LXL04_022685 | RubberDandelionOmics

Gene overview

LXL04_022685

Reference: OH-1004 Chr: Chr05 Coordinates: 4779672-4781628 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1867 bp · LXL04_022685|LXL04_022685|OH1004|cDNA

TTTGACTTTCATTTGTTTCCTATACCATTTATCTCTCAAAAATCTTCGAAATATCCATGGTTATTAATTAAGCTATTCATGAATTCTGCAGGTTTGACTTTTCAAAAGATTCGTTCTTGGTTCATTTTATTTCCAGGATCTTGAATTTTTCATCAGGTTTGATTTCCACAAAACGATTGAAATCATGGTAGAAGATCAGGATAAAGAGAAAGAGGTCGCGGTTGACTTCTGGTCAACCGAAGAATGGCTGTCCCATGCAA...

CDS

Download CDS FASTA

1683 bp · LXL04_022685|LXL04_022685|OH1004|CDS

ATGGTAGAAGATCAGGATAAAGAGAAAGAGGTCGCGGTTGACTTCTGGTCAACCGAAGAATGGCTGTCCCATGCAAAAGATCTTGTACCACTGGCTCTCAAAAAGGCCCGAAAAGTTAACGGGTTTCCAGGCAGGTGGAAAATGATCATATCAAAATTAGAACAAATCCCGACTCGATTATCAGATTTATCAAGCCATCCGTGTTTTTCAAAGAACACATTATGCAAAGAACAACTTCAATCGGTTTCAAAAACATTAAA...

Protein

Download Protein FASTA

560 aa · LXL04_022685|LXL04_022685|OH1004|PROTEIN

MVEDQDKEKEVAVDFWSTEEWLSHAKDLVPLALKKARKVNGFPGRWKMIISKLEQIPTRLSDLSSHPCFSKNTLCKEQLQSVSKTLNEIIKMAEKCLKEKQEGKLQMQSDLDALSGKIDLNLRDCGLLIKTGVLSEVALSTCTLTAPEGTSHGSCSVTELLARLQIGHLDAKHKALDCLVDVMKEDEKTVLPFLGRSSISALVQLLTATSPRIRETTVTLICTLTESGGCDDLLVSEGVLPPLIRLLESGSSVGREKSAI...

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_022685`
TK1151 ID	TkA06G465960
OH-1004 ID	LXL04_022685
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.400
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_022685

Location Chr05:4779672-4781628 (-)

Description Similar to VAC8: Vacuolar protein 8 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g23140`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At3g54790`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g67340`	Functions as an E3 ubiquitin ligase.	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_022685 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000045 autophagosome assembly Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0048364 root development Biological Process

GO:0048658 anther wall tapetum development Biological Process

GO:0071562 nucleus-vacuole junction assembly Biological Process

GO:1904821 chloroplast disassembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0043495 protein-membrane adaptor activity Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT2G23140

ath:AT3G54790

kla:KLLA0_A11286g

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.

Cytoplasm0.526

Rank 1 · LXL04_022685 · OH-1004

Nucleus0.355

Rank 2 · LXL04_022685 · OH-1004

Cell membrane0.215

Rank 3 · LXL04_022685 · OH-1004

Endoplasmic reticulum0.051

Rank 4 · LXL04_022685 · OH-1004

Golgi apparatus0.044

Rank 5 · LXL04_022685 · 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.

PF23005.2DUF703224-133 aa

PF25598.2ARM_PUB175-363 aa

PF24768.2ARM_ARMC5270-468 aa

PF25598.2ARM_PUB273-527 aa

PF00514.30Arm310-349 aa

PF24768.2ARM_ARMC5393-533 aa

PF00514.30Arm430-468 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022685	`PF23005.2`	DUF7032	24	133	3.7e-38	130.6
LXL04_022685	`PF25598.2`	ARM_PUB	175	363	1.2e-09	38.8
LXL04_022685	`PF24768.2`	ARM_ARMC5	270	468	1.1e-16	61.7
LXL04_022685	`PF25598.2`	ARM_PUB	273	527	1.2e-09	38.8
LXL04_022685	`PF00514.30`	Arm	310	349	6.2e-34	115.6
LXL04_022685	`PF24768.2`	ARM_ARMC5	393	533	1.1e-16	61.7
LXL04_022685	`PF00514.30`	Arm	430	468	6.2e-34	115.6

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
`O22193`	Arabidopsis thaliana	U-box domain-containing protein 4	26.087%	Swiss-Prot	weak database homology
`Q8GWV5`	Arabidopsis thaliana	U-box domain-containing protein 3	25.899%	Swiss-Prot	weak database homology
`Q5XEZ8`	Arabidopsis thaliana	U-box domain-containing protein 2	27.632%	Swiss-Prot	weak database homology

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