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. 2021 Nov 12:2021:10.17912/micropub.biology.000474.
doi: 10.17912/micropub.biology.000474. eCollection 2021.

Drosophila yakuba - Tsc1

Bailey Lose  1 , Abigail Myers  1 , Savanah Fondse  2 , Ian Alberts  3 , Joyce Stamm  3 , James J Youngblom  2 , Chinmay P Rele  1 , Laura K Reed  1
Affiliations

Drosophila yakuba - Tsc1

Bailey Lose et al. MicroPubl Biol. .

Abstract

Gene Model for the ortholog of Tsc1 in the Drosophila yakuba DyakCAF1 assembly (GCA_000005975.1).

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Figures

Figure 1
Figure 1
(A) Synteny between D. melanogaster and D. yakuba in the genomic neighborhood around our focal gene, Tsc1: the thin arrows at the back indicate the strand in each species, whereas the thick arrows with the gene names in them indicate direction relative to Tsc1. The top line of text in the D. yakuba gene arrows indicates the locus identifiers specific to D. yakuba genes while the bottom line of text indicates the orthologous gene in D. melanogaster; (B) Gene Model in Apollo: A screenshot of the Apollo instance housing the gene model, containing student annotations, D. mel Proteins, NCBI RefSeq Genes, TransDecoder Transcripts, RNA-Seq tracks (Yang et al., 2018; SRP006203) and splice junctions, exon reading frames are indicated in blue, green, and red as in legend; (C) Dot Plot of gene in D. melanogaster (x-axis) vs. the gene in D. yakuba (y-axis), the numbers on the bottom and left correspond to amino acid position, and the numbers on the top and right correspond to exon number, the vertical and horizontal stripes of color highlight the exon corresponding to each number, the purple boxes represent a lack of sequence similarity in the protein sequences within coding exons three and six; (D) An image of exon three in the gene model from the GEP mirror of the UCSC Genome Browser for D. yakuba. The Conservation Track of 28 Drosophila species compared to exon three in D. melanogaster Tsc1-RA contains regions lacking sequence similarity (vertical red box; D. yakuba is highlighted in the horizontal red box). The gray scale at the top of the image represents the three reading frames, where Tsc1-RA is in reading frame +2 of Drosophila melanogaster. In the grayscale, the red boxes are stop codons and the green represent start codons. The maroon, green, and purple/pink tracks above the species alignments represent the ROAST alignments and conservation (28 Drosophila species), PhastCons Scores Based on Four-fold Degenerate Sites, and PhyloP Scores Based on Four-fold Degenerate Sites, respectively. For the Drosophila conservation track for 28 Drosophila species at the bottom of the figure, darker values to indicate higher levels of overall conservation as scored by phastCons.
See this image and copyright information in PMC

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