LXL04_013229 | RubberDandelionOmics

Gene overview

LXL04_013229

Reference: OH-1004 Chr: Chr03 Coordinates: 26327314-26329561 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1287 bp · LXL04_013229|LXL04_013229|OH1004|cDNA

ATGAACTTGAATGTGAACTCGGTGGATTCACTGGTGGCTGAAATACAAGGGTTATCGGGAAGTTCTCAAGATGTAAATCACTTGAACAATCTTTTGAAACAATCCGAGGACATAATTCGCTCTCAGCCTACAACTTTTGCTACATGCATCACTCAACTTGACCCTTCCCTTCATTCCCTTGGTTACCTTTACATTCTGGAAGCATGTACAGCAGGTCCAATTCCAGAACCACAGGCAAACGAACTAGTTCTTTCTGTTGT...

CDS

Download CDS FASTA

1287 bp · LXL04_013229|LXL04_013229|OH1004|CDS

ATGAACTTGAATGTGAACTCGGTGGATTCACTGGTGGCTGAAATACAAGGGTTATCGGGAAGTTCTCAAGATGTAAATCACTTGAACAATCTTTTGAAACAATCCGAGGACATAATTCGCTCTCAGCCTACAACTTTTGCTACATGCATCACTCAACTTGACCCTTCCCTTCATTCCCTTGGTTACCTTTACATTCTGGAAGCATGTACAGCAGGTCCAATTCCAGAACCACAGGCAAACGAACTAGTTCTTTCTGTTGT...

Protein

Download Protein FASTA

428 aa · LXL04_013229|LXL04_013229|OH1004|PROTEIN

MNLNVNSVDSLVAEIQGLSGSSQDVNHLNNLLKQSEDIIRSQPTTFATCITQLDPSLHSLGYLYILEACTAGPIPEPQANELVLSVVRFIDVCSAEQIRLVPDKFISVCKRLHEQVMVLGAPIRAVAPLLTAIRKIQPSSEHLTPLHPDFLQVCVSSKCYKIGYSILEDDIYEVDQPRDFFLYCYYGGMICIGQKRFAKALELFHNVVTAPMSAMNAIAVEAYKKYILVSLIHLRQFSATFPKYTSAVAQRNLKNFSQPY...

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_013229`
TK1151 ID	TkA02G510660
OH-1004 ID	LXL04_013229
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
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_013229

Location Chr03:26327314-26329561 (+)

Description Similar to CSN3: COP9 signalosome complex subunit 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g14250`	Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses.	A role of Arabidopsis COP9 signalosome in multifaceted developmental processes revealed by the characterization of its subunit 3.2001 · DOI: 10.1242/dev.128.21.4277

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013229 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000338 protein deneddylation Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0010971 positive regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0008180 COP9 signalosome Cellular Component

GO:0048471 perinuclear region of cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT5G14250

bta:507932

dre:335720

mmu:26572

pon:100171418

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.

Nucleus0.645

Rank 1 · LXL04_013229 · OH-1004

Cytoplasm0.548

Rank 2 · LXL04_013229 · OH-1004

Lysosome / Vacuole0.044

Rank 3 · LXL04_013229 · OH-1004

Endoplasmic reticulum0.035

Rank 4 · LXL04_013229 · OH-1004

Cell membrane0.033

Rank 5 · LXL04_013229 · 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.

PF22788.3COP9_hel_rpt23-248 aa

PF01399.34PCI287-360 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013229	`PF22788.3`	COP9_hel_rpt	23	248	2.6e-64	217.7
LXL04_013229	`PF01399.34`	PCI	287	360	4.4e-17	62.8

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
`Q8W575`	Arabidopsis thaliana	COP9 signalosome complex subunit 3	62.588%	Swiss-Prot	strong database homology

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