LXL04_033137 | RubberDandelionOmics

Gene overview

LXL04_033137

Reference: OH-1004 Chr: Chr07 Coordinates: 36939539-36946164 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2547 bp · LXL04_033137|LXL04_033137|OH1004|cDNA

ATGGGTCCCGGTGGTAACATCTTCCAAGACGTTACTGAATCGCGAGCTGATTATAATCTTAAATCTGCAAACATAGAAGGACGAAGCTGCCTGAGATTATGCGGATCCGCCGGTGGACGGCAGGGACTGGCTTCAAACAGCGCAGTCCATGAACTACTCGAGTGTCCCGTATGTCTTAACATAATGCACCCCCCAATTCATCAATGTCCAAATGGCCACACGATATGTGTGGTATGCAAATCGAAAGTACAAAACAGCTG...

CDS

Download CDS FASTA

2547 bp · LXL04_033137|LXL04_033137|OH1004|CDS

ATGGGTCCCGGTGGTAACATCTTCCAAGACGTTACTGAATCGCGAGCTGATTATAATCTTAAATCTGCAAACATAGAAGGACGAAGCTGCCTGAGATTATGCGGATCCGCCGGTGGACGGCAGGGACTGGCTTCAAACAGCGCAGTCCATGAACTACTCGAGTGTCCCGTATGTCTTAACATAATGCACCCCCCAATTCATCAATGTCCAAATGGCCACACGATATGTGTGGTATGCAAATCGAAAGTACAAAACAGCTG...

Protein

Download Protein FASTA

848 aa · LXL04_033137|LXL04_033137|OH1004|PROTEIN

MGPGGNIFQDVTESRADYNLKSANIEGRSCLRLCGSAGGRQGLASNSAVHELLECPVCLNIMHPPIHQCPNGHTICVVCKSKVQNSCPICRQELGNIRCLALEKVAESIELPCTECHVTGDIPFLVAHLKSDHNVDMHDGSTFNHRYVKPNPHEIENATWMLTIFNCFGYQFCLHFEAFHLGMAPVYMAFLRFMGDENDASKFSYSLEVGGNGRKLKWQGVPRSIRDGHKTAGAQVESGRPDLERTGLKVEPVMPIMVEI...

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_033137`
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_033137

Location Chr07:36939539-36946164 (+)

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
`At4g27880`	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

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033137 · 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:2000785 regulation of autophagosome assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005776 autophagosome Cellular Component

GO:0005886 plasma membrane 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:AT4G27880

ath:AT5G53360

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.

Mitochondrion0.475

Rank 1 · LXL04_033137 · OH-1004

Plastid0.253

Rank 2 · LXL04_033137 · OH-1004

Nucleus0.192

Rank 3 · LXL04_033137 · OH-1004

Cytoplasm0.083

Rank 4 · LXL04_033137 · OH-1004

Cell membrane0.025

Rank 5 · LXL04_033137 · 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_RING55-90 aa

PF03145.23Sina_TRAF165-233 aa

PF28564.1GEP3_N417-503 aa

PF01926.30MMR_HSR1584-659 aa

PF21516.3YqeH-like_C700-798 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_033137	`PF21362.4`	Sina_RING	55	90	6.1e-12	46.2
LXL04_033137	`PF03145.23`	Sina_TRAF	165	233	4.9e-24	85.4
LXL04_033137	`PF28564.1`	GEP3_N	417	503	2.9e-10	41.5
LXL04_033137	`PF01926.30`	MMR_HSR1	584	659	2e-09	38.3
LXL04_033137	`PF21516.3`	YqeH-like_C	700	798	3e-12	47.6

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
`Q9M2P4`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT2	62.454%	Swiss-Prot	weak database homology
`P93748`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase SINAT1	61.049%	Swiss-Prot	weak database homology
`Q84JL3`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT3	63.514%	Swiss-Prot	weak database homology
`Q9STN8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT4	62.389%	Swiss-Prot	weak database homology
`Q8S3N1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase SINAT5	62.844%	Swiss-Prot	weak database homology

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