LXL04_025102 | RubberDandelionOmics

Gene overview

LXL04_025102

Reference: OH-1004 Chr: Chr05 Coordinates: 105989364-105991007 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1068 bp · LXL04_025102|LXL04_025102|OH1004|cDNA

ATGGCGGAGATGTCAACGGAGACAACCGCGCCGTTACTCAGGCCACGGCAGGCTGCCGGAGAATCACAATCAGGGGAAGGTGGCAGGCCGACTACGCTCGCTCTTCTTCTGGGCCGTGCTTCGGGACGGCGTGGAGCGTCTATGCTGGTGCGCGAGACTGCAGCGCGACAACTGGAGGAGAGGCGAGCCGACTGGGGCTACTCGAAACCAGTTGTTGCCCTAGACATGACATGGAACCTCGCCTTCGTAGCGGTTTCGGT...

CDS

Download CDS FASTA

1068 bp · LXL04_025102|LXL04_025102|OH1004|CDS

ATGGCGGAGATGTCAACGGAGACAACCGCGCCGTTACTCAGGCCACGGCAGGCTGCCGGAGAATCACAATCAGGGGAAGGTGGCAGGCCGACTACGCTCGCTCTTCTTCTGGGCCGTGCTTCGGGACGGCGTGGAGCGTCTATGCTGGTGCGCGAGACTGCAGCGCGACAACTGGAGGAGAGGCGAGCCGACTGGGGCTACTCGAAACCAGTTGTTGCCCTAGACATGACATGGAACCTCGCCTTCGTAGCGGTTTCGGT...

Protein

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355 aa · LXL04_025102|LXL04_025102|OH1004|PROTEIN

MAEMSTETTAPLLRPRQAAGESQSGEGGRPTTLALLLGRASGRRGASMLVRETAARQLEERRADWGYSKPVVALDMTWNLAFVAVSVVLLICTLEEKPNVPIRVWICGYALQCAVHAVLVWLEYSRRSRRLHEEETTGGSESNYNDSEDDDGRIGAFLTSNTISYTKRCENLNTMVSFVWWLIGFYWMVSGGEILLHNAPRLYWLTVVFLAFDVFFAIFCVVLACLIGIALCCCLPCIIAILYAVAGQEGASEADLNILP...

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_025102`
TK1151 ID	TkAUNG024000
OH-1004 ID	LXL04_025102
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	100.000
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_025102

Location Chr05:105989364-105991007 (-)

Description Similar to RIE1: E3 ubiquitin protein ligase RIE1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g01735`	Probable E3 ubiquitin-protein ligase required for embryo development.	A RING-H2 zinc-finger protein gene RIE1 is essential for seed development in Arabidopsis.2003 · DOI: 10.1023/b:plan.0000009256.01620.a6
`At4g11680`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g12760`	Mediates E2-dependent protein ubiquitination in vitro.	No verified direct reference in this release
`At1g63170`	Mediates E2-dependent protein ubiquitination.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025102 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0016020 membrane Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G12760

ath:AT1G63170

ath:AT2G01735

ath:AT4G11680

dre:767686

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.

Lysosome / Vacuole0.311

Rank 1 · LXL04_025102 · OH-1004

Cell membrane0.240

Rank 2 · LXL04_025102 · OH-1004

Cytoplasm0.234

Rank 3 · LXL04_025102 · OH-1004

Endoplasmic reticulum0.233

Rank 4 · LXL04_025102 · OH-1004

Golgi apparatus0.213

Rank 5 · LXL04_025102 · 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.

PF13639.13zf-RING_2303-345 aa

PF17123.12zf-RING_11303-331 aa

PF12678.14zf-rbx1303-345 aa

PF13923.13zf-C3HC4_2304-344 aa

PF00097.32zf-C3HC4304-344 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025102	`PF13639.13`	zf-RING_2	303	345	8.5e-15	55.5
LXL04_025102	`PF17123.12`	zf-RING_11	303	331	2.6e-08	34.1
LXL04_025102	`PF12678.14`	zf-rbx1	303	345	4.2e-08	34.0
LXL04_025102	`PF13923.13`	zf-C3HC4_2	304	344	9.9e-07	29.2
LXL04_025102	`PF00097.32`	zf-C3HC4	304	344	4e-06	27.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8GUU2`	Arabidopsis thaliana	E3 ubiquitin protein ligase RIE1	61.878%	Swiss-Prot	strong database homology
`Q93Z92`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At4g11680	53.823%	Swiss-Prot	strong database homology
`Q9LN71`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g12760	52.023%	Swiss-Prot	strong database homology
`Q8LDB8`	Arabidopsis thaliana	E3 ubiquitin-protein ligase At1g63170	51.585%	Swiss-Prot	strong database homology

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