Y chromosomal fertility genes of Drosophila: a new type of eukaryotic genes

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 561-571 ◽  
Author(s):  
Wolfgang Hennig ◽  
Reindert C. Brand ◽  
Johannes Hackstein ◽  
Ron Hochstenbach ◽  
Hannie Kremer ◽  
...  
Keyword(s):  
Repeated Sequence ◽  
Protein Coding ◽  
Chromosomal Proteins ◽  
Coding Regions ◽  
Eukaryotic Genes ◽  
Chromosomal Genes ◽  
Specific Proteins ◽  
New Type ◽  
Fertility Genes ◽  
Lampbrush Loops

The Y chromosomal fertility genes of Drosophila are required for sperm differentiation. They are active only in primary spermatocytes where they form giant lampbrush loops. The molecular structure of these genes was investigated and revealed an unusual composition of DNA. Short, tandemly repeated sequence clusters are interrupted by longer and more heterogeneous sequences, which probably all represent transposable elements. No indication of the presence of protein-coding regions has been found within the fertility genes. However, the lampbrush loops bind site-specific proteins recognized by immunofluorescence techniques. This, together with other experimental data, led to the hypothesis that the Y chromosomal genes have a function in binding chromosomal proteins. The data and arguments in support of this gene model are summarized in this paper.Key words: Y chromosome, Drosophila, fertility genes, gene structure, lampbrush loops, spermatogenesis.

scholarly journals Emergence of multiple variants of SARS-CoV-2 with signature structural changes

2020 ◽  
Author(s):  
Debaleena Bhowmik ◽  
Sourav Pal ◽  
Abhishake Lahiri ◽  
Arindam Talukdar ◽  
Sandip Paul
Keyword(s):  
Structural Changes ◽  
Phylogenomic Analysis ◽  
Genetic Studies ◽  
Protein Coding ◽  
Coding Regions ◽  
Emergent Groups ◽  
Specific Proteins ◽  
Modelling Techniques ◽  
Divergence Pattern ◽  
The Impact

AbstractThis study explores the divergence pattern of SARS-CoV-2 using whole genome sequences of the isolates from various COVID-19 affected countries. The phylogenomic analysis indicates the presence of at least four distinct groups of the SARS-CoV-2 genomes. The emergent groups have been found to be associated with signature structural changes in specific proteins. Also, this study reveals the differential levels of divergence patterns for the protein coding regions. Moreover, we have predicted the impact of structural changes on a couple of important viral proteins via structural modelling techniques. This study further advocates for more viral genetic studies with associated clinical outcomes and hosts’ response for better understanding of SARS-CoV-2 pathogenesis enabling better mitigation of this pandemic situation.

scholarly journals The open targets post-GWAS analysis pipeline

2020 ◽  
Vol 36 (9) ◽  
pp. 2936-2937 ◽  
Author(s):  
Gareth Peat ◽  
William Jones ◽  
Michael Nuhn ◽  
José Carlos Marugán ◽  
William Newell ◽  
...  
Keyword(s):  
Drug Targets ◽  
Gene Expression Regulation ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Protein Coding ◽  
Data Resource ◽  
Coding Regions ◽  
Genome Wide ◽  
Causal Genes ◽  
Interactive Data

Abstract Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

scholarly journals Nucleotide sequence of the putative regulatory region of mouse lactate dehydrogenase-A gene

1986 ◽  
Vol 235 (2) ◽  
pp. 435-439 ◽  
Author(s):  
K M Fukasawa ◽  
S S L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Nucleotide Sequence ◽  
Cyclic Amp ◽  
Regulatory Region ◽  
Base Pairs ◽  
Protein Coding ◽  
Untranslated Sequence ◽  
Eukaryotic Genes ◽  
Putative Regulatory Region ◽  
Processed Pseudogene

The nucleotide sequence of approx. 3 kilobases including the regulatory region, a non-coding exon and the first protein-coding exon from mouse lactate dehydrogenase-A (LDH-A) gene has been determined. The putative initiation sites of transcription and translation were deduced by comparing the nucleotide sequence of mouse LDH-A gene with those of a mouse LDH-A processed pseudogene and the LDH-A full-length cDNAs from rat and human. The tentative TATA and CAAT boxes, and the hexanucleotides CCGCCC have been identified. The sequence of AAATCTTGCTCAA of mouse LDH-A gene has also been found to show striking homology to the cyclic AMP-responsive sequences of eukaryotic genes regulated by cyclic AMP. It has been reported previously that the protein-coding sequence of mouse LDH-A gene is interrupted by six introns and the 3′ untranslated sequence of 485 nucleotides is not interrupted [Li, Tiano, Fukasawa, Yagi, Shimiza, Sharief, Nakashima & Pan (1985) Eur. J. Biochem. 149, 215-225]. An additional intron of 1653 base-pairs was found in the 5′ untranslated sequence of 101 nucleotides at 24 nucleotides upstream to the translation start site. Thus, mouse LDH-A gene containing seven introns spans approx. 11 kilobases and its length of mature mRNA is 1582 nucleotides, excluding the poly(A) tail.

scholarly journals Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

Biochimie ◽  
2011 ◽  
Vol 93 (11) ◽  
pp. 2019-2023 ◽  
Author(s):  
Sven Findeiß ◽  
Jan Engelhardt ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Secondary Structures ◽  
Protein Coding ◽  
Rna Secondary Structures ◽  
Coding Regions

Structure and expression of canary myc family genes

1991 ◽  
Vol 11 (3) ◽  
pp. 1770-1776
Author(s):  
R G Collum ◽  
D F Clayton ◽  
F W Alt
Keyword(s):  
Untranslated Region ◽  
Untranslated Regions ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Neuronal Precursors ◽  
Myc Gene ◽  
Mature Neurons

We found that the canary N-myc gene is highly related to mammalian N-myc genes in both the protein-coding region and the long 3' untranslated region. Examined coding regions of the canary c-myc gene were also highly related to their mammalian counterparts, but in contrast to N-myc, the canary and mammalian c-myc genes were quite divergent in their 3' untranslated regions. We readily detected N-myc and c-myc expression in the adult canary brain and found N-myc expression both at sites of proliferating neuronal precursors and in mature neurons.

scholarly journals Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05

2010 ◽  
Vol 11 (3) ◽  
pp. 243
Author(s):  
Saber Jelokhani-Niaraki ◽  
Majid Esmaelizad ◽  
Morteza Daliri ◽  
Rasoul Vaez-Torshizi ◽  
Morteza Kamalzadeh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Protein Coding ◽  
Coding Regions ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Subtype A ◽  
Virus Subtype

scholarly journals Genome Sequence of Rheinheimera salexigens sp. nov. Isolated from a Fishing Hook off O‘ahu, Hawai‘i

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Xuehua Wan ◽  
Shaobin Hou ◽  
Kazukuni Hayashi ◽  
James Anderson ◽  
Stuart P. Donachie
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Coding Sequences ◽  
Coding Regions ◽  
Roche 454

Rheinheimera salexigens KH87 T is an obligately halophilic gammaproteobacterium. The strain’s draft genome sequence, generated by the Roche 454 GS FLX+ platform, comprises two scaffolds of ~3.4 Mbp and ~3 kbp, with 3,030 protein-coding sequences and 58 tRNA coding regions. The G+C content is 42 mol%.

scholarly journals Gene prediction by multiple syntenic alignment

2005 ◽  
Vol 2 (1) ◽  
pp. 38-47
Author(s):  
Said S. Adi ◽  
Carlos E. Ferreira
Keyword(s):  
Computer Program ◽  
Genomic Dna ◽  
Gene Prediction ◽  
Genomic Sequences ◽  
Prediction Problem ◽  
Huge Amount ◽  
Protein Coding ◽  
Coding Regions ◽  
Conserved Regions ◽  
Similarity Information

Summary Given the increasing number of available genomic sequences, one now faces the task of identifying their functional parts, like the protein coding regions. The gene prediction problem can be addressed in several ways. One of the most promising methods makes use of similarity information between the genomic DNA and previously annotated sequences (proteins, cDNAs and ESTs). Recently, given the huge amount of newly sequenced genomes, new similarity-based methods are being successfully applied in the task of gene prediction. The so-called comparative-based methods lie in the similarities shared by regions of two evolutionary related genomic sequences. Despite the number of different gene prediction approaches in the literature, this problem remains challenging. In this paper we present a new comparative-based approach to the gene prediction problem. It is based on a syntenic alignment of three or more genomic sequences. With syntenic alignment we mean an alignment that is constructed taking into account the fact that the involved sequences include conserved regions intervened by unconserved ones. We have implemented the proposed algorithm in a computer program and confirm the validity of the approach on a benchmark including triples of human, mouse and rat genomic sequences.

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