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. 2025 Jan 29:2025:10.17912/micropub.biology.001020.
doi: 10.17912/micropub.biology.001020. eCollection 2025.

Gene model for the ortholog of eIF4E1 in Drosophila yakuba

Bailey Lose  1 , Jeremy Girard  2 , Josephine Hayes  3 , Lane Weast  3 , Natalie Minkovsky  4 , Sarah Justice  5 , Jack A Vincent  6 , James J Youngblom  2 , Lindsey J Long  3 , Chinmay P Rele  1 , Laura K Reed  1
Affiliations

Gene model for the ortholog of eIF4E1 in Drosophila yakuba

Bailey Lose et al. MicroPubl Biol. .

Abstract

Gene model for the ortholog of eukaryotic translation initiation factor 4E1 ( eIF4E1 ) in the Dyak_CAF1 Genome Assembly (GenBank Accession: GCA_000005975.1 ) of Drosophila yakuba . This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

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Conflict of interest statement

The authors declare that there are no conflicts of interest present.

Figures

Figure 1. Genomic neighborhood and gene model for <i>eIF4E1 </i> in <i> D. yakuba</i>
Figure 1. Genomic neighborhood and gene model for eIF4E1 in D. yakuba
(A) Synteny comparison of the genomic neighborhoods for eIF4E1 in Drosophila melanogaster and D. yakuba . Thin underlying arrows indicate the DNA strand within which the reference gene– eIF4E1 –is located in D. melanogaster (top) and D. yakuba (bottom) genomes. The thin arrow pointing to the right indicates that eIF4E1 is on the positive (+) strand in D. melanogaster , and the thin arrow pointing to the left indicates that eIF4E1 is on the negative (-) strand in D. yakuba The wide gene arrows pointing in the same direction as eIF4E1 are on the same strand relative to the thin underlying arrows, while wide gene arrows pointing in the opposite direction of eIF4E1 are on the opposite strand relative to the thin underlying arrows. White gene arrows in D. yakuba indicate orthology to the corresponding gene in D. melanogaster . Gene symbols given in the D. yakuba gene arrows indicate the orthologous gene in D. melanogaster , while the locus identifiers are specific to D. yakuba . (B) Gene Model in GEP UCSC Track Data Hub (Raney et al., 2014). The coding-regions of eIF4E1 in D. yakuba are displayed in the User Supplied Track (black); CDS are depicted by thick rectangles and introns by thin lines with arrows indicating the direction of transcription. Subsequent evidence tracks include BLAT Alignments of NCBI RefSeq Genes (dark blue, alignment of Ref-Seq genes for D. yakuba ), Spaln of D. melanogaster Proteins (purple, alignment of Ref-Seq proteins from D. melanogaster ), Transcripts and Coding Regions Predicted by TransDecoder (dark green), RNA-Seq from Adult Females and Adult Males (red and light blue, respectively; alignment of Illumina RNA-Seq reads from D. yakuba ), and Splice Junctions Predicted by regtools using D. yakuba RNA-Seq (SRP006203 - Graveley et al, 2010). Splice junctions shown have a read-depth of 232, 500-999 and >1000 supporting reads in pink, brown and red, respectively. (C) Dot Plot of eIF4E1-PB in D. melanogaster ( x -axis) vs. the orthologous peptide in D. yakuba ( y -axis). Amino acid number is indicated along the left and bottom; CDS number is indicated along the top and right, and CDS are also highlighted with alternating colors. A region with a reduced sequence similarity is circled in red. (D) Dot Plot of eIF4E1-PC in D. melanogaster (x-axis) vs. the orthologous peptide in D. yakuba (y-axis). A region with reduced sequence similarity is circled in red.
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