Updated sequence information for this Drosophila species is no longer provided by FlyBase. Gene model annotations for this species are now updated and maintained at NCBI, using the gnomon automated annotation pipeline. See the NCBI page ‘Eukaryotic genomes annotated at NCBI’.
The FlyBase BLAST tool will continue to support queries against the reference genome of this species, but not queries against annotated transcripts or proteins. For the current release, there is no JBrowse or GBrowse view of the gene model annotations for this species.
The FlyBase archived release FB2017_05 includes the last NCBI annotation update for this species that was imported into FlyBase. That sequence data can be accessed from archived gene reports, via the archived GBrowse tool, and via archived bulk-data downloads.
Up-to-date information on gene product function can be found by searching UniProtKB for proteins or RNAcentral for non-coding RNAs.
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dyak\per using the Feature Mapper tool.
The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).
JBrowse - Visual display of RNA-Seq signals
View Dyak\per in JBrowsePlease Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.
For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.
Annotation GE16270 eliminated in release 1.04 of the Drosophila yakuba genome annotation; not predicted by NCBI Gnomon predictions dated 2014.03.14).
Quantifying rates of protein sequence divergence within and between species reveals that the Drosophila genome harbors a substantial proportion of genes with a very high divergence rate.
Dyak\per gene has been cloned and sequenced: comparison of the coding regions reveals a pattern of highly diverged areas interwoven with large conserved regions. Transformation experiments involving the Thr-Gly encoding region of per (Yu, Nature 326:765 ) suggest that the Thr-Gly repeat may play a role in determining song cycles, Dyak\per has 15 Thr-Gly pairs and has a long 80 second song rhythm.
The DNA sequence and presumed protein sequence was compared to per from D.melanogaster. The divergence observed in the less well conserved regions of the per protein is principally due to selective constraint. The level of silent substitution is comparable to the level of silent substitution previously reported between D.yakuba and D.melanogaster mitochondrial genes. This result suggests that silent sites are evolving at a similar rate in mitochondrial and nuclear genes of Drosophila.
Comments on Gene Model: Merge with nearby annotations supported.
