LXL04_026167 | RubberDandelionOmics

Gene overview

LXL04_026167

Reference: OH-1004 Chr: Chr05 Coordinates: 122102145-122104316 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2091 bp · LXL04_026167|LXL04_026167|OH1004|cDNA

ATGGGTTGCACTGTTAGAGAAAAGCACATCCGCACAAATCGAAGGCCTAGGCCTTTGAAATCCGATTCTGATGGGATGGATAAAGCTCTGGCTAACAAATCTACTTTAAACGCATTGAATTTCCAATTGGGATTCAACGAATCAGCTCAAAATCCCAATTCAAACCCTAATTTCGACGACAGTGGTTGGGGTTACTGCACGGAGGAACAATTAGAAGAGATTTTGTTGAAGAATTTGGAGTTTCTGTATAACGAGGCGAT...

CDS

Download CDS FASTA

2091 bp · LXL04_026167|LXL04_026167|OH1004|CDS

ATGGGTTGCACTGTTAGAGAAAAGCACATCCGCACAAATCGAAGGCCTAGGCCTTTGAAATCCGATTCTGATGGGATGGATAAAGCTCTGGCTAACAAATCTACTTTAAACGCATTGAATTTCCAATTGGGATTCAACGAATCAGCTCAAAATCCCAATTCAAACCCTAATTTCGACGACAGTGGTTGGGGTTACTGCACGGAGGAACAATTAGAAGAGATTTTGTTGAAGAATTTGGAGTTTCTGTATAACGAGGCGAT...

Protein

Download Protein FASTA

696 aa · LXL04_026167|LXL04_026167|OH1004|PROTEIN

MGCTVREKHIRTNRRPRPLKSDSDGMDKALANKSTLNALNFQLGFNESAQNPNSNPNFDDSGWGYCTEEQLEEILLKNLEFLYNEAIVKLVALGYEEEVALNAILRNGHCYGGMDVLTNILHNSLAFLNSGSTVNEGDPDEGEQIFADLRQLEEYSLAGMVCLLQQIKPQLSKGDAMWCLLMSDLHVGRASVMEIPIPSNPNTDSYTNSSESTSPIVNVNDDSVGVTPALCRFHGGWGFGNGGTSDFPVNRFLSYAASEM...

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_026167`
TK1151 ID	TkA06G023320
OH-1004 ID	LXL04_026167
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_026167

Location Chr05:122102145-122104316 (+)

Description Similar to MIP1: MND1-interacting protein 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g32530`	MND1-interacting protein 1.	No verified direct reference in this release
`At4g03000`	Putative E3 ubiquitin-protein ligase RF298.	No verified direct reference in this release
`At1g03365`	Putative E3 ubiquitin-protein ligase RF4.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026167 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0008270 zinc ion binding Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G03365

ath:AT1G32530

ath:AT4G03000

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.601

Rank 1 · LXL04_026167 · OH-1004

Cytoplasm0.360

Rank 2 · LXL04_026167 · OH-1004

Cell membrane0.092

Rank 3 · LXL04_026167 · OH-1004

Plastid0.040

Rank 4 · LXL04_026167 · OH-1004

Endoplasmic reticulum0.040

Rank 5 · LXL04_026167 · 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.

PF20235.4PIR2-like_helical78-191 aa

PF13920.13zf-C3HC4_3642-687 aa

PF14447.13Prok-RING_4645-688 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026167	`PF20235.4`	PIR2-like_helical	78	191	1.3e-25	90.6
LXL04_026167	`PF13920.13`	zf-C3HC4_3	642	687	6.4e-13	49.0
LXL04_026167	`PF14447.13`	Prok-RING_4	645	688	2.5e-06	28.0

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
`Q8RX22`	Arabidopsis thaliana	MND1-interacting protein 1	52.538%	Swiss-Prot	strong database homology
`Q0WPJ7`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase RF298	33.523%	Swiss-Prot	weak database homology
`Q9ZVT8`	Arabidopsis thaliana	Putative E3 ubiquitin-protein ligase RF4	35.345%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card