A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes II: the importance of mRNA secondary structure in assessing the functionality of 3′ UTR variants

2006 ◽  
Vol 120 (3) ◽  
pp. 301-333 ◽  
Author(s):  
Jian-Min Chen ◽  
Claude Férec ◽  
David N. Cooper
Keyword(s):  
Secondary Structure ◽  
Human Protein ◽  
Mrna Secondary Structure ◽  
Regulatory Regions ◽  
Systematic Analysis ◽  
Protein Coding ◽  
Protein Coding Genes

Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽  
2021 ◽  
Vol 4952 (2) ◽  
pp. 331-353
Author(s):  
CHAO YANG ◽  
LE ZHAO ◽  
QINGXIONG WANG ◽  
HAO YUAN ◽  
XUEJUAN LI ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Protein Coding Genes ◽  
Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies. 

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

2011 ◽  
Vol 18 (9) ◽  
pp. 1075-1082 ◽  
Author(s):  
Eivind Valen ◽  
Pascal Preker ◽  
Peter Refsing Andersen ◽  
Xiaobei Zhao ◽  
Yun Chen ◽  
...  
Keyword(s):  
Small Rnas ◽  
Human Protein ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

2019 ◽  
Vol 34 (1-2) ◽  
pp. 132-145 ◽  
Author(s):  
Joshua D. Eaton ◽  
Laura Francis ◽  
Lee Davidson ◽  
Steven West
Keyword(s):  
Human Protein ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Transcriptional Termination

scholarly journals Overlapping protein-coding genes in human genome and their coincidental expression in tissues

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao-Hsin Chen ◽  
Chao-Yu Pan ◽  
Wen-chang Lin
Keyword(s):  
Human Genome ◽  
Expression Profiles ◽  
Tissue Expression ◽  
Human Protein ◽  
Clear Understanding ◽  
Overlapping Genes ◽  
Genome Sequences ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Overlapping Gene

Abstract The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5ʹ-tandem overlapping and 3ʹ-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

Systematic Analysis of Missing Proteins Provides Clues to Help Define All of the Protein-Coding Genes on Human Chromosome 1

2013 ◽  
Vol 13 (1) ◽  
pp. 114-125 ◽  
Author(s):  
Chengpu Zhang ◽  
Ning Li ◽  
Linhui Zhai ◽  
Shaohang Xu ◽  
Xiaohui Liu ◽  
...  
Keyword(s):  
Human Chromosome ◽  
Chromosome 1 ◽  
Systematic Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Human Chromosome 1
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