LXL04_036348 | RubberDandelionOmics

Gene overview

LXL04_036348

Reference: OH-1004 Chr: Chr08 Coordinates: 40551279-40552331 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

900 bp · LXL04_036348|LXL04_036348|OH1004|cDNA

ATGACTCGAGGTGGTGTTTGCAAGGATGTTACTGAATCTCACCCTAAAATCGTATCAACTTCAAAACCCGACCCTAAAACCAATATTATCACAAAAACAACCGAAAACCACACCATTTCTTCAACTCATGTGGTTTACGAGCTTCTAGAATGTCCCATGTGCCGAAAGTTAATGTACCCTCCTATTCTTCAGTGTCGAAACGGCCATACATTATGCTCAAATTGCAAATCAAAAGTCCACAATTGTTGCCCAATGTGCCA...

CDS

Download CDS FASTA

900 bp · LXL04_036348|LXL04_036348|OH1004|CDS

ATGACTCGAGGTGGTGTTTGCAAGGATGTTACTGAATCTCACCCTAAAATCGTATCAACTTCAAAACCCGACCCTAAAACCAATATTATCACAAAAACAACCGAAAACCACACCATTTCTTCAACTCATGTGGTTTACGAGCTTCTAGAATGTCCCATGTGCCGAAAGTTAATGTACCCTCCTATTCTTCAGTGTCGAAACGGCCATACATTATGCTCAAATTGCAAATCAAAAGTCCACAATTGTTGCCCAATGTGCCA...

Protein

Download Protein FASTA

299 aa · LXL04_036348|LXL04_036348|OH1004|PROTEIN

MTRGGVCKDVTESHPKIVSTSKPDPKTNIITKTTENHTISSTHVVYELLECPMCRKLMYPPILQCRNGHTLCSNCKSKVHNCCPMCHCELGNIRCLALEKVAESLDLPCRHKPLGCHEIFPYYSKLNHEVKCRFRPYNCPYAGSKCSVTADVANLVTHLKNDHNVDMHDGCTFNHRYVKSNPHEVENATWMLTVFNCYGRQFCLHFEAFQLGMAPVYISFLRFIGEDSEAKNFSYSLEVGGYGRKLTWQGVPRSIRDSHQ...

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_036348`
TK1151 ID	TkA01G611310
OH-1004 ID	LXL04_036348
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	70.200
Protein coverage (%)	TK1151 95.897 / OH-1004 62.207 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_036348

Location Chr08:40551279-40552331 (+)

Description Similar to SINAT2: E3 ubiquitin-protein ligase SINAT2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g58040`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis.2017 · DOI: 10.1105/tpc.17.00056 SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267
`At2g41980`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	TRAF Family Proteins Regulate Autophagy Dynamics by Modulating AUTOPHAGY PROTEIN6 Stability in Arabidopsis.2017 · DOI: 10.1105/tpc.17.00056 SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267 SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants.2020 · DOI: 10.1111/jipb.13005
`At3g61790`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	SINAT E3 Ubiquitin Ligases Mediate FREE1 and VPS23A Degradation to Modulate Abscisic Acid Signaling.2020 · DOI: 10.1105/tpc.20.00267
`At5g53360`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	SINAT5 promotes ubiquitin-related degradation of NAC1 to attenuate auxin signals.2002 · DOI: 10.1038/nature00998 SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants.2020 · DOI: 10.1111/jipb.13005

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0356414`	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins.	The SINA E3 ligase OsDIS1 negatively regulates drought response in rice.2011 · DOI: 10.1104/pp.111.180893

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036348 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0080148 negative regulation of response to water deprivation Biological Process

GO:2000785 regulation of autophagosome assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005776 autophagosome Cellular Component

GO:0012505 endomembrane system Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G41980

ath:AT3G58040

ath:AT3G61790

ath:AT5G53360

dosa:Os03g0356414

osa:9266295

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.

Cytoplasm0.586

Rank 1 · LXL04_036348 · OH-1004

Nucleus0.411

Rank 2 · LXL04_036348 · OH-1004

Cell membrane0.079

Rank 3 · LXL04_036348 · OH-1004

Mitochondrion0.065

Rank 4 · LXL04_036348 · OH-1004

Endoplasmic reticulum0.055

Rank 5 · LXL04_036348 · 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.

PF21362.4Sina_RING51-86 aa

PF21361.4Sina_ZnF100-175 aa

PF03145.23Sina_TRAF195-291 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036348	`PF21362.4`	Sina_RING	51	86	6.7e-12	46.1
LXL04_036348	`PF21361.4`	Sina_ZnF	100	175	1.7e-28	99.6
LXL04_036348	`PF03145.23`	Sina_TRAF	195	291	2.7e-32	111.8

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
`Q9M2P4`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT2	71.711%	Swiss-Prot	strong database homology
`P93748`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINAT1	69.435%	Swiss-Prot	strong database homology
`Q84JL3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT3	74.330%	Swiss-Prot	strong database homology
`Q8S3N1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT5	72.414%	Swiss-Prot	strong database homology
`Q10L91`	Oryza sativa subsp. japonica	E3 ubiquitin-protein ligase DIS1	69.072%	Swiss-Prot	strong database homology

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