https://www.researchgate.net/publication/13778815_Identification_of_a_novel_splice-site_mutation_of_the_BRCA1_gene_in_two_breast_cancer_families_Screening_reveals_low_frequency_in_Icelandic_breast_cancer_ ...
The results of the oligonucleotide hybridisations are shown in figs 2B-E. Whereas the normal control sample only showed the expected exon IIIc splice product (fig 2B, lane N), two additional shorter products were identifiable in the patient sample. DNA sequencing and hybridisation to specific oligonucleotides showed that one of these arose from direct splicing of exon IIIa to exon 12 (fig 2E), whereas the other utilised a cryptic splice site within exon IIIc (5′-CGGgtaatt-3′; new intronic nucleotides in lower case) (figs 2B, C). This cryptic splice site was previously known, both because it is activated by the pathogenic synonymous substitution 1032G→A in exon IIIc (Ala344Ala mutation),4 creating the donor splice site 5′-CAGgtaatt-3′12,13 and because the wild-type cryptic sequence is utilised in a mutant allele with a 6 nucleotide insertion that destroys the normal 5′ splice site.14 There was no evidence for ectopic expression of the alternatively spliced IIIb exon (fig 2D).7. The ...
A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included. Introns are supposed to be removed, while the exons are expressed. The mutation must occur at the specific site at which intron splicing occurs: within non-coding sites in a gene, directly next to the location of the exon. The mutation can be an insertion, deletion, frame shift, etc. The splicing process itself is controlled by the given sequences, known as splice-donor and splice-acceptor ...
TY - JOUR. T1 - Severe Hb S-β°-thalassaemia with a T→C substitution in the donor splice site of the first intron of the β-globin gene. AU - Gonzalez-Redondo, J. M.. AU - Stoming, T. A.. AU - Kutlar, Ferdane. AU - Kutlar, Abdullah. AU - McKie, V. C.. AU - McKie, K. M.. AU - Huisman, T. H.J.. PY - 1989/1/1. Y1 - 1989/1/1. N2 - Through direct sequencing and dot-blot analyses with synthetic oligonucleotide probes of amplified DNA, a new nucleotide substitution was discovered in a Black teenager with severe Hb S-β°-thalassaemia. The substitution involved a T→C replacement at the second position of the donor splice site of the first intervening sequence of the β-globin gene. The clinical and haematological observations made in Black subjects with Hb S-β°-thalassaemia, with different types of thalassaemia, suggest severe disease resembling sickle cell anaemia. Only an occasional patient had a milder clinical course, perhaps because of a greatly increased production of fetal ...
In this study, we describe the clinical features and provide experimental analyses of a novel point mutation affecting the penultimate nucleotide of the first exon of the HBA2 (HBA2: c.94A,G) gene identified in a 26-year-old female who also carries a heterozygous Hb E (HBB: c.79G,A) variant. The aim of the study was to investigate the impact of this point mutation on the transcriptional activity of the HBA2 gene using a combination of an initial in silico prediction followed by in vitro mutagenesis and transcriptional activity assessment. The analyses revealed that the HBA2: c.94A,G point mutation causes the activation of a cryptic splice site located 49bp upstream of the exon1-intron1 boundary in both HBA2 long and short isoforms, thus generating a frameshift and a premature termination codon between codons 48 and 49 in the second exon. A rapid degradation of the aberrantly spliced transcripts by the nonsense mediated decay (NMD) surveillance system is highly indicative of an a-thalassemia ...
In this thesis, I describe investigations into the evolution of splicing in mammals. I first investigate a small class of alternative splicing events, tandem splice sites, and show how they are used to introduce and remove ...
Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. [PMID 18634151] No association between systemic sclerosis and C77G polymorphism in the human PTPRC (CD45) gene. [PMID 20158892 ...
This sequence change affects a donor splice site in intron 4 of the WT1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs771527206, ExAC 0.002%). This variant has not been reported in the literature in individuals with WT1-related disease. ClinVar contains an entry for this variant (Variation ID: 661942). Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in WT1 are known to be pathogenic (PMID: 15150775). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic ...
Parameters: -f ,filename, potential splice sites in gff format -g ,filename, genome file in fasta format -c ,integer, defines the number of potential splice site every potential splice site itself is compared with -t ,float, has to be between 0 and 1 and defines how much the average coverage may differ -m ,integer, defines how many bases around the splice site should be checked -d enables debugging output -i ,integer, maximum length an Intron can be, default 500000 (human genome ...
Donor showed classic features of progeria. The biopsy was taken antemortem on 2/14/75 from skin of the thorax area. The culture was initiated using explants of minced skin tissue. The cell morphology is fibroblastlike. The karyotype is 46,XX; normal diploid female with 6% of cells examined showing random chromosome loss. Donor subject has a de novo single base substitution, a C>T change at nucleotide 2036 (2036C>T), which results in a silent change at codon 608 [Gly608Gly (G608G)] in exon 11 of the Lamin A gene (LMNA). This substitution creates an exonic consensus splice donor sequence and results in activation of a cryptic splice site which in turn causes skipping of 150 bp of the LMNA mRNA leading to the deletion of 50 amino acids from the protein. This altered LMNA protein was detected on western blots [Eriksson et al., Nature 423:293 (2003)]. From Fibroblast line AG01972. ...
Burge Lab MaxEntScan::score3ss scores 23 mers using different 3ss models To score 5 splice sites go to MaxEntScan::score5ss To build your own MaxEntScan models as described in the paper (below) refer to MaxEntScan::build Reference ...
Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5 splice site ...
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The adenovirus major late transcription unit (MLTU) is an example of a complex alternatively spliced gene, in which more than 15 different 3 splice sites can be joined to a common 5 splice site. Maturation of the full repertoire of possible mRNAs requires late viral protein synthesis and occurs only at late stages of the infectious cycle (16-24 hpi). We are trying to decipher the mechanisms regulating alternative 3 splice site choice during the infectious cycle. Therefore, we examined the splicing activity of several 3 splice sites from the MLTU in vitro in nuclear extracts prepared from adenovirus infected cells (Ad NE) and from uninfected cells. The results suggest that pre-mRNAs with "weak" 3 splice sites (short, atypical polypyrimidine tracts) are activated and pre-mRNAs with long, prototypical polypyrimidine tracts are repressed in Ad NE. In fact, our data show a reciprocal correlation between the strength of a polypyrimidine tract, defined by its affinity for U2AF65K in vitro, and the ...
Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced dinoflagellate genomic tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR-based contigs. The sequence contains an intron-rich set of five highly-expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice-site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3 splice site are repeated by an identical two to nine base pairs around the 5 splice site. The 5 and 3 splice sites are in the same locations within each repeat so that the ...
Asa BH, Cheng SO and Sonnenburg S (2008). Support vector machines and kernels for computational biology. PLoS 4: 1-10. Baten AK, Chang BC, Halgamuge SK and Li J (2006). Splice site identification using probabilistic parameters and SVM classification. BMC Bioinformatics 7 (Suppl 5): S15. http://dx.doi.org/10.1186/1471-2105-7-S5-S15 PMid:17254299 PMCid:1764471 Baten AK, Halgamuge SK, Chang B and Wickramarachchi N (2007). Biological sequence data preprocessing for classification: A case study in splice site identification. Adv. Neural Netw. 4492: 1221-1230. Baten AK, Halgamuge SK and Chang BC (2008). Fast splice site detection using information content and feature reduction. BMC Bioinformatics 9 (Suppl 12): S8. http://dx.doi.org/10.1186/1471-2105-9-S12-S8 PMid:19091031 PMCid:2638148 Burset M, Seledtsov IA and Solovyev VV (2000). Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 28: 4364-4375. http://dx.doi.org/10.1093/nar/28.21.4364 PMid:11058137 ...
Recognition of the 3′-splice site is a key step in pre-mRNA splicing and accomplished by a dynamic complex comprising splicing factor 1 (SF1) and the U2 snRNP auxiliary factor 65-kDa subunit (U2AF65). Both proteins mediate protein-protein and protein-RNA interactions for cooperative RNA-binding during spliceosome assembly. Here, we report the solution structure of a novel helix-hairpin domain in the N-terminal region of SF1 (SF1NTD). The nuclear magnetic resonance- and small-angle X-ray scattering-derived structure of a complex of the SF1NTD with the C-terminal U2AF homology motif domain of U2AF65 (U2AF65UHM) reveals that, in addition to the known U2AF65UHM-SF1 interaction, the helix-hairpin domain forms a secondary, hydrophobic interface with U2AF65UHM, which locks the orientation of the two subunits. Mutational analysis shows that the helix hairpin is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. We further show that tandem serine phosphorylation of a conserved ...
1991) Baudry et al. (2000) Ge et al. (2000) Kwabi-Addo et al. (2001) Lin et al. (1998) NOS Ich-1 ischemia Catania et al. (2001) Daoud et al. 1 Gene Transfer Methods Type I and II mutations either destroy splice sites or activate cryptic splice sites. Antisense nucleic acids can suppress point mutations and promote the formation of the normal gene products. Special chemistries were devised to prevent RNAseH-mediated cleavage of the RNA and to lower toxicity (Sazani and Kole 2003). Oligonucleotides have been used to target cryptic splice sites that are activated in beta thalassemias (Lacerra et al. Nature 409: 860-921 Le K, Mitsouras K, Roy M, Wang Q, Xu Q, Nelson SF, Lee C (2004) Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res 32: e180 Lee C, Wang Q (2005) Bioinformatics analysis of alternative splicing. Brief Bioinform. 6: 23-33. Levitin F, Baruch A, Weiss M, Stiegman K, Hartmann ML, Yoeli-Lerner M, Ziv R, Zrihan-Licht S, ...
Core splice site motifs and splicing regulatory elements function together to regulate splicing decisions. We are beginning to explore the functional interactions between classes of splicing regulatory elements, using genomic/comparative genomic analyses together with splicing reporter assays. One direction involves identifying pairs of elements that preferentially occur together in adjacent gene regions. This approach has led to the identification of a pair of intronic motifs that can function cooperatively to silence the splicing of intervening exons. Pairs of co-occurring motifs in other gene regions are also being explored. Patterns of evolutionary compensation between different classes of splicing regulatory elements can also provide clues to functional interactions. We are exploring in depth a pattern in which intronic splicing enhancers (ISEs) enhance the splicing of exons whose 5 splice sites have moderate intrinsic strength much more strongly than for other exons whose splice sites are ...
The proteome expanding effects of alternative pre-mRNA splicing have had a profound impact on eukaryotic evolution. The events that create this diversity can be placed into four major classes: exon skipping, intron retention, alternative 5′ splice sites, and alternative 3′ splice sites. Although the regulatory mechanisms and evolutionary pressures among alternative splicing classes clearly differ, how these differences affect the evolution of splicing regulation remains poorly characterized. We used RNA-seq to investigate splicing differences in D. simulans, D. sechellia, and three strains of D. melanogaster. Regulation of exon skipping and tandem alternative 3′ splice sites (NAGNAGs) were more divergent than other splicing classes. Splicing regulation was most divergent in frame-preserving events and events in noncoding regions. We further determined the contributions of cis- and trans-acting changes in splicing regulatory networks by comparing allele-specific splicing in F1 interspecific hybrids
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Component of the spliceosome A complex. Regulates alternative splicing of a number of mRNAs. May modulate splice site pairing after recruitment of the U1 and U2 snRNPs to the 5 and 3 splice sites of the intron. May both positively and negatively regulate apoptosis by regulating the alternative splicing of several genes involved in this process, including FAS and CASP2/caspase-2. In the case of FAS, promotes exclusion of exon 6 thereby producing a soluble form of FAS that inhibits apoptosis. In the case of CASP2/caspase-2, promotes exclusion of exon 9 thereby producing a catalytically active form of CASP2/Caspase-2 that induces apoptosis ...
There has been a bug discovered regarding the use of single-reads. When the new code was added for improved long pair-reads, it was not updated for single-reads by me (John Mu). Very sorry about that! There have been a number of problems as a result of this for people who use single-reads, including not discovering many junctions. A fixed version will be out in a few days, with an announcement. Please note: If you use pair-reads, there is nothing to be worried about. It is fine. ...
SC-JBS-L-A SPLICE CONNECTION WITH JUNCTION BOX INSTALLATION INSTRUCTIONS SC-JBP-L-A Class I, Division, Groups A, B, C, D Class II, Division 1 and, Groups E, F, G Type 4X Temp Code T (1) For use only with
Y" Splice adapter to gang two fixtures on one circuit. Economical made from yellow 12/3 STW cable, 18" overall length, with molded L5-20 twist-lock connectors ...
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Four separate CETP gene mutations have been published previously. Of the four mutations, the intron 14 donor splice site mutation4 and the Asp442-to-Gly mutation in exon 1528 are both known to be very common in the Japanese population.7 8 9 10 29 The other two mutations, the Gln309-to-Stop mutation in exon 1026 and a 1-bp insertion in intron 14,7 are probably sporadic mutations. Except for the Asp442-to-Gly mutation that causes partial CETP deficiency, the other three seemed to have null allelic effects, although exact mechanisms underlying the null effects have not been studied. In the present study, we demonstrated that the primary abnormality due to the intron 14 donor splice site mutation is the exon skipping of mRNA, which decreases the level of mRNA and produces a truncated protein that should be degraded intracellularly. These observations clearly explain the molecular basis of the complete CETP deficiency found not only in patients with the common intron 14 splicing mutation but also in ...
Vol. 204, No. 4, April 16, 2007. Pages 853-863.. Please note that an error appeared in Fig. 4 B, which displays the genomic sequence with the Unc13djinx point mutation. The sequence displayed in Fig. 4 B is from the minus strand (The NCBI GenBank reference assembly for the linear genomic DNA sequence of Unc13d [Locus NC_000077] is considered the plus strand). The indicated mutation is correct, but the indicated position of the resulting new donor splice site is incorrect. The correct position of the mutation and new donor splice site within intron 26, shown in the plus strand, is below:. 11311 ctccaaggct cacgagtCag tggcatgttg 11340 (C57BL/6J). 11311 ctccaaggct cacgagtAag tggcatgttg 11340 (jinx). The sequence shown is from GenBank genomic region NC_000077 for the linear genomic DNA sequence of Unc13d. The mutated C is shown in a bold capital letter, and the new donor splice site is underlined.. ...
Non-catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5 and 3 splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2,3 cyclic phosphate and 5-OH termini. There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events ...
Although nonsense mutations have been associated with the skipping of specific constitutively spliced exons in selected genes, notably the fibrillin gene, the basis for this association is unclear. Now, using chimaeric constructs in a model in vivo expression system, premature termination codons are …
about Alamut. "We are very pleased with Alamut since it conveniently streamlines post-sequencing analyses of detected variants. We value the programme user friendliness and its all-in one approach to variant analysis.". PROF. MILAN MACEK Jr. M.D. Ph.D ...
Ubiquitination close to the active site of RNAPII occurs in response to RNA processing events and is linked to transcriptional pausing, which is released following Bre5-Ubp3 mediated deubiquitination associated with the nascent transcript.
upstream sequence) g.5009 aagcacaga c.-301 . . . . . . g.5069 gccactagattagtctgtgagggaaggagatgcctcttccttcccttcaatagtgggtta c.-241 . . . , 02 . . g.7616 aacccagctggcaccctctggaactacgg , gaacaatattcttcaagagaaggtcactcta c.-181 . . . . . . / g.7676 ccaaagccaggagcacagtattctcaggatctcaacaaggaagagcagaccaag / gttgct c.-121 alternative splice site ^ . . . . . . g.7736 tctgattccttacaaccttccgtaattccaggcttgtggccccaaattcagggccccacc c.-61 . . . . . . g.7796 cttccaggaacaaatcattatagtaataatttgccttcatcttccatataccaactaagc c.-1 . . . . . . g.7856 ATGTTTAACTACGAACGTCCAAAACACTTCATCCAGTCCCAAAACCCATGTGGCTCCAGA c.60 M F N Y E R P K H F I Q S Q N P C G S R p.20 . . . . . . g.7916 TTGCAGCCTCCTGGACCAGAAACCTCCAGCTTCTCTAGCCAGACCAAACAGTCTTCCATT c.120 L Q P P G P E T S S F S S Q T K Q S S I p.40 . . . . . . g.7976 ATCATCCAGCCCCGCCAGTGTACAGAGCAAAGATTTTCTGCCTCCTCAACACTGAGCTCT c.180 I I Q P R Q C T E Q R F S A S S T L S S p.60 . . . . . . g.8036 CACATCACCATGTCCTCCTCTGCTTTCCCTGCTTCTCCCCAGCAGCATGCTGGCTCCAAC c.240 H I T M S S S A F P ...
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2M24: NMR structure of the 5 splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition.
Im only halfway through my college career, but I feel like I am a decent English major. Ive taken all the classes on grammar that Im going to take and I can write a solid essay under the right circumstances. For me, learning grammar wasnt the desirable part of being an English major. I was interested in finding out how meaning is conveyed in a story. I was interested in learning how authors weave language into emotion. I was not interested in learning about comma splices and semicolons. The professors here taught me smidgens of grammar despite my resistance. I wont be diagramming your sentences anytime soon and if you read this blog you will find typographical and grammatical errors aplenty, but comma splices are a particularly grievous error I attempt to avoid. In the same way that listening to the Pachelbel Rant makes it so you cant unhear Pachelbels canon in every modern pop song and the Death Star will always look like the AT&T logo after someone points it out, once you know what a ...
3VAH: U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs.
When Krainer and postdoctoral researcher Xavier Roca, Ph.D., analyzed SpliceRack, a comprehensive database of all ~200,000 known, functional splice sites found at the beginning of every intron in human genes, they were surprised to find many of these sites that didnt appear to have the right sequence of RNA bases to match U1. Experimental testing of particular examples of these sites showed, however, that they were in fact recognized by U1 and effectively used. These "atypical" sites, in other words, could be spliced to make the correct messenger RNA, despite the apparent mismatch ...
MIT biologists find that alternative splicing of RNA rewires signaling in different tissues and may often contribute to species differences.
The interactions established at the 5-splice site during spliceosome assembly are likely to be important for both precise recognition of the upstream intron boundary and for positioning this site in the active center of the spliceosome. Definition of the RNA-RNA and the RNA-protein interactions at the 5 splice site would be facilitated by the use of a small substrate amenable to modification during chemical synthesis. We describe a trans-splicing reaction performed in Saccharomyces cerevisiae extracts in which the 5 splice site and the 3 splice site are on separate molecules. The RNA contributing the 5 splice site is only 20 nucleotides long and was synthesized chemically. The trans-splicing reaction is accurate and has the same sequence, ATP, and Mg^2+ requirements as cis-splicing. We also report how deoxy substitutions around the 5-splice site affect trans-splicing efficiency. ...
Production of mRNA in eukaryotic cells involves not only transcription but also various processing reactions such as splicing. Recent experiments have indicated that there are direct physical connections between components of the transcription and processing machinery, supporting previous suggestions that pre-mRNA splicing occurs co-transcriptionally. Here we have used a novel functional approach to demonstrate co-transcriptional regulation of alternative splicing. Exon 3 of the alpha-tropomyosin gene is specifically repressed in smooth muscle cells. By delaying synthesis of an essential downstream inhibitory element, we show that the decision to splice or repress exon 3 occurs during a limited window of opportunity following transcription, indicating that splice site selection proceeds rapidly after transcription.
IVS17DS,T>G,+6; In a family with 2 affected sibs and in 2 patients with mucolipidosis IIIA (252900), Kudo et al. (Am J Hum Genet 78:451-463, 2006) described a donor splice site mutation in intron 17 of the GNPTAB gene, IVS17+6T-G, that results in skipping of exon 17 and frameshift with a premature termination at residue 1085 (P1084fsX1172). This same result was observed in another intron 17 splice site mutation in a patient with ML II (607840.0012). The former intron 17 splice site mutation was designated type I and the latter type II. Although the mRNA sequences derived from these 2 mutations are the same, the GlcNAc-phosphotransferase activities and clinical outcomes are different; fibroblasts with the type I mutation exhibited less than 0.1% activity, whereas those carrying the type II mutation exhibited 1 to 3% GlcNAc-phosphotransferase activity. That the type II mutation was located outside the invariant splice site was suggested as a possible cause of the greater activity ...
The Ewing sarcoma protein EWS is an RNA and DNA binding protein implicated in transcription, pre-mRNA splicing, and DNA damage response. Using CLIP-seq, we identified EWS RNA binding sites in exonic regions near 5′ splice sites. A prominent target was exon 6 of the FAS/CD95 receptor, which is alternatively spliced to generate isoforms with opposing activities in programmed cell death. Depletion and overexpression experiments showed that EWS promotes exon 6 inclusion and consequently the synthesis of the proapoptotic FAS/CD95 isoform, whereas an EWS-FLI1 fusion protein characteristic of Ewing sarcomas shows decreased activity. Biochemical analyses revealed that EWS binding promotes the recruitment of U1snRNP and U2AF65 to the splice sites flanking exon 6 and therefore exon definition. Consistent with a role for EWS in the regulation of programmed cell death, cells depleted of EWS show decreased sensitivity to FAS-induced apoptosis, and elevated EWS expression enhances apoptosis in ...
We report here the results of genetic studies on Müllerian aplasia, namely, results of TBX6 and LHX1 mutation screening in 112 MA patients and CNV analysis in a subset of them.. Sequencing of TBX6 (located in 16p11.2) revealed a splice mutation in two patients and rare missense variants in 15 patients (13.4%). TBX6 is a transcription factor that functions in early embryogenesis. It resides on the minus strand with a full-length transcript of 1806 bp, encoding a 436 aminoacid protein (NP_004599.2). TBX6 is a member of a phylogenetically well-conserved T-box gene family, where all members share the similar N-terminal DNA-binding domain, the T-box [55]. We identified a c.622-2A,T splice site mutation in two patients (one with MRKH and the other with total MA and with ovarian aplasia) and a rare homozygous missense variant in exon 4 and exon 6 in two patients. The splice site mutation is situated in the highly conserved splice acceptor site (AG) of exon 5. According to the in silico prediction ...
Lucero Rogel. PREP Program. Lab Group: Alan Zahler. PREP Research: The Zahler lab works to investigate the mechanism of RNA splicing by utilizing C. elegans as a model organism. Accurate splicing of pre-mRNA is a critical step in the gene expression pathway in eukaryotes carried out by a large ribonucleoprotein complex known as the spliceosome. The spliceosome consists of 5 RNAs (U1, U2, U4, U5, and U6) that assemble onto the pre-mRNA by recognizing conserved sequence elements that define the beginning and ends of introns, known as 5 and 3 splice sites. To facilitate the interactions between the pre-mRNA and the 5 RNAs, over 150 proteins are employed to aid in the process. Currently in the lab, I am working on elucidating the role of spliceosomal protein SNRP-27 in 5 splice site selection by uncovering differential interactions that a mutant and wild type form of this factor have with the splicing machinery.. Undergraduate Major: Biochemistry and Molecular Biology. Undergraduate Institution: ...
This site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Introns present special problems for the annotation of eukaryotic genomes. Splice sites are information-poor, and their recognition by the splicing apparatus is highly context-dependent and regulated, making identification by computational gene prediction programs a challenge. At present we do not understand splice site context well enough to predict which potential splice sites will be used, and thus how the genomic sequences will be expressed. Understanding the how and why of introns will require genome level information about splicing. One element of this will involve understanding splicing patterns and how they are regulated globally. Another element will involve understanding how splicing patterns change during evolution. To begin we study yeast, since it has the simplest known eukaryotic genome. In these pages we have listed known spliceosomal introns in the yeast genome and documented the ...
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