scholarly journals Episialin, a carcinoma-associated mucin, is generated by a polymorphic gene encoding splice variants with alternative amino termini.

1990 ◽  
Vol 265 (10) ◽  
pp. 5573-5578 ◽  
Author(s):  
M J Ligtenberg ◽  
H L Vos ◽  
A M Gennissen ◽  
J Hilkens
Keyword(s):  
Splice Variants ◽  
Gene Encoding ◽  
Polymorphic Gene

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 Bovine Muc1 is a highly polymorphic gene encoding an extensively glycosylated mucin that binds bacteria

2009 ◽  
Vol 92 (10) ◽  
pp. 5276-5291 ◽  
Author(s):  
L. Sando ◽  
R. Pearson ◽  
C. Gray ◽  
P. Parker ◽  
R. Hawken ◽  
...  
Keyword(s):  
Gene Encoding ◽  
Polymorphic Gene

Computational Analysis of the Messenger RNA Variants Encoding Two Isoforms of the High-mobility Group box 1 Protein

2021 ◽  
Vol 30 (3) ◽  
pp. 243-252
Author(s):  
Luchezar Karagyozov ◽  
◽  
Jordana Todorova ◽  
Keyword(s):  
Messenger Rna ◽  
Computational Analysis ◽  
Splice Variants ◽  
Inflammatory Diseases ◽  
High Mobility ◽  
High Mobility Group ◽  
Dual Function ◽  
Chromosomal Protein ◽  
Hmgb1 Protein ◽  
Gene Encoding

High-mobility group box 1 protein (HMGB1) is a multifunctional nonhistone chromosomal protein. This widespread nuclear protein has a dual function-in the nucleus - it binds DNA and participates in practically all DNA-dependent processes. On the other hand, the protein plays an important role in the extracellular matrix as an “alarmin”, which interacts with certain receptors and stimulates biochemical pathways, associated with carcinogenesis and metastasis. HMGB1 is a critical damage-associated molecular pattern molecule, has been implicated in several inflammatory diseases and cancer types. This universality makes it an attractive target for innovative therapeutic strategies in the treatment of various diseases. The updated database for the HMGB1 gene, encoding the high-mobility group box 1 protein, was used for computational analysis of the annotated mRNA splice variants. Results showed that five of the splice variants encode an HMGB1 protein, containing 215 amino acid residues. However, two of the splice variants encode a shorter HMGB1 protein with 158 residues. Presently, the existence of a shorter HMGB1 protein is not registered in the protein databanks. This inconsistency is not yet resolved.

scholarly journals Multiple regions within the promoter of the murine Ifnar-2 gene confer basal and inducible expression

2002 ◽  
Vol 365 (2) ◽  
pp. 355-367 ◽  
Author(s):  
Matthew P. HARDY ◽  
Paul J. HERTZOG ◽  
Catherine M. OWCZAREK
Keyword(s):  
Splice Variants ◽  
Regulatory Region ◽  
Distal Region ◽  
Inducible Expression ◽  
Luciferase Reporter ◽  
Type I ◽  
Type I Ifn ◽  
Mrna Isoforms ◽  
Gene Encoding ◽  
Multiple Regions

The (murine) type I interferon (IFN) receptor, muIfnar-2, is expressed ubiquitously, and exists as both transmembrane and soluble forms. In the present study we show that the gene encoding muIfnar-2 spans approx. 33kb on mouse chromosome 16, and consists of nine exons and eight introns. The three mRNA splice variants resulting in one transmembrane (muIfnar-2c) and two soluble (muIfnar-2a/2a′) mRNA isoforms are generated by alternative RNA processing of the muIfnar-2 gene. Treatment of a range of murine cell lines with a combination of type I and II IFN showed that the muIfnar-2a and −2c mRNA isoforms were up-regulated independently of each other in L929 fibroblasts and hepa-1c1c7 hepatoma cells, but not in M1 myeloid leukaemia cells. Analysis of the 5′ flanking region of muIfnar-2 using promoter—luciferase reporter constructs defined three regulatory regions: a region proximal to exon 1, conferring high basal expression, a distal region conferring inducible expression, and a negative regulatory region between the two. These data represent the first promoter analysis of a type I IFN receptor and, taken together with our previous data demonstrating high expression levels and dual biological functions for muIfnar-2a protein, suggests that the regulation of muIfnar-2 isoform expression may be an important way of modulating type I IFN responses.

scholarly journals Structural organization and splice variants of the POLE1 gene encoding the catalytic subunit of human DNA polymerase ε

1999 ◽  
Vol 339 (3) ◽  
pp. 657-665 ◽  
Author(s):  
Deqi HUANG ◽  
Helmut POSPIECH ◽  
Tapio KESTI ◽  
Juhani E. SYVÄOJA
Keyword(s):  
Dna Polymerase ◽  
Nuclear Dna ◽  
Splice Variants ◽  
Cpg Island ◽  
Signal Sequence ◽  
Catalytic Subunit ◽  
Promoter Regions ◽  
Gene Encoding ◽  
Alternative Transcripts ◽  
Human Dna

The catalytic subunit of human DNA polymerase ϵ, an enzyme involved in nuclear DNA replication and repair, is encoded by the POLE1 gene. This gene is composed of 51 exons spanning at least 97 kb of genomic DNA. It was found to encode three alternative mRNA splice variants that differ in their 5ʹ-terminal sequences and in the N-termini of the predicted proteins. A CpG island covers the promoter region for the major transcript in HeLa cells. This promoter is TATA-less and contains several putative binding sites for transcription factors typical of S-phase-up-regulated and serum-responsive promoters. Potential promoter regions were also identified for the two other alternative transcripts. Interestingly, no nuclear polyadenylation signal sequence was detected in the 3ʹ-untranslated region, although a poly(A) tail was present. These results suggest a complicated regulatory machinery for the expression of the human POLE1 gene, including three alternative transcripts expressed from three promoters.

scholarly journals Identification of a Polymorphic Gene, BCL2A1, Encoding Two Novel Hematopoietic Lineage-specific Minor Histocompatibility Antigens

2003 ◽  
Vol 197 (11) ◽  
pp. 1489-1500 ◽  
Author(s):  
Yoshiki Akatsuka ◽  
Tetsuya Nishida ◽  
Eisei Kondo ◽  
Mikinori Miyazaki ◽  
Hirohumi Taji ◽  
...  
Keyword(s):  
Hematopoietic Cell Transplantation ◽  
Cytotoxic T Lymphocyte ◽  
Single Gene ◽  
Nucleotide Polymorphisms ◽  
Histocompatibility Antigens ◽  
Gene Encoding ◽  
Minor Histocompatibility Antigens ◽  
Leukocyte Antigen ◽  
Hematopoietic Lineage ◽  
Polymorphic Gene

We report the identification of two novel minor histocompatibility antigens (mHAgs), encoded by two separate single nucleotide polymorphisms on a single gene, BCL2A1, and restricted by human histocompatibility leukocyte antigen (HLA)-A*2402 (the most common HLA-A allele in Japanese) and B*4403, respectively. Two cytotoxic T lymphocyte (CTL) clones specific for these mHAgs were first isolated from two distinct recipients after hematopoietic cell transplantation. Both clones lyse only normal and malignant cells within the hematopoietic lineage. To localize the gene encoding the mHAgs, two-point linkage analysis was performed on the CTL lytic patterns of restricting HLA-transfected B lymphoblastoid cell lines obtained from Centre d'Etude du Polymorphisme Humain. Both CTL clones showed a completely identical lytic pattern for 4 pedigrees and the gene was localized within a 3.6-cM interval of 15q24.3–25.1 region that encodes at least 46 genes. Of those, only BCL2A1 has been reported to be expressed in hematopoietic cells and possess three nonsynonymous nucleotide changes. Minigene transfection and epitope reconstitution assays with synthetic peptides identified both HLA-A*2402– and B*4403-restricted mHAg epitopes to be encoded by distinct polymorphisms within BCL2A1.

scholarly journals Development of Molecular Marker Linked with Bacterial Fruit Blotch Resistance in Melon (Cucumis melo L.)

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 220 ◽  
Author(s):  
Md. Rafiqul Islam ◽  
Mohammad Rashed Hossain ◽  
Denison Michael Immanuel Jesse ◽  
Hee-Jeong Jung ◽  
Hoy-Taek Kim ◽  
...  
Keyword(s):  
Dominant Gene ◽  
Indel Marker ◽  
Chromosome 9 ◽  
Detection Accuracy ◽  
Nucleotide Polymorphisms ◽  
Marketable Yield ◽  
Gene Encoding ◽  
Bacterial Fruit Blotch ◽  
Polymorphic Gene ◽  
Lrr Domain

Bacterial fruit blotch (BFB) causes losses in melon marketable yield. However, until now, there has been no information about the genetic loci responsible for resistance to the disease or their pattern of inheritance. We determined the inheritance pattern of BFB resistance from a segregating population of 491 F2 individuals raised by crossing BFB-resistant (PI 353814) and susceptible (PI 614596) parental accessions. All F1 plants were resistant to Acidovorax citrulli strain KACC18782, and F2 plants segregated with a 3:1 ratio for resistant and susceptible phenotypes, respectively, in a seedling bioassay experiment, indicating that BFB resistance is controlled by a monogenic dominant gene. In an investigation of 57 putative disease-resistance related genes across the melon genome, only the MELO3C022157 gene (encoding TIR-NBS-LRR domain), showing polymorphism between resistant and susceptible parents, revealed as a good candidate for further investigation. Cloning, sequencing and quantitative RT-PCR expression of the polymorphic gene MELO3C022157 located on chromosome 9 revealed multiple insertion/deletions (InDels) and single nucleotide polymorphisms (SNPs), of which the SNP A2035T in the second exon of the gene caused loss of the LRR domain and truncated protein in the susceptible accession. The InDel marker MB157-2, based on the large (504 bp) insertion in the first intron of the susceptible accession, was able to distinguish resistant and susceptible accessions among 491 F2 and 22 landraces/inbred accessions with 98.17% and 100% detection accuracy, respectively. This novel PCR-based, co-dominant InDel marker represents a practical tool for marker-assisted breeding aimed at developing BFB-resistant melon accessions.

scholarly journals Tissue and cell-type specific expression of a splice variant in the II-III cytoplasmic loop ofCacna1b

2019 ◽  
Author(s):  
Bunda Alexandra ◽  
LaCarubba Brianna ◽  
Akiki Marie ◽  
Andrade Arturo
Keyword(s):  
Motor Neurons ◽  
Splice Variants ◽  
Gene Encoding ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Alternatively Spliced ◽  
Cell Type Specific ◽  
Alternatively Spliced Exons ◽  
Cerebellar Cells

ABSTRACTPresynaptic CaV2.2 (N-type) channels are fundamental for transmitter release across the nervous system. The gene encoding CaV2.2 channels,Cacna1b, contains alternatively spliced exons that originate functionally distinct splice variants (e18a, e24a, e31a and 37a/37b). Alternative splicing of the cassette exon 18a generates two mRNA transcripts (+e18a-Cacna1band Δe18a-Cacna1b). In this study, using novel mouse genetic models and in situ hybridization (BaseScope™), we confirmed that +e18a-Cacna1bsplice variants are expressed in monoaminergic regions of midbrain. We expanded these studies and identified +e18a-Cacna1bmRNA in deep cerebellar cells and spinal cord motor neurons. Furthermore, we determined that +e18a-Cacna1bis enriched in cholecystokinin expressing interneurons. Our results provide key information to understand cell-specific functions of CaV2.2 channels.

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