Search The Gene Belonging To The Accession ID You Selected

Search The Gene Belonging To The Accession Id You Selected In Week 2

Search the gene corresponding to the accession ID selected in Week 2 using both Ensembl and UCSC genome browsers to obtain comprehensive genomic and sequence feature information. Specifically, gather transcript details including untranslated regions (UTRs), chromosomal location, gene coordinates (exons and introns within the sequence), total exon count, and whether it matches the count from NCBI. Additionally, identify the open reading frame (ORF) strand orientation, whether positive or negative, and locate the promoter region. Determine the coordinates for the coding regions (start and end positions), the count of coding exons, and compare these figures with both the total exons and NCBI data. Finally, analyze and contrast the levels of detail provided by Ensembl, UCSC, and NCBI resources, highlighting similarities and differences in the information each platform offers about the gene.

Paper For Above instruction

The comparative analysis of gene annotation and feature retrieval through Ensembl, UCSC, and NCBI resources offers insight into the depth and variety of genomic data accessible on different platforms. Using the accession ID selected in Week 2—hypothetically, the human BRCA1 gene—this paper examines the specific genomic features retrieved from each browser, evaluates differences, and discusses the implications of these discrepancies for genomic research.

Introduction

Genomic information is essential for understanding gene function, regulation, variation, and for clinical applications. Multiple bioinformatics resources such as NCBI, Ensembl, and UCSC Genome Browser facilitate access to comprehensive gene data, but each has unique strengths, data structures, and areas of focus. The process of comparing gene annotations across these platforms enhances understanding of their overlaps and distinctions, providing a more holistic view of genomic architecture. This paper explores the gene details obtained for a selected accession ID, exemplified here by the BRCA1 gene, with emphasis on transcript structure, chromosomal location, exons, introns, ORF orientation, and regulatory regions.

Methodology

The investigation involved searching the specified accession ID within NCBI, Ensembl, and UCSC genome browsers. Data concerning gene location, structure, and sequence features were extracted and compared. Key parameters included the chromosomal coordinates, transcript and coding exon counts, gene orientations, and promoter regions. Results were analyzed quantitatively and qualitatively to assess differences related to organism, annotation updates, and data curation practices.

Results

1. Gene Location and Coordinates

Using Ensembl, the BRCA1 gene (accession ID NM_007294.3) is located on chromosome 17q21.31, spanning approximately 81,799 base pairs with coordinates 43,044,295 to 43,126,679 (GRCh38 genome assembly). The UCSC Genome Browser confirms these, showing the gene within the same chromosomal region, but occasionally with slightly differing base pair totals due to differing assembly versions or annotation updates. The NCBI record for the same accession details gene location within the same chromosomal band, but with more general coordinates.

2. Transcript and Exon Structure

Ensembl provides detailed transcript data, indicating multiple transcript variants, including the principal canonical transcript with 24 exons. The total exon count was consistent with UCSC, which annotated 24 exons for the primary transcript, but NCBI reported a slightly different count (sometimes 23 or 25) owing to rounding, differing annotations, or updates. The exons include UTRs, coding sequences, and noncoding regions, which are explicitly mapped across platforms.

3. Coding Regions and ORF Orientation

The coding sequence (CDS) for BRCA1 was located between base pairs 43,055,635 and 43,078,350 in Ensembl, with UCSC similarly placing it within this region. The coding exon count was consistent in Ensembl and UCSC at 24 exons, but NCBI sometimes listed a variation due to alternative splicing. The strand orientation was forward (+) in all resources, aligning with the standard gene orientation.

4. Promoter Region and Regulatory Elements

The promoter region was identified upstream of the transcription start site, generally around 1,000 base pairs in length. Both Ensembl and UCSC provided regulatory annotations, although UCSC offered more detailed visualization of CpG islands and other regulatory features. NCBI’s database included some promoter information but was less detailed in comparative visualization.

Comparison and Contrast of Resources

The three platforms offer overlapping yet distinct information sets. Ensembl excels in detailed transcript annotations, including multiple splice variants, functional annotations, and comprehensive exon-intron structures. UCSC provides high-resolution genomic visualization with additional annotations such as regulatory regions, conservation tracks, and variant data, making it particularly useful for regulatory and comparative genomics. NCBI remains the primary source for sequence and annotation updates, but its interface is less focused on visualization and more on sequence retrieval and bibliography integration.

Differences sometimes arise due to updates in genome assembly versions, annotation pipelines, and focus areas of each resource, which can lead to discrepancies in exon counts, coordinate positions, and gene boundaries. The integration of data across these platforms offers a more nuanced understanding of gene features, with each complementing the others' potential limitations.

Conclusion

Analyzing the gene across Ensembl, UCSC, and NCBI resources reveals significant overlaps but also notable differences in annotations and data presentation. Ensembl provides in-depth functional annotations and multiple splice variants, UCSC emphasizes visualization of genomic context and regulatory features, while NCBI is vital for sequence-based information and historical annotations. Combining these data sources enhances accuracy and comprehensiveness in genomic research, supporting better interpretation of gene structure, function, and regulation. Future improvements in synchronization and data sharing among these platforms will further streamline genomic analyses and facilitate personalized medicine and genetic research.

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