LXL04_026411 | RubberDandelionOmics

Gene overview

LXL04_026411

Reference: OH-1004 Chr: Chr05 Coordinates: 125946974-125949445 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1548 bp · LXL04_026411|LXL04_026411|OH1004|cDNA

ATGACCCTTTTGGCCGGAATTAGTCACCGGTGTATATGTAATCGCCTGTTTTGCCTTGTTATACGTTATCTCCACCATCGGCAACACCAGTCCATACAACACCGTGATCGAATACGGCGTGAATATCTGTTTCACCAACAGAAACGCGACGCTGGTGAGGACGCCGATCACCGCCGTGATCGAATACAACGCAGGGAGGCGGAAGATTCCGCATGCGTAGAGAAAGTCGTCGACGCCGGTGTGGACGCCGATCACCGCCG...

CDS

Download CDS FASTA

1548 bp · LXL04_026411|LXL04_026411|OH1004|CDS

ATGACCCTTTTGGCCGGAATTAGTCACCGGTGTATATGTAATCGCCTGTTTTGCCTTGTTATACGTTATCTCCACCATCGGCAACACCAGTCCATACAACACCGTGATCGAATACGGCGTGAATATCTGTTTCACCAACAGAAACGCGACGCTGGTGAGGACGCCGATCACCGCCGTGATCGAATACAACGCAGGGAGGCGGAAGATTCCGCATGCGTAGAGAAAGTCGTCGACGCCGGTGTGGACGCCGATCACCGCCG...

Protein

Download Protein FASTA

515 aa · LXL04_026411|LXL04_026411|OH1004|PROTEIN

MTLLAGISHRCICNRLFCLVIRYLHHRQHQSIQHRDRIRREYLFHQQKRDAGEDADHRRDRIQRREAEDSACVEKVVDAGVDADHRRCEKHPWTHVLDGGSGQKGHMRTILKSSWKNASLKAEKGTLSPLSVSAMDPYSFSSSAAMAQQTWELENNIVTMEAPQSSESDAIFYYDESAQSKFQQEKPWSNDPHYFKRVKVSALALLKMVVHARSGGTIEVMGLMQGKTDGDAIIVMDAFALPVEGTETRVNAQADAYEYM...

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_026411`
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_026411

Location Chr05:125946974-125949445 (+)

Description Similar to CSN5B: COP9 signalosome complex subunit 5b

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71230`	Probable protease subunit of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses.	Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations.1998 · DOI: 10.1105/tpc.10.11.1779
`At1g22920`	Probable protease subunit of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses.	Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations.1998 · DOI: 10.1105/tpc.10.11.1779

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0654700`	Probable protease subunit of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and response to hormones (By similarity).	CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa.2016 · DOI: 10.1038/srep25485

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026411 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000338 protein deneddylation Biological Process

GO:0006412 translation Biological Process

GO:0006508 proteolysis Biological Process

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

GO:0009640 photomorphogenesis Biological Process

GO:0009733 response to auxin Biological Process

GO:0010093 specification of floral organ identity Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010387 COP9 signalosome assembly Biological Process

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

GO:0019954 asexual reproduction Biological Process

GO:0031347 regulation of defense response Biological Process

KEGG gene cross-reference

ath:AT1G22920

ath:AT1G71230

ddi:DDB_G0284597

dosa:Os04g0654700

hsa:10987

osa:4337249

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.

Cytoplasm0.436

Rank 1 · LXL04_026411 · OH-1004

Nucleus0.403

Rank 2 · LXL04_026411 · OH-1004

Cell membrane0.110

Rank 3 · LXL04_026411 · OH-1004

Golgi apparatus0.108

Rank 4 · LXL04_026411 · OH-1004

Endoplasmic reticulum0.108

Rank 5 · LXL04_026411 · 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.

PF01398.27JAB194-306 aa

PF18323.7CSN5_C394-474 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026411	`PF01398.27`	JAB	194	306	1.7e-36	125.3
LXL04_026411	`PF18323.7`	CSN5_C	394	474	3.2e-29	102.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9FVU9`	Arabidopsis thaliana	COP9 signalosome complex subunit 5b	84.770%	Swiss-Prot	moderate database homology
`Q8LAZ7`	Arabidopsis thaliana	COP9 signalosome complex subunit 5a	84.483%	Swiss-Prot	moderate database homology
`Q8H936`	Oryza sativa subsp. japonica	COP9 signalosome complex subunit 5	82.961%	Swiss-Prot	moderate database homology

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