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Abstract <p>In this study, promoter sequences predicted by the MAHDS method in the <i>Oryza sativa</i> genome were analyzed using three genome annotations: RefSeq NCBI, Rice Genome Annotation Project, and Ensembl. Part of the predicted promoters was found to be located near annotated genes, which indicates their potential functional role. The remaining sequences, considered as potentially novel regulatory elements, were examined using YAPP for the presence of core promoter motifs and their functional combinations. All analyzed predicted promoters contain either an Inr or a TATA motif—the key elements involved in transcription initiation. The identified motif combinations suggest a high likelihood of transcriptional activity in these sequences, and the consistency of the results with annotated data and CAGE-seq signals supports the reliability and applicability of the MAHDS method.</p>

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Effect of a Comparative Analysis of Different Annotations of the Oryza sativa Rice Genome for In Silico Verification of Predicted Promoter Sequences

  • 期刊论文

  • 发表日期：

    2025年8月1日

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  • A. N. Bubnova,
  • I. V. Yakovleva,
  • A. M. Kamionskaya

摘要

Abstract

In this study, promoter sequences predicted by the MAHDS method in the Oryza sativa genome were analyzed using three genome annotations: RefSeq NCBI, Rice Genome Annotation Project, and Ensembl. Part of the predicted promoters was found to be located near annotated genes, which indicates their potential functional role. The remaining sequences, considered as potentially novel regulatory elements, were examined using YAPP for the presence of core promoter motifs and their functional combinations. All analyzed predicted promoters contain either an Inr or a TATA motif—the key elements involved in transcription initiation. The identified motif combinations suggest a high likelihood of transcriptional activity in these sequences, and the consistency of the results with annotated data and CAGE-seq signals supports the reliability and applicability of the MAHDS method.