scholarly journals Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Majid Mehravar ◽  
Fatemeh Ghaemimanesh ◽  
Ensieh M. Poursani
Keyword(s):  
Human Genome ◽  
Splice Variants ◽  
Biological Significance ◽  
In Silico Analysis ◽  
Overlapping Genes ◽  
Overlapping Gene ◽  
Domains Of Life ◽  
New Form ◽  
Genomic Regions ◽  
Expressed Sequence

Abstract Background Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome. Results By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants. Conclusions This new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms.

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.

scholarly journals SSRD: Simple Sequence Repeats Database of the Human Genome

2003 ◽  
Vol 4 (3) ◽  
pp. 342-345 ◽  
Author(s):  
Subbaya Subramanian ◽  
Vamsi M. Madgula ◽  
Ranjan George ◽  
Satish Kumar ◽  
Madhusudhan W. Pandit ◽  
...  
Keyword(s):  
Human Genome ◽  
Simple Sequence Repeats ◽  
Biological Significance ◽  
Repeat Sequence ◽  
Easy Access ◽  
Evolutionary Significance ◽  
Intergenic Regions ◽  
Genomic Regions ◽  
Abundance And Distribution ◽  
Simple Sequence

Simple sequence repeats are predominantly found in most organisms. They play a major role in studies of genetic diversity, and are useful as diagnostic markers for many diseases. The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance. The data includes the abundance and distribution of SSRs in the coding and non-coding regions of the genome, as well as their association with the UTRs of genes. The exact locations of repeats with respect to genomic regions (such as UTRs, exons, introns or intergenic regions) and their association with STS markers are also highlighted. The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats. SSRD is available through two websites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr.

scholarly journals A Scan for Linkage Disequilibrium Across the Human Genome

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1711-1722 ◽  
Author(s):  
Gavin A Huttley ◽  
Michael W Smith ◽  
Mary Carrington ◽  
Stephen J O’Brien
Keyword(s):  
Linkage Disequilibrium ◽  
Human Genome ◽  
Pedigree Analysis ◽  
Exact Test ◽  
Genomic Scale ◽  
Genomic Regions ◽  
Formal Test ◽  
Scale Data ◽  
Short Tandem ◽  
Tandem Repeat Polymorphism

Abstract Linkage disequilibrium (LD), the tendency for alleles of linked loci to co-occur nonrandomly on chromosomal haplotypes, is an increasingly useful phenomenon for (1) revealing historic perturbation of populations including founder effects, admixture, or incomplete selective sweeps; (2) estimating elapsed time since such events based on time-dependent decay of LD; and (3) disease and phenotype mapping, particularly for traits not amenable to traditional pedigree analysis. Because few descriptions of LD for most regions of the human genome exist, we searched the human genome for the amount and extent of LD among 5048 autosomal short tandem repeat polymorphism (STRP) loci ascertained as specific haplotypes in the European CEPH mapping families. Evidence is presented indicating that ∼4% of STRP loci separated by <4.0 cM are in LD. The fraction of locus pairs within these intervals that display small Fisher’s exact test (FET) probabilities is directly proportional to the inverse of recombination distance between them (1/cM). The distribution of LD is nonuniform on a chromosomal scale and in a marker density-independent fashion, with chromosomes 2, 15, and 18 being significantly different from the genome average. Furthermore, a stepwise (locus-by-locus) 5-cM sliding-window analysis across 22 autosomes revealed nine genomic regions (2.2-6.4 cM), where the frequency of small FET probabilities among loci was greater than or equal to that presented by the HLA on chromosome 6, a region known to have extensive LD. Although the spatial heterogeneity of LD we detect in Europeans is consistent with the operation of natural selection, absence of a formal test for such genomic scale data prevents eliminating neutral processes as the evolutionary origin of the LD.

In Silico Analysis of the CST6 Tumor Suppressor Gene

2013 ◽  
Vol 2 (3) ◽  
pp. 42-58
Author(s):  
Athanasia Pavlopoulou ◽  
Georgios Tsaramirsis
Keyword(s):  
Tumor Suppressor ◽  
Splice Variants ◽  
Cpg Island ◽  
Mammalian Species ◽  
Gene Promoter ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Suppressor Gene ◽  
Differentially Expressed ◽  
Gene Encoding

The gene encoding cystatin E/M, CST6, is a Class II tumor suppressor. Using bioinformatics tools for database mining and virtual gene expression profiling, the authors showed that CST6 is differentially expressed in various types of cancer. Moreover, epigenetic silencing mediated by hypermethylation of the CpG island located at the CST6 promoter was found to be conserved in mammalian species. Comprehensive analyses of animal genomes led to the identification of novel CST6 transcript orthologs and splice variants that enabled us to trace the evolutionary origin of CST6. Moreover, eight novel and potentially regulatory SNPs were identified in CST6 gene. Conserved cancer-relevant regulatory elements were identified in the CST6 gene promoter. In addition, miRNAs that are differentially expressed in human cancers were identified as putative posttranscriptional regulators of CST6. Collectively, the authors suggest that expression of CST6 in normal and cancer cells is coordinately regulated by genomic, transcriptional and post-transcriptional mechanisms.

scholarly journals DMSO Reductase Family: Phylogenetics and Applications of Extremophiles

2019 ◽  
Vol 20 (13) ◽  
pp. 3349 ◽  
Author(s):  
Jose María Miralles-Robledillo ◽  
Javier Torregrosa-Crespo ◽  
Rosa María Martínez-Espinosa ◽  
Carmen Pire
Keyword(s):  
Redox Reactions ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Anaerobic Respiration ◽  
Biogeochemical Cycles ◽  
Free Software ◽  
Transfer Processes ◽  
Expression Of Genes ◽  
Potential Applications ◽  
Domains Of Life

Dimethyl sulfoxide reductases (DMSO) are molybdoenzymes widespread in all domains of life. They catalyse not only redox reactions, but also hydroxylation/hydration and oxygen transfer processes. Although literature on DMSO is abundant, the biological significance of these enzymes in anaerobic respiration and the molecular mechanisms beyond the expression of genes coding for them are still scarce. In this review, a deep revision of the literature reported on DMSO as well as the use of bioinformatics tools and free software has been developed in order to highlight the relevance of DMSO reductases on anaerobic processes connected to different biogeochemical cycles. Special emphasis has been addressed to DMSO from extremophilic organisms and their role in nitrogen cycle. Besides, an updated overview of phylogeny of DMSOs as well as potential applications of some DMSO reductases on bioremediation approaches are also described.

scholarly journals Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

PLoS ONE ◽  
2013 ◽  
Vol 8 (8) ◽  
pp. e70582 ◽  
Author(s):  
Adrián Ochoa-Leyva ◽  
Gabriela Montero-Morán ◽  
Gloria Saab-Rincón ◽  
Luis G. Brieba ◽  
Xavier Soberón
Keyword(s):  
Human Genome ◽  
Alternative Splice ◽  
Splice Variants ◽  
Protein Fold ◽  
Tim Barrel ◽  
Alternative Splice Variants

scholarly journals Mammalian Septins Nomenclature

2002 ◽  
Vol 13 (12) ◽  
pp. 4111-4113 ◽  
Author(s):  
Ian G. Macara ◽  
Richard Baldarelli ◽  
Christine M. Field ◽  
Michael Glotzer ◽  
Yasuhide Hayashi ◽  
...  
Keyword(s):  
Human Genome ◽  
Gene Product ◽  
Genome Organization ◽  
Splice Variants ◽  
Gene Products ◽  
Gene Nomenclature ◽  
Nomenclature System ◽  
Nomenclature Committee ◽  
Human And Mouse ◽  
Mouse Genomic

There are 10 known mammalian septin genes, some of which produce multiple splice variants. The current nomenclature for the genes and gene products is very confusing, with several different names having been given to the same gene product and distinct names given to splice variants of the same gene. Moreover, some names are based on those of yeast or Drosophilaseptins that are not the closest homologues. Therefore, we suggest that the mammalian septin field adopt a common nomenclature system, based on that adopted by the Mouse Genomic Nomenclature Committee and accepted by the Human Genome Organization Gene Nomenclature Committee. The human and mouse septin genes will be namedSEPT1–SEPT10 and Sept1–Sept10, respectively. Splice variants will be designated by an underscore followed by a lowercase “v” and a number, e.g., SEPT4_v1.

scholarly journals Triplet repeats in human genome: distribution and their association with genes and other genomic regions

2003 ◽  
Vol 19 (5) ◽  
pp. 549-552 ◽  
Author(s):  
S. Subramanian ◽  
V. M. Madgula ◽  
R. George ◽  
R. K. Mishra ◽  
M. W. Pandit ◽  
...  
Keyword(s):  
Human Genome ◽  
Triplet Repeats ◽  
Genomic Regions
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