LXL04_001598 | RubberDandelionOmics

Gene overview

LXL04_001598

Reference: OH-1004 Chr: Chr01 Coordinates: 29822753-29827340 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3375 bp · LXL04_001598|LXL04_001598|OH1004|cDNA

ATGCCATATCATCAGCGTACCTGGATCGTAAATAAAATAAAAGGTAAGGGCATAAACCTAATTAACGCAATTTCCATCGATCCCCACAACTTTCGTTCTCGTAACCGTCTCGCTCCGATTCCAGCCTCCATCGCCATCACAGAGAGAGGATCTCGAGTAGAGGAGAGGGAATCTCGCCTGAAATCTTACATGGCGAACGAACAACCGGTTCTGCCGGCAGACGACAGAGTGCGAGATGTCGCTGTCGATGCGCCagtttc...

CDS

Download CDS FASTA

3354 bp · LXL04_001598|LXL04_001598|OH1004|CDS

ATGCCATATCATCAGCGTACCTGGATCGTAAATAAAATAAAAGGTAAGGGCATAAACCTAATTAACGCAATTTCCATCGATCCCCACAACTTTCGTTCTCGTAACCGTCTCGCTCCGATTCCAGCCTCCATCGCCATCACAGAGAGAGGATCTCGAGTAGAGGAGAGGGAATCTCGCCTGAAATCTTACATGGCGAACGAACAACCGGTTCTGCCGGCAGACGACAGAGTGCGAGATGTCGCTGTCGATGCGCCAGTTTC...

Protein

Download Protein FASTA

1117 aa · LXL04_001598|LXL04_001598|OH1004|PROTEIN

MPYHQRTWIVNKIKGKGINLINAISIDPHNFRSRNRLAPIPASIAITERGSRVEERESRLKSYMANEQPVLPADDRVRDVAVDAPVSSSSSSSGSSASILTSESVLDNANNGKNLSNTMYDDDDDEEGDVCRICRNPGDADNPLRYPCACSGSIKFVHQDCLLQWLNHSNARQCEVCKHPFSFSPVYAENAPAKLPFQEFVVGMSMKACHILQFFLRLTFVLSVWLVIIPFITFWIWRFSFVRTFKEAQKLFLTHISTTI...

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_001598`
TK1151 ID	TkA01G522970
OH-1004 ID	LXL04_001598
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.700
Protein coverage (%)	TK1151 100.000 / OH-1004 94.360 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_001598

Location Chr01:29822753-29827340 (-)

Description Similar to SUD1: Probable E3 ubiquitin ligase SUD1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34100`	Probable E3 ubiquitin ligase acting as a positive post-transcriptional regulator of 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity.	Arabidopsis ECERIFERUM9 involvement in cuticle formation and maintenance of plant water status.2012 · DOI: 10.1104/pp.112.198697 The SUD1 gene encodes a putative E3 ubiquitin ligase and is a positive regulator of 3-hydroxy-3-methylglutaryl coenzyme a reductase activity in Arabidopsis.2013 · DOI: 10.1105/tpc.112.108696

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001598 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008299 isoprenoid biosynthetic process Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0010025 wax biosynthetic process Biological Process

GO:0010143 cutin biosynthetic process Biological Process

GO:0010345 suberin biosynthetic process Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0036503 ERAD pathway Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

GO:0045541 negative regulation of cholesterol biosynthetic process Biological Process

GO:0070936 protein K48-linked ubiquitination Biological Process

GO:1900486 positive regulation of isopentenyl diphosphate biosynthetic process, mevalonate pathway Biological Process

KEGG gene cross-reference

ath:AT4G34100

hsa:10299

mmu:223455

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.

Endoplasmic reticulum0.606

Rank 1 · LXL04_001598 · OH-1004

Nucleus0.172

Rank 2 · LXL04_001598 · OH-1004

Golgi apparatus0.163

Rank 3 · LXL04_001598 · OH-1004

Cytoplasm0.118

Rank 4 · LXL04_001598 · OH-1004

Cell membrane0.085

Rank 5 · LXL04_001598 · 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.

PF12906.14RINGv131-177 aa

PF23113.2MARCHF6_C913-1090 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001598	`PF12906.14`	RINGv	131	177	6.9e-17	62.0
LXL04_001598	`PF23113.2`	MARCHF6_C	913	1090	2.9e-48	164.7

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
`F4JKK0`	Arabidopsis thaliana	Probable E3 ubiquitin ligase SUD1	73.088%	Swiss-Prot	strong database homology

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