ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Martelli, Pier Luigi; D’Antonio, Mattia; Bonizzoni, Paola; Castrignanò, Tiziana; D’Erchia, Anna Maria; Meo, Paolo D’Onorio De; Fariselli, Piero; Finelli, Michele; Licciulli, Flavio; Mangiulli, Marina; Mignone, Flavio; Pavesi, Giulio; Picardi, Ernesto; Rizzi, Raffaella; Rossi, Ivan; Valletti, Alessio; Zauli, Andrea; Zambelli, Federico; Casadio, Rita; Pesole, Graziano

doi:10.1093/nar/gkq1073

Cited by 39 publications

(29 citation statements)

References 41 publications

(66 reference statements)

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“…Using the parental genes of the IR-type duplicates that contain one or more of the parental introns (seven in Drosophila spp., 55 in human, 92 in rice, and 200 in Arabidopsis), we searched the AS databases (DEDB [Lee et al, 2004] for Drosophila spp., ASPicDB [Martelli et al, 2011] for human, and ASIP [Wang and Brendel, 2006] for rice and Arabidopsis), which use RNA sequencing, EST, and cDNA support to identify AS isoforms, following the steps detailed in "Materials and Methods." We identified three, 86, 47, and 32 parental genes with intron retention AS isoforms for Drosophila spp., human, rice, and Arabidopsis, respectively.…”

Section: As Parental Isoforms Support As-based Modelmentioning

confidence: 99%

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Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes

Chen

Gschwend

Ouyang³

et al. 2014

Plant Physiology

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The structure of eukaryotic genes evolves extensively by intron loss or gain. Previous studies have revealed two models for gene structure evolution through the loss of introns: RNA-based gene conversion, dubbed the Fink model and retroposition model. However, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. We detected hundreds of retroduplicationderived genes in human (Homo sapiens), fly (Drosophila melanogaster), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplicated genes that have at least lost one and retained one intron compared with the parental copy (intron-retaining [IR] type). Our new model attributes intron retention alternative splicing to the generation of these IR-type gene pairs. We presented 25 parental genes that have an intron retention isoform and have retained introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis. Our alternative-splicing-based model in conjunction with the retroposition and Fink models can explain the IR-type gene observed. We discovered a greater percentage of IR-type genes in plants than in animals, which may be due to the abundance of intron retention cases in plants. Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures.

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Section: As Parental Isoforms Support As-based Modelmentioning

confidence: 99%

“…plantgdb.org/ASIP/; 2007 version; Brendel, 2006), human (2028) from ASPicDB (http://t.caspur.it/ASPicDB/; Martelli et al, 2011), and Drosophila spp. (2386) from DEDB (http://proline.bic.nus.edu.sg/dedb; Lee et al, 2004).…”

Section: Identifying Ir-type Genes With As Supportmentioning

confidence: 99%

Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes

Chen

Gschwend

Ouyang³

et al. 2014

Plant Physiology

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“…Sequence alignment was performed with the programs of MultAlin and ESPript. were predicted (39,40). We checked the alternative transcripts of these PA28 members deposited in GenBank, and found that four transcript variants of PA28α, one transcript variant of PA28β and four transcript variants of PA28γ have been reported.…”

Section: Discussionmentioning

confidence: 99%

“…Among them, three homologs of proteasome activator PA28α, PA28β, and PA28γ were shown to have upregulated mRNA levels in oral squamous cell carcinoma (OSCC) cells relative to oral keratinocytes (38). In this study, we analyzed alternative splicing of PA28γ using the alternative splicing prediction data base ASPicDB (39,40), and found that there are theoretically nearly 50 alternative transcripts. we therefore tried cloning these predicted splice variants.…”

Section: Introductionmentioning

confidence: 99%

A novel transcript variant of proteasome activator 28γ: Identification and function in oral cancer cells

Liu

et al. 2015

International Journal of Oncology

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Abstract. Proteasome activator 28γ (PA28γ) binds to and activates the proteasome in an ATP-independent manner to promote mainly ubiquitin-independent protein degradation in cells. Previously, four transcript variants of PA28γ have been identified, which have been closely correlated with the progression of cancers. In the present study, we predicted the alternative splicing of PA28γ via the bioinformatics tool ASPicDB and 49 splices were predicted. Then, we cloned some new segment according to predication in oral cancer cells using reverse transcription PCR and a novel variant of PA28γ was found. The novel transcript encodes a truncated form compared with other isoforms of PA28γ. However, it contains most of the conserved residues and the 'activation loop' of the PA28γ family. In order to explore its function, we overexpressed the variant in HEK293 cells and demonstrated that this variant is likely to further regulate cell cycle and apoptosis via regulating p53 and the mouse double minute2 homolog (Mdm2).

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“…Moreover, we have extracted from the literature the relevant information on the genome coordinates of RNA binding sites (or experimentally validated non-binding sites), type of binding assay, gene information and the context-specific splicing effects of splicing factor binding in terms of exonization or intronization. Furthermore, binding site information have been also reported in the transcript view of ASPicDB [1,3].…”

Section: Methodsmentioning

confidence: 99%

SpliceAid-F: a database of human splicing factors and their RNA binding sites

Giulietti

Piva

D’Antonio³

et al. 2012

EMBnet j.

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MotivationsThe pre-mRNA sequences of eukaryotes harbour multiple information layers in addition to the one specifying the aminoacid sequence. Indeed, specific signals regulating the splicing process, RNA folding, capping, polyadenylation, stability and nuclear export, overlap each other and with the coding information. Mutagenesis experiments have highlighted that splicing regulatory elements are scattered in the entire pre-mRNA sequence and that all nucleotide positions are potentially involved in the generation of the specific splicing pattern through the specific interaction with trans-acting RNA-binding proteins. In particular, the identification of cis-regulatory motifs in exonic regions, such as exonic splicing enhancers (ESEs) or silencers (ESSs), superimposed on the coding sequence of the gene can be driven by the observation of purifying selection occurring at synonymous codons [5]. The coordinated binding of combinations of regulatory proteins to their binding sites modulate the expression of specific transcript isoforms in a cell/tissue type-, development stage-, disease-and/or other condition-specific manners and may also promote or repress the formation of the spliceosome, the large (~60S) RNA-protein machinery that catalyzes intron removal. A growing list of mammalian protein factors involved in splicing regulation and their target sites in the pre-mRNA has been reported in the literature [2]. In order to establish a curated and retrievable repository of splicing regulatory factors and target sites for human genes we have recently created SpliceAid [4] that can also be used to find putative regulatory motifs in user submitted sequences. As a further evolution of SpliceAid, we present here SpliceAid-F, a database compilation of splicing regulatory factors and their experimentally validated target RNAs extracted from an exhaustive hand-curated literature search.

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ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Cited by 39 publications

References 41 publications

Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes

Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes

A novel transcript variant of proteasome activator 28γ: Identification and function in oral cancer cells

SpliceAid-F: a database of human splicing factors and their RNA binding sites

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