LXL04_008440 | RubberDandelionOmics

Gene overview

LXL04_008440

Reference: OH-1004 Chr: Chr02 Coordinates: 99769806-99770234 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

429 bp · LXL04_008440|LXL04_008440|OH1004|cDNA

ATGTCGACGGACACGATCCTTACGCTGAAGTCGAGCGACAATCAACTTTTCACCGTCGAAAAGGAGATCGCAATCAAATCCACGACGCTCAAAAACCTGTTGGAAGATGGCTGTGTTTCGCCTGTGATCCCTCTCCCGAACCTCGATTCCAAAATCCTATCCGTAGTTCTTGAATTACTCAATAAAGAGAACGACGATCAGAAAAAATCTGTTGAAAATCTGCAGATTTCTACGCTGGTGGATCTCGCAAAAGCTGCTAA...

CDS

Download CDS FASTA

429 bp · LXL04_008440|LXL04_008440|OH1004|CDS

ATGTCGACGGACACGATCCTTACGCTGAAGTCGAGCGACAATCAACTTTTCACCGTCGAAAAGGAGATCGCAATCAAATCCACGACGCTCAAAAACCTGTTGGAAGATGGCTGTGTTTCGCCTGTGATCCCTCTCCCGAACCTCGATTCCAAAATCCTATCCGTAGTTCTTGAATTACTCAATAAAGAGAACGACGATCAGAAAAAATCTGTTGAAAATCTGCAGATTTCTACGCTGGTGGATCTCGCAAAAGCTGCTAA...

Protein

Download Protein FASTA

142 aa · LXL04_008440|LXL04_008440|OH1004|PROTEIN

MSTDTILTLKSSDNQLFTVEKEIAIKSTTLKNLLEDGCVSPVIPLPNLDSKILSVVLELLNKENDDQKKSVENLQISTLVDLAKAANYMEIKDMLDVVCQRTADLIKDKTVEDVRAIFGIVNDFTPEEEHAIRAEYEWAFEI

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_008440`
TK1151 ID	TkA03G371950
OH-1004 ID	LXL04_008440
Relationship / confidence	Multi Candidate From Tk1151 / Complex relationship
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_008440

Location Chr02:99769806-99770234 (-)

Description Similar to ASK11: SKP1-like protein 11

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34210`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	Members of the Arabidopsis-SKP1-like gene family exhibit a variety of expression patterns and may play diverse roles in Arabidopsis.2003 · DOI: 10.1104/pp.103.024703
`At4g34470`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At3g21860`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At3g21850`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At1g20140`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	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_008440 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007346 regulation of mitotic cell cycle Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009753 response to jasmonic acid Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0019005 SCF ubiquitin ligase complex Cellular Component

KEGG gene cross-reference

ath:AT1G20140

ath:AT3G21850

ath:AT3G21860

ath:AT4G34210

ath:AT4G34470

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.

Cytoplasm0.709

Rank 1 · LXL04_008440 · OH-1004

Nucleus0.405

Rank 2 · LXL04_008440 · OH-1004

Mitochondrion0.054

Rank 3 · LXL04_008440 · OH-1004

Cell membrane0.035

Rank 4 · LXL04_008440 · OH-1004

Endoplasmic reticulum0.031

Rank 5 · LXL04_008440 · 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.

PF03931.22Skp1_POZ7-64 aa

PF01466.25Skp192-139 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008440	`PF03931.22`	Skp1_POZ	7	64	2.2e-17	63.7
LXL04_008440	`PF01466.25`	Skp1	92	139	3e-22	78.9

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
`O49484`	Arabidopsis thaliana	SKP1-like protein 11	45.270%	Swiss-Prot	moderate database homology
`O65674`	Arabidopsis thaliana	SKP1-like protein 12	44.595%	Swiss-Prot	moderate database homology
`Q9LSX8`	Arabidopsis thaliana	SKP1-like protein 10	45.455%	Swiss-Prot	moderate database homology
`Q9LSX9`	Arabidopsis thaliana	SKP1-like protein 9	44.805%	Swiss-Prot	moderate database homology
`Q9LNT9`	Arabidopsis thaliana	SKP1-like protein 4	40.000%	Swiss-Prot	moderate database homology

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