protein-coding genes
Site-to-site Rate Variation in Protein Coding Genes
... 13 protein coding genes from the completed mitochondrial genomes of a total of 111 taxa sampled from ten animal clades, we find extensive variability of synonymous rates in the majority of ...
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A subset of conserved mammalian long non coding RNAs are fossils of ancestral protein coding genes
... of protein-coding potential loss occurring at several time points during vertebrate evolution, we focused on six vertebrate species found at intermediate distances from human and mouse and used those as ...
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Recent de novo origin of human protein coding genes
... new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or ...new genes from noncoding DNA is extremely rare, and very few ...
8
Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs
... and protein cod- ing genes and their transcripts were ...and protein coding genic regions and their flanking ...tein coding and lncRNA genes in pigs, and a similar trend of LINEs ...
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Human protein coding genes and gene feature statistics in 2019
... Due to the continuous increase of data deposited in genomic repositories, a revision and analysis of their con- tent is recommended. We provide here a tabulated set of data about human nuclear ...
5
Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes
... mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal ...rRNA genes, but there is a lack of a standard nomenclature for introns present in ...
8
Conserved syntenic clusters of protein coding genes are missing in birds
... 18,596 protein coding genes in lizard, 12,113 are predicted to have 1-to-1 orthologs in ...1,559 genes that are potential candi- dates for missing genes in birds (Table ...conserved ...
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Tracing the De Novo Origin of Protein Coding Genes in Yeast
... novo genes between any subpopulations were determined by Fisher’s exact test (P ⬍ ...novo genes. Reconstruction of ancestral state. The 1,000 single-copy genes that are universally present in all ...
11
De novo origin of protein coding genes in murine rodents
... of genes arising partly though duplication, and partly through de novo mechanisms, is the evolution of the antifreeze glycoprotein in Arctic cod and in Antarctic notothenioid fish ...novel genes from ...
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Detecting positive selection in protein coding genes
... Kreitman, 1991) for protein coding data has been more successful at detecting selection. The basic idea behind MK test is similar to that underlying HKA test. The MK test compares the ratio of nonsynonym ...
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Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates
... Ndh5 were used for estimating branch lengths by the maxi- mum likelihood method; a general reversible model of nucle- otide substitution and gammadistributed substitution-[r] ...
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Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)
... of protein-coding genes ...mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny ...COI genes are more ...
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The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes
... the protein- coding genes are compared to protein families ...The protein se- quences are compared to COG PSSMs obtained from the CDD database [10] using the program RPS-BLAST at an ...
5
The mitochondrial genome of Parascaris univalens implications for a “forgotten” parasite
... 36 genes: 12 protein-coding genes (adenosine triphosphatase subunit 6 [atp6], the cyto- chrome c oxidase subunits 1, 2 and 3 [cox1-cox3], cyto- chrome b (cytb) and the nicotinamide ...
8
Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens
... for the total hypothetical micF RNA structure used con- sisted of a rho-independent termination motif at 35–85 nt downstream from the 3' end of the 13 nt sequence. The P. luminescens genome was scanned and sequences ...
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The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: Its composition and comparative analysis
... known genes, including 89 protein-coding genes, 8 ribosomal RNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species), with 18 of them located in the inverted repeat ...
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Identification of Genes Potentially Involved in the Increased Risk of Malignancy in NF1-Microdeleted Patients
... 16 protein-coding genes and the 2 microRNAs located in the ...Five genes were significantly upregulated: OMG and SUZ12 in plexiform neurofibromas and ATAD5, EVI2A and C17orf79 in ...two ...
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Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma
... of protein-coding genes and non-coding RNAs may contribute to delineate molecular heterogeneity within ccRCC and may help guiding treatment of ...
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Biological function in the twilight zone of sequence conservation
... most protein-coding genes placed at one extreme because of their strong degree of constraint, then long non-coding RNAs (lncRNAs) are located at the other: most multi- exonic lncRNA loci ...
9
The complete sequences and gene organisation of the mitochondrial genomes of the heterodont bivalves Acanthocardia tuberculata and Hiatella arctica – and the first record for a putative Atpase subunit 8 gene in marine bivalves
... typical protein coding genes, lacking the Atpase subunit 8 (atp8) gene, as all published marine ...all genes on the same strand and have an additional ...with genes located on both ...
14