVCRSCTVDEEEDVIPLESDSDLDSQGTETDDEDDNSGNQEYEGSEGHPQSDHPAAHAIPAVLTDPDVLDCSICLEPLCAPIYQCENGHIACSSCCTKTNKKCPSCCLTIGFNRCR...

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_013687`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_013687

Location Chr03:34140037-34147250 (-)

Description Similar to At5g37930: E3 ubiquitin-protein ligase SINA-like 10

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g37930`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37870`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37890`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At1g66630`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g37910`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	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_013687 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009411 response to UV Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G66630

ath:AT5G37870

ath:AT5G37890

ath:AT5G37910

ath:AT5G37930

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.719

Rank 1 · LXL04_013687 · OH-1004

Cytoplasm0.315

Rank 2 · LXL04_013687 · OH-1004

Cell membrane0.066

Rank 3 · LXL04_013687 · OH-1004

Endoplasmic reticulum0.047

Rank 4 · LXL04_013687 · OH-1004

Mitochondrion0.033

Rank 5 · LXL04_013687 · 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.

PF21362.4Sina_RING215-250 aa

PF21361.4Sina_ZnF264-326 aa

PF00505.26HMG_box507-573 aa

PF29561.1DUF8566586-782 aa

PF10536.15PMD653-813 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013687	`PF21362.4`	Sina_RING	215	250	7.7e-09	36.3
LXL04_013687	`PF21361.4`	Sina_ZnF	264	326	3.9e-09	37.5
LXL04_013687	`PF00505.26`	HMG_box	507	573	1e-08	36.2
LXL04_013687	`PF29561.1`	DUF8566	586	782	4.5e-65	220.0
LXL04_013687	`PF10536.15`	PMD	653	813	6.7e-12	46.0

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
`Q84K34`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 10	32.836%	Swiss-Prot	weak database homology
`Q9FKD9`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINA-like 6	34.783%	Swiss-Prot	weak database homology
`Q9FKD7`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 7	35.965%	Swiss-Prot	weak database homology
`Q9C6H2`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINA-like 3	38.693%	Swiss-Prot	weak database homology
`Q9FKD5`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINA-like 9	35.242%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card