Validation of Human Alternative Splice Forms Using the EASED Platform and Multiple Splice Site Discriminating Features

Abstract Alternative splicing is one of the most important mechanisms to generate a large number of mRNA and protein isoforms from a small number of genes. Its study became one of the hot topics in computational genome analysis. The repository EASED (Extended Alternatively Spliced EST Database, http://eased.bioinf.mdc-berlin.de/) stores a large collection of splice variants predicted from comparing the human genome against EST databases. It enables finding new unpublished splice forms that could be interesting candidate genes for stage specific, diseases specific or tissue specific splicing. The main idea behind selecting specific splice forms is to compare the number and the origin of ESTs confirming one isoform with the number and the origin of ESTs confirming the opposite isoform. A measure asDcs is introduced to take into account the unequal distribution of ESTs per splice site on one hand, and the possible uncertainties due to the relatively low quality of EST data on the other hand. First, the number of ESTs per splice site is scaled with a modified Hill function. The measure asDcs computes in the second step the distance of each pair of ESTs from equipartition. Equipartition exists if for every number of adult ESTs the same number of embryonic ESTs. The effect of several input parameters for the scaling of true EST values is analysed and can be reproduced on http://cardigan.zbh.uni-hamburg.de/asDcs. Some of the obtained best scoring hits for selected parameters (transcription factor P65, drebrin, and fetuin) have been already described in literature as been involved in embryonic development. This result shows the plausibility of this approach and looks promising for the identification of unplublished embryo specific alternative splice sites in human.

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Factors That Influence Alternative Splice Site Selection in Vitro

Molecular Biology of RNA ◽

10.1016/b978-0-12-372483-0.50010-7 ◽

1987 ◽

pp. 97-112 ◽

Cited By ~ 1

Author(s):

JAMES L. MANLEY ◽

JONATHAN C.S. NOBLE ◽

XIN-YUAN FU ◽

HUI GE

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Site Selection ◽

Splice Site Selection ◽

Alternative Splice Site

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EST analysis online: WWW tools for detection of SNPs and alternative splice forms

Trends in Genetics ◽

10.1016/s0168-9525(00)02089-8 ◽

2000 ◽

Vol 16 (9) ◽

pp. 416-418 ◽

Cited By ~ 11

Author(s):

D Brett

Keyword(s):

Alternative Splice ◽

Est Analysis ◽

Splice Forms

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The concentration of B52, an essential splicing factor and regulator of splice site choice in vitro, is critical for Drosophila development.

Molecular and Cellular Biology ◽

10.1128/mcb.14.8.5360 ◽

1994 ◽

Vol 14 (8) ◽

pp. 5360-5370 ◽

Cited By ~ 25

Author(s):

M E Kraus ◽

J T Lis

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Developmental Stages ◽

Immunoblot Analysis ◽

Splicing Factor ◽

Dependent Manner ◽

Concentration Dependent Manner ◽

Alternative Splice Site

B52 is a Drosophila melanogaster protein that plays a role in general and alternative splicing in vitro. It is homologous to the human splicing factor ASF/SF2 which is essential for an early step(s) in spliceosome assembly in vitro and also regulates 5' and 3' alternative splice site choice in a concentration-dependent manner. In vitro, B52 can function as both a general splicing factor and a regulator of 5' alternative splice site choice. Its activity in vivo, however, is largely uncharacterized. In this study, we have further characterized B52 in vivo. Using Western blot (immunoblot) analysis and whole-mount immunofluorescence, we demonstrate that B52 is widely expressed throughout development, although some developmental stages and tissues appear to have higher B52 levels than others do. In particular, B52 accumulates in ovaries, where it is packaged into the developing egg and is localized to nuclei by the late blastoderm stage of embryonic development. We also overexpressed this protein in transgenic flies in a variety of developmental and tissue-specific patterns to examine the effects of altering the concentration of this splicing factor in vivo. We show that, in many cell types, changing the concentration of B52 adversely affects the development of the organism. We discuss the significance of these observations with regard to previous in vitro results.

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Molecular and Cellular Characterization of a New α-Thalassemia Mutation (HBA2:c.94A>C) Generating an Alternative Splice Site and a Premature Stop Codon

Hemoglobin ◽

10.3109/03630269.2012.670683 ◽

2012 ◽

Vol 36 (3) ◽

pp. 244-252 ◽

Cited By ~ 3

Author(s):

Talal Qadah ◽

Jill Finlayson ◽

Christopher Newbound ◽

Nicole Pell ◽

Michelle Pascoe ◽

...

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Stop Codon ◽

Premature Stop Codon ◽

Alternative Splice Site ◽

Thalassemia Mutation

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Prevalent skipping of an individual exon accounts for shortened protein 4.1 Presles

Blood ◽

10.1182/blood.v80.11.2925.2925 ◽

1992 ◽

Vol 80 (11) ◽

pp. 2925-2930 ◽

Cited By ~ 1

Author(s):

S Feddal ◽

S Hayette ◽

F Baklouti ◽

R Rimokh ◽

R Wilmotte ◽

...

Keyword(s):

Red Blood Cells ◽

Alternative Splice ◽

Splice Site ◽

Blood Cells ◽

Protein 4.1 ◽

Alternative Splice Site ◽

Alternatively Spliced ◽

Domain Protein

Abstract An asymptomatic shortened variant of protein 4.1 (-8.5 Kd) was first recognized in the red blood cells and designated protein 4.1 Presles. We show here that the missing segment belongs to the 22/24 Kd domain. Protein 4.1 cDNA from reticulocytes was amplified, mapped, and sequenced. The truncation appeared to result from the prevalent skipping of an individual and alternatively spliced exon, also called motif II, whereas this motif is preferentially retained under normal conditions. The same phenomenon was observed in lympho-blastoid cells. Sequencing over 80 bp of intronic sequences 5′ and 3′ of motif II failed to reveal any change. A new alternative splice site was incidently found 81 nucleotide downstream of motif II in both normal and truncated 4.1 mRNA.

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half pint Regulates Alternative Splice Site Selection in Drosophila

Developmental Cell ◽

10.1016/s1534-5807(02)00128-4 ◽

2002 ◽

Vol 2 (3) ◽

pp. 343-353 ◽

Cited By ~ 57

Author(s):

Cheryl Van Buskirk ◽

Trudi Schüpbach

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Site Selection ◽

Splice Site Selection ◽

Alternative Splice Site

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Temporal and spatial expression of alternative splice-forms of the α1(XI) collagen gene in fetal rat cartilage

Developmental Dynamics ◽

10.1002/(sici)1097-0177(199809)213:1<12::aid-aja2>3.0.co;2-0 ◽

1998 ◽

Vol 213 (1) ◽

pp. 12-26 ◽

Cited By ~ 22

Author(s):

Gillian B.M. Davies ◽

Julia T. Oxford ◽

Lauri C. Hausafus ◽

Barbara F. Smoody ◽

Nicholas P. Morris

Keyword(s):

Alternative Splice ◽

Collagen Gene ◽

Spatial Expression ◽

Fetal Rat ◽

Temporal And Spatial ◽

Splice Forms

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CHARACTERIZATION OF THE SPLICE SITES IN GT–AG AND GC–AG INTRONS IN HIGHER EUKARYOTES USING FULL-LENGTH cDNAs

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720004000570 ◽

2004 ◽

Vol 02 (02) ◽

pp. 309-331 ◽

Cited By ~ 21

Author(s):

SUMIE KITAMURA–ABE ◽

HITOMI ITOH ◽

TAKANORI WASHIO ◽

AKIHIRO TSUTSUMI ◽

MASARU TOMITA

Keyword(s):

Alternative Splice ◽

Splice Site ◽

Consensus Sequence ◽

Full Length ◽

Splice Sites ◽

Consensus Sequences ◽

Full Length Cdna ◽

Strong Consensus ◽

Higher Eukaryotes

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT–AG and GC–AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT–AG and GC–AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC–AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.

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