LXL04_009663 | RubberDandelionOmics

Gene overview

LXL04_009663

Reference: OH-1004 Chr: Chr02 Coordinates: 130897275-130898280 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

471 bp · LXL04_009663|LXL04_009663|OH1004|cDNA

atgtcttcttcatcgaAGGTTATCGTTTTGAAAAGTTCTGATGGAGAAACCTTCGAGGTTGAAGAAGCGGTGGCGTTGGAGTCACAGACGATTAAGCATATGATTGAAGACGACTGTGCCGACACTAGTATTCCTCTCCCCAACGTCACTAGCAAGATCCTCTCAAAGGTTATTGAGTACTGTAAGAAACATGTGGAGACACCGAAGACCGACGATAAGGCAGCTGAGGACGATCTGAAATCGTTTGATGTCGAGTTTGT...

CDS

Download CDS FASTA

471 bp · LXL04_009663|LXL04_009663|OH1004|CDS

ATGTCTTCTTCATCGAAGGTTATCGTTTTGAAAAGTTCTGATGGAGAAACCTTCGAGGTTGAAGAAGCGGTGGCGTTGGAGTCACAGACGATTAAGCATATGATTGAAGACGACTGTGCCGACACTAGTATTCCTCTCCCCAACGTCACTAGCAAGATCCTCTCAAAGGTTATTGAGTACTGTAAGAAACATGTGGAGACACCGAAGACCGACGATAAGGCAGCTGAGGACGATCTGAAATCGTTTGATGTCGAGTTTGT...

Protein

Download Protein FASTA

156 aa · LXL04_009663|LXL04_009663|OH1004|PROTEIN

MSSSSKVIVLKSSDGETFEVEEAVALESQTIKHMIEDDCADTSIPLPNVTSKILSKVIEYCKKHVETPKTDDKAAEDDLKSFDVEFVKVDQGTLFDLILAANYLNIKSLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENAWAFE

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_009663`
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_009663

Location Chr02:130897275-130898280 (+)

Description Similar to SKP1A: SKP1-like protein 1A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g75950`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	The Arabidopsis SKP1-LIKE1 gene is essential for male meiosis and may control homologue separation.1999 · DOI: 10.1073/pnas.96.20.11416 The ASK1 gene regulates development and interacts with the UFO gene to control floral organ identity in Arabidopsis.1999 · DOI: 10.1002/(sici)1520-6408(1999)25:3<209::aid-dvg4>3.0.co;2-o The ASK1 gene regulates B function gene expression in cooperation with UFO and LEAFY in Arabidopsis.2001 · DOI: 10.1242/dev.128.14.2735 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 The ASK1 and ASK2 genes are essential for Arabidopsis early development.2004 · DOI: 10.1105/tpc.017772
`At1g20140`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At5g42190`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0539500`	Involved in ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009663 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000226 microtubule cytoskeleton organization Biological Process

GO:0000278 mitotic cell cycle Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007059 chromosome segregation Biological Process

GO:0007140 male meiotic nuclear division 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:0009793 embryo development ending in seed dormancy Biological Process

GO:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0016567 protein ubiquitination Biological Process

KEGG gene cross-reference

ath:AT1G20140

ath:AT1G75950

ath:AT4G34210

ath:AT5G42190

dosa:Os09g0539500

osa:4347721

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.

Cytoplasm0.692

Rank 1 · LXL04_009663 · OH-1004

Nucleus0.420

Rank 2 · LXL04_009663 · OH-1004

Mitochondrion0.083

Rank 3 · LXL04_009663 · OH-1004

Cell membrane0.080

Rank 4 · LXL04_009663 · OH-1004

Endoplasmic reticulum0.046

Rank 5 · LXL04_009663 · 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_POZ6-65 aa

PF01466.25Skp1107-154 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009663	`PF03931.22`	Skp1_POZ	6	65	2.9e-31	108.1
LXL04_009663	`PF01466.25`	Skp1	107	154	2.1e-31	108.2

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
`Q39255`	Arabidopsis thaliana	SKP1-like protein 1A	77.358%	Swiss-Prot	strong database homology
`Q9LNT9`	Arabidopsis thaliana	SKP1-like protein 4	69.939%	Swiss-Prot	strong database homology
`Q9FHW7`	Arabidopsis thaliana	SKP1-like protein 1B	73.529%	Swiss-Prot	strong database homology
`O49484`	Arabidopsis thaliana	SKP1-like protein 11	71.242%	Swiss-Prot	strong database homology
`Q651E8`	Oryza sativa subsp. japonica	SKP1-like protein 20	71.345%	Swiss-Prot	strong database homology

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