A gene belonging to the Sm family of snRNP core proteins maps within the mouse MHC

Bedian, Vahe; Adams, Tasha A.; Geiger, Elizabeth A.; Gasser, David L.

doi:10.1007/s002510050297

Cited by 5 publications

(7 citation statements)

References 13 publications

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“…An example of this is drawn from a sequence in the mouse MHC region that was associated with a hormone-induced cleft palate phenotype. As reported previously (Bedian et al 1997), framework annotation demonstrated a cluster of ESTs not overlapping a known transcript. This cluster provided an initial model of exon structure, including potential alternative splicing, which was extended by further sequencing of cDNA clones associated with the ESTs.…”

Section: Initial Experiencementioning

confidence: 68%

GAIA: Framework Annotation of Genomic Sequence

et al. 1998

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As increasing amounts of genomic sequence from many organisms become available, and as DNA sequences become a primary reagent in biologic investigations, the role of annotation as a prospective guide for laboratory experiments will expand rapidly. Here we describe a process of high-throughput, reliable annotation, called framework annotation, which is designed to provide a foundation for initial biologic characterization of previously unexamined sequence. To examine this concept in practice, we have constructed Genome Annotation and Information Analysis (GAIA), a prototype software architecture that implements several elements important for framework annotation. The center of GAIA consists of an annotation database and the associated data management subsystem that forms the software bus along which other components communicate. The schema for this database defines three principal concepts: (1) Entries, consisting of sequence and associated historical data; (2) Features, comprising information of biologic interest; and (3) Experiments, describing the evidence that supports Features. The database permits tracking of annotation results over time, as well as assessment of the reliability of particular results. New framework annotation is produced by CARTA, a set of autonomous sensors that perform automatic analyses and assert results into the annotation database. These results are available via a Web-based query interface that uses graphical Java applets as well as text-based HTML pages to display data at different levels of resolution and permit interactive exploration of annotation. We present results for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and discuss ways in which the current prototype can be improved. The prototype is available for public use and comment at

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Section: Initial Experiencementioning

confidence: 68%

GAIA: Framework Annotation of Genomic Sequence

et al. 1998

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“…The coding sequence for the protein SmX5 human (AF196468) is identical to the mouse SnRNP core protein SmX5 [27,28] and highly homologue to the AmphiBRF43 from Branchiostoma floridae (Florida lancelet) [29], and the SmX5 protein from Arabidopsis thaliana.…”

Section: Human Snrnp Core Protein Smx5mentioning

confidence: 99%

Determination of Protein-Protein Interactions of ICln by the Yeast Two-Hybrid System

Schmarda

Fresser²,

Gschwentner³

et al. 2001

Cell Physiol Biochem

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ICln is a ubiquitously expressed eukaryotic protein. Expression of the protein in Xenopus laevis oocytes, the knocking-down of the protein in fibroblasts, or the reconstitution of the protein in lipid bilayer led to the assumption that this protein is an ionic channel or a significant part thereof. However, other possible roles for ICln in potential regulatory mechanisms have been postulated, as diverse as regulator of cell morphology by interacting with the Skb1 protein and/or interaction with core spliceosomal proteins. Here we show that ICln is able to interact with SnRNP core proteins SmD1, SmD2, SmD3, SmX5 and SmB/B’.

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“…First, it reduces the likelihood that the model is based on a rare artifact such as cloning of genomic DNA into a cDNA library. Second, multiple ESTs may also identify patterns consistent with alternative exon usage (Bedian et al 1997). Third, the positions of ESTs from each end of different cDNA clones may reveal different portions of the gene, and, by comparison of cDNA size to separation of ESTs on the genomic sequence, provide clues about exon/intron structure.…”

Section: Clustering Of Ests Over Annotated Genesmentioning

confidence: 99%

“…Variant or additional transcripts in the sequence may remain unidentified, or, if identified, uncharacterized or unpublished. For example, even in regions such as the HLA gene cluster, where an extensive body of work has accumulated, available annotation does not yet completely describe the gene content of the sequence (Bedian et al 1997). Therefore, it was necessary to restrict this set to a small number of sequences for which there was clear evidence of exhaustive transcript mapping: ∼170 kb from the DiGeorge syndrome minimal critical region (Gong et al 1996; DGCR, IC accession nos.…”

Section: Construction Of Genomic Test Setsmentioning

confidence: 99%

“…In this context, the most important characteristic is high positive predictive value, so that the resulting annotation forms a reliable resource, and does not lead to the frequent misapplication of laboratory efforts. Once an area of interest has been so identified, additional similarity data, obtained from both high and low stringency analysis of nucleotide and predicted amino acid sequences, can add further information about gene structure, variation, and potential function (Bedian et al 1997;Wolfsberg and Landsman 1997). Such information may be used not only to further biologic evaluation of specific genes, but as the basis for preliminary investigations of genome-wide structure and function.…”

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Analysis of EST-Driven Gene Annotation in Human Genomic Sequence

Searls²,

Gc³

1998

Genome Res.

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We have performed a systematic analysis of gene identification in genomic sequence by similarity search against expressed sequence tags (ESTs) to assess the suitability of this method for automated annotation of the human genome. A BLAST-based strategy was constructed to examine the potential of this approach, and was applied to test sets containing all human genomic sequences longer than 5 kb in public databases, plus 300 kb of exhaustively characterized benchmark sequence. At high stringency, 70%-90% of all annotated genes are detected by near-identity to EST sequence; >95% of ESTs aligning with well-annotated sequences overlap a gene. These ESTs provide immediate access to the corresponding cDNA clones for follow-up laboratory verification and subsequent biologic analysis. At lower stringency, up to 97% of annotated genes were identified by similarity to ESTs. The apparent false-positive rate rose to 55% of ESTs among all sequences and 20% among benchmark sequences at the lowest stringency, indicating that many genes in public database entries are unannotated. Approximately half of the alignments span multiple exons, and thus aid in the construction of gene predictions and elucidation of alternative splicing. In addition, ESTs from multiple cDNA libraries frequently cluster over genes, providing a starting point for crude expression profiles. Clone IDs may be used to form EST pairs, and particularly to extend models by associating alignments of lower stringency with high-quality alignments. These results demonstrate that EST similarity search is a practical general-purpose annotation technique that complements pattern recognition methods as a tool for gene characterization.

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A gene belonging to the Sm family of snRNP core proteins maps within the mouse MHC

Cited by 5 publications

References 13 publications

GAIA: Framework Annotation of Genomic Sequence

GAIA: Framework Annotation of Genomic Sequence

Determination of Protein-Protein Interactions of ICln by the Yeast Two-Hybrid System

Analysis of EST-Driven Gene Annotation in Human Genomic Sequence

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