Faculty Opinions recommendation of Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes.

Author(s):  
Thomas Mitchell-Olds
2019 ◽  
Vol 36 (4) ◽  
pp. 861-862 ◽  
Author(s):  
Celine Scornavacca ◽  
Khalid Belkhir ◽  
Jimmy Lopez ◽  
Rémy Dernat ◽  
Frédéric Delsuc ◽  
...  

Abstract We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface.


2018 ◽  
Author(s):  
Elizabeth J. Adams ◽  
Rami Khoriaty ◽  
Anna Kiseleva ◽  
Audrey C. A. Cleuren ◽  
Kärt Tomberg ◽  
...  

ABSTRACTThe COPII component SEC24 mediates the recruitment of transmembrane cargoes or cargo adaptors into newly forming COPII vesicles on the ER membrane. Mammalian genomes encode fourSec24paralogs (Sec24a-d), with two subfamilies based on sequence homology (SEC24A/B and C/D), though little is known about their comparative functions and cargo-specificities. Complete deficiency forSec24dresults in very early embryonic lethality in mice (before the 8 cell stage), with later embryonic lethality (E 7.5) observed inSec24cnull mice. To test the potential overlap in function between SEC24C/D, we employed dual recombinase mediated cassette exchange to generate aSec24cc-dallele, in which the C-terminal 90% of SEC24C has been replaced by SEC24D coding sequence. In contrast to the embryonic lethality at E7.5 of SEC24C-deficiency,Sec24cc-d/c-dpups survive to term, though dying shortly after birth.Sec24cc-d/c-dpups are smaller in size, but exhibit no obvious developmental abnormality. These results suggest that tissue-specific and/or stage-specific expression of theSec24c/dgenes rather than differences in cargo function explain the early embryonic requirements for SEC24C and SEC24D.


2008 ◽  
Vol 59 (11) ◽  
Author(s):  
Vasile V. Morariu

The length of coding sequence (CDS) series in bacterial genomes were regarded as a fluctuating system and characterized by the methods of statistical physics. The distribution and the correlation properties of CDS for 47 genomes were investigated. The distribution was found to be approximated by an exponential function while the correlation analysis revealed short range correlations.


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