Prototypic sequences for human repetitive DNA

Jurka, Jerzy; Walichiewicz, Jolanta; Milosavljević, Aleksandar

doi:10.1007/bf00161166

Cited by 151 publications

(77 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…On the other hand, our analysis grouped quenced with universal primers with the dideoxy chain termination D6S276 in a cluster mapped 4 cM telomerically and method by Taq polymerase (AmpliCycle kit, Perkin-Elmer). The sequences were then checked for their repetitive content by compari-placed D6S258 and D6S265 in the proximity of son with human repetitive elements (Jurka et al, 1992). Primers D6S273.…”

Section: Methodsmentioning

confidence: 99%

Construction of a YAC Contig Covering Human Chromosome 6p22

et al. 1996

View full text Add to dashboard Cite

et al. (1995) it is still represented by two separate paths A contig covering human chromosome 6p22 that con-of levels 3 and 1, respectively. In the STS-based map sists of 134 YAC clones aligned based on the presence/ of the human genome (Hudson et al., 1995) two ''doubly absence of 52 DNA markers is presented. This contig linked'' contigs overlap this region. overlaps with the 6p23 contig at its telomeric end andSeveral genes have been assigned to 6p22. By using with the 6p21.3 contig at its centromeric end. The or-panels of somatic cell hybrids, Albig et al. (1993) asder of loci within the contig resolves the relative posi-signed to this band the cluster of H1 histone genes; tions of several genetically mapped markers. Among Abbott and Povey (1991) assigned the prolactin gene; the additional markers used here, there are eight Durkin et al. (1994) assigned brain-specific ESTs by novel PCR assays. The 12 known genes and anonymous PCR;and Pappas et al. (1995) found six ESTs mapping ESTs located within the contig establish a first step to 6p21.3-p23, one of which was identified as a zinc toward a transcriptional map of this region. The insta-finger protein. A number of disease causing genes or bility of YAC clones observed during this work is also cDNAs linked to the MHC are reported in OMIM with discussed. ᭧

show abstract

Section: Methodsmentioning

confidence: 99%

Construction of a YAC Contig Covering Human Chromosome 6p22

et al. 1996

View full text Add to dashboard Cite

show abstract

“…Eight of these Alu sequences are oriented in the opposite direction of the ZAG, whereas the remaining one (Alu-6) is oriented in the same direction (32). In addition, two MER sequences belonging to subfamilies 12 and 14 (33) and one MIR element (34) were found in the first and second introns of the gene, respectively.…”

Section: Gene Structure and Regulationmentioning

confidence: 99%

Zinc α2-Glycoprotein: A Multidisciplinary Protein

Hassan

Waheed

Yadav

et al. 2008

Molecular Cancer Research

215

204

View full text Add to dashboard Cite

Zinc A2-glycoprotein (ZAG) is a protein of interest because of its ability to play many important functions in the human body, including fertilization and lipid mobilization. After the discovery of this molecule, during the last 5 decades, various studies have been documented on its structure and functions, but still, it is considered as a protein with an unknown function. Its expression is regulated by glucocorticoids. Due to its high sequence homology with lipid-mobilizing factor and high expression in cancer cachexia, it is considered as a novel adipokine. On the other hand, structural organization and fold is similar to MHC class I antigen-presenting molecule; hence, ZAG may have a role in the expression of the immune response. The function of ZAG under physiologic and cancerous conditions remains mysterious but is considered as a tumor biomarker for various carcinomas. There are several unrelated functions that are attributed to ZAG, such as RNase activity, regulation of melanin production, hindering tumor proliferation, and transport of nephritic by-products. This article deals with the discussion of the major aspects of ZAG from its gene structure to function and metabolism. (Mol Cancer Res 2008;6(6):892 -906)

show abstract

“…The first of the similarity-based sensors is IREsense, which detects interspersed repeat elements (IREs), simple sequence repeats, and cloning vector sequence, using the CENSOR package (Jurka et al 1996) as the analytical engine and a set of repeat templates based on Repbase (Jurka et al 1992). Subtyping of Alu repeats is done by use of PYTHIA (Milosavljevic and Jurka 1993).…”

Section: Initial Sensorsmentioning

confidence: 99%

“…Repeat templates consisted of a collection of species-specific repeat elements (v5.0, Jurka et al 1992), simple repeat elements (v3.0, Jurka and Pethiyagoda 1995), and the cloning vector pUC19. CENSOR was run once with a linear gap penalty and again with a logarithmic gap penalty, to better identify partial repeats; the default alignment parameters were used at each step.…”

Section: Iresensementioning

confidence: 99%

GAIA: Framework Annotation of Genomic Sequence

et al. 1998

View full text Add to dashboard Cite

As increasing amounts of genomic sequence from many organisms become available, and as DNA sequences become a primary reagent in biologic investigations, the role of annotation as a prospective guide for laboratory experiments will expand rapidly. Here we describe a process of high-throughput, reliable annotation, called framework annotation, which is designed to provide a foundation for initial biologic characterization of previously unexamined sequence. To examine this concept in practice, we have constructed Genome Annotation and Information Analysis (GAIA), a prototype software architecture that implements several elements important for framework annotation. The center of GAIA consists of an annotation database and the associated data management subsystem that forms the software bus along which other components communicate. The schema for this database defines three principal concepts: (1) Entries, consisting of sequence and associated historical data; (2) Features, comprising information of biologic interest; and (3) Experiments, describing the evidence that supports Features. The database permits tracking of annotation results over time, as well as assessment of the reliability of particular results. New framework annotation is produced by CARTA, a set of autonomous sensors that perform automatic analyses and assert results into the annotation database. These results are available via a Web-based query interface that uses graphical Java applets as well as text-based HTML pages to display data at different levels of resolution and permit interactive exploration of annotation. We present results for initial application of framework annotation to a set of test sequences, demonstrating its effectiveness in providing a starting point for biologic investigation, and discuss ways in which the current prototype can be improved. The prototype is available for public use and comment at

show abstract

Prototypic sequences for human repetitive DNA

Cited by 151 publications

References 59 publications

Construction of a YAC Contig Covering Human Chromosome 6p22

Construction of a YAC Contig Covering Human Chromosome 6p22

Zinc α2-Glycoprotein: A Multidisciplinary Protein

GAIA: Framework Annotation of Genomic Sequence

Contact Info

Product

Resources

About