LXL04_030253 | RubberDandelionOmics

Gene overview

LXL04_030253

Reference: OH-1004 Chr: Chr06 Coordinates: 112442140-112443708 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1218 bp · LXL04_030253|LXL04_030253|OH1004|cDNA

ATGTTTACCGGCTTCAACGAGCTCATCAGCTTAAACTTTGCCCTTCAAAAACACTCTCCTTCTACCGGAGCTATTTGGTACGCCGCCGGTCCTATAGCTGTACTCATGTTCGCCTCTCTTGTCTACTCAATTTCGTCCAAAAATAAGAAGGAATTGAACATCGGAAGGTATGATGATGTCTCGGTAGAGATTGCAGAGGCGGCCAGAGGCTCGTTTCAGAGATCTGATGACGACGAAGTTTCCTGGAAATCTGCAAGCGA...

CDS

Download CDS FASTA

1218 bp · LXL04_030253|LXL04_030253|OH1004|CDS

ATGTTTACCGGCTTCAACGAGCTCATCAGCTTAAACTTTGCCCTTCAAAAACACTCTCCTTCTACCGGAGCTATTTGGTACGCCGCCGGTCCTATAGCTGTACTCATGTTCGCCTCTCTTGTCTACTCAATTTCGTCCAAAAATAAGAAGGAATTGAACATCGGAAGGTATGATGATGTCTCGGTAGAGATTGCAGAGGCGGCCAGAGGCTCGTTTCAGAGATCTGATGACGACGAAGTTTCCTGGAAATCTGCAAGCGA...

Protein

Download Protein FASTA

405 aa · LXL04_030253|LXL04_030253|OH1004|PROTEIN

MFTGFNELISLNFALQKHSPSTGAIWYAAGPIAVLMFASLVYSISSKNKKELNIGRYDDVSVEIAEAARGSFQRSDDDEVSWKSASDGVVCGFCHFFGVSVDFMLIHHCAFTSSVTLPAMNTIAEVIELFRTLNLPVLFQEDNNDIISEADAKYAEEIQIQEALLASIFSSQTKTNASTSSLKTRSSLSSLLKTTESTETTCKICLENHEQWQMFKNPTCSHSFCYTCTSKHATTKIHESKNTITCPESNCKSTLDPYTL...

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_030253`
TK1151 ID	TkA07G390150
OH-1004 ID	LXL04_030253
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	87.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_030253

Location Chr06:112442140-112443708 (+)

Description Similar to Arih1: E3 ubiquitin-protein ligase ARIH1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g26130`	Acts as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.	A forward genetic approach in Arabidopsis thaliana identifies a RING-type ubiquitin ligase as a novel determinant of seed longevity.2014 · DOI: 10.1016/j.plantsci.2013.11.004

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030253 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000209 protein polyubiquitination Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010431 seed maturation Biological Process

GO:0010476 gibberellin mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0039585 PKR/eIFalpha signaling Biological Process

GO:0140547 acquisition of seed longevity Biological Process

GO:0000151 ubiquitin ligase complex Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT2G26130

bta:508410

dre:405859

hsa:25820

mmu:23806

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.

Nucleus0.512

Rank 1 · LXL04_030253 · OH-1004

Cytoplasm0.417

Rank 2 · LXL04_030253 · OH-1004

Cell membrane0.092

Rank 3 · LXL04_030253 · OH-1004

Endoplasmic reticulum0.086

Rank 4 · LXL04_030253 · OH-1004

Mitochondrion0.045

Rank 5 · LXL04_030253 · 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.

PF01485.28IBR271-331 aa

PF01485.28IBR353-401 aa

PF22191.3IBR_1358-396 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030253	`PF01485.28`	IBR	271	331	1.7e-18	67.2
LXL04_030253	`PF01485.28`	IBR	353	401	1.7e-18	67.2
LXL04_030253	`PF22191.3`	IBR_1	358	396	5.1e-08	33.4

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
`F4ITM1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase RSL1	30.846%	Swiss-Prot	weak database homology

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