LXL04_035089 | RubberDandelionOmics

Gene overview

LXL04_035089

Reference: OH-1004 Chr: Chr08 Coordinates: 13926641-13928324 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

741 bp · LXL04_035089|LXL04_035089|OH1004|cDNA

ATGGCCTGTGTGGAAGGAATGACAGCATCATCTTGCTCGGACTCCTCCAACAGCACCACAACAGACGAACTTATAACAGAATCACTGCTATTGAttcaaaacaacaaaaataaGGGCGATGAAGGTGATCTAAATCGCAACATAGAAGAAGGTTGTTCAAAGATGGTGAACAGGGAGTGTAGAATATGCCAAGAAGAAGATGGAGAGCACGAATTGGAATCTCCTTGTGCCTGTAATGGCACCCTCAAGTTTGCTCATAG...

CDS

Download CDS FASTA

741 bp · LXL04_035089|LXL04_035089|OH1004|CDS

ATGGCCTGTGTGGAAGGAATGACAGCATCATCTTGCTCGGACTCCTCCAACAGCACCACAACAGACGAACTTATAACAGAATCACTGCTATTGATTCAAAACAACAAAAATAAGGGCGATGAAGGTGATCTAAATCGCAACATAGAAGAAGGTTGTTCAAAGATGGTGAACAGGGAGTGTAGAATATGCCAAGAAGAAGATGGAGAGCACGAATTGGAATCTCCTTGTGCCTGTAATGGCACCCTCAAGTTTGCTCATAG...

Protein

Download Protein FASTA

246 aa · LXL04_035089|LXL04_035089|OH1004|PROTEIN

MACVEGMTASSCSDSSNSTTTDELITESLLLIQNNKNKGDEGDLNRNIEEGCSKMVNRECRICQEEDGEHELESPCACNGTLKFAHRKCIQKWCNKKGDITCEICNQVYSPNYALPPAITNPNPHVMTIDIRHAWAPHIDLRDTHFLAFTSEHQFLEQDYDVSSNTSIVYLRFMALILMFILLVRQALLITRDLGMVPVSSKIFNFQVSVLQLAGFLLPCYVVSRSWLMILRQRRRQVSQFIYPFF

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_035089`
TK1151 ID	TkA04G169480
OH-1004 ID	LXL04_035089
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.300
Protein coverage (%)	TK1151 99.587 / OH-1004 96.748 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_035089

Location Chr08:13926641-13928324 (+)

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_035089 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006897 endocytosis Biological Process

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:0016567 protein ubiquitination Biological Process

GO:0036503 ERAD pathway Biological Process

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

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

GO:0005764 lysosome Cellular Component

GO:0005768 endosome Cellular Component

KEGG gene cross-reference

ath:AT4G34100

mmu:320253

rno:364878

xla:779329

xtr:493225

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.

Cell membrane0.309

Rank 1 · LXL04_035089 · OH-1004

Lysosome / Vacuole0.277

Rank 2 · LXL04_035089 · OH-1004

Endoplasmic reticulum0.209

Rank 3 · LXL04_035089 · OH-1004

Cytoplasm0.207

Rank 4 · LXL04_035089 · OH-1004

Nucleus0.162

Rank 5 · LXL04_035089 · 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.

PF12906.14RINGv60-105 aa

PF12428.14DUF3675111-226 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035089	`PF12906.14`	RINGv	60	105	7.2e-14	52.4
LXL04_035089	`PF12428.14`	DUF3675	111	226	3.6e-24	86.3

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
`F4JKK0`	Arabidopsis thaliana	Probable E3 ubiquitin ligase SUD1	41.379%	Swiss-Prot	weak database homology

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