Description
Introduction
The Ras homolog enriched in brain (
Rheb
) encodes a Ras homolog (Karassek
et al.
2010). Ras is family of genes that make proteins involved in cell signaling pathways that control cell growth and cell death (Banerjee and Resat 2016).
The gene model reported here (dgri_Rheb) was developed for the May 2011 assembly of
D. grimshawi
Agencourt dgri_caf1/DgriCAF1 (GCA_000005155.1) to describe the ortholog to
D. melanogaster Rheb
(FBgn0041191) at the locus previously annotated as XM_001989756.1. The general protocol and datasets for the genome browser tracks used to establish this reported gene model are reported in Rele
et al.
2020. Additional tools and resources used in generating and confirming this model include HISAT (Kim
et al.
2015), BEDTools (Quinlan
et al.
2010), and the Sequence Read Archive (trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP073087)
.
Synteny
The
Rheb
gene on chromosome 3R in
D. melanogaster
is surrounded by the genes
CG12746
,
CG2931
,
CRMP
, and
CG2926
. Upon a
tblastn
search, the
Rheb
ortholog gene in
D. grimshawi
, on scaffold 14906, is surrounded by the genes XM_001989754.1, XM_001989755.1, XM_001989575.1, and XM_001989576.1 (orthologous to
Cenp-C
,
CLS
,
Nup93-2
, and
CG2519)
in
D. melanogaster
, Figure 1A). Though none of these flanking genes appear to be orthologous between the two species, we determined this region to contain the ortholog for
Rheb
in
D. grimshawi
because this location had a substantially better
blastp
hit to the
Rheb
protein sequence than to the second-best hit.
Gene Model
This gene model contains two isoforms of the
Rheb
protein in
D. grimshawi
, Rheb-PA and ­Rheb-PB (Figure 1B). Each of these isoforms contains five identical coding exons. The model in
D. melanogaste
r and
D. grimshawi
have the same length and number of exons, and are similar in peptide sequence. However, there is a dissimilarity at the start of the third exon; but the peptides replacing the ones in
D. melanogaster
have similar properties. The coordinates of the corrected gene model can be found in NCBI at GenBank/BankIt using the accession BK014396 and archived in CaltechData
here
.
Special Characters of Gene Model
Improper alignment at start of coding exon three
: As shown in Figure 1D, there is a stretch of amino acids (Figure 1D) that are not identical (black color), but similar (gray/white), between
D. melanogaster
and
D. grimshawi
. This pattern is also evident in a few other species as compared to
D. melanogaster
(Figure 1D). Though this is more obvious in
D. kikkawai, D. serrata, D. obscura, D. pseudoobscura, D. persimilis
, and
D. miranda
(Figure 1D) as compared to
D. grimshawi
(Figure 1D), it nonetheless exists.
Changes in the splice donor site for coding exon four
: Rheb-PA in
D. grimshawi
has a canonical GT splice donor site at the end of coding exon four. In contrast, the end of coding exon four of Rheb-PA in
D. melanogaster
, and in most of the other
Drosophila
species across the genus
Sophophora
, use a non-canonical GC splice donor site.
Extended data:
Fasta (.faa and .fna) and GFF files are archived and available on CaltechData:
D_grimshawi_Rheb_geneModel_gff_faa_fna
.
This file contains
Peptide Sequence of
Rheb
in
D. grimshawi
Nucleotide Sequence of
Rheb
in
D. grimshawi
GFF of
Rheb
in
D. grimshawi