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At least 991 records · Page 55Linked to original sources
PubMed1995

A 100-kb physical and transcriptional map around the EDH17B2 gene: identification of three novel genes and a pseudogene of a human homologue of the rat PRL-1 tyrosine phosphatase.

In this paper, we describe the physical map and transcriptional organisation of a 100-kb region with the BRCA1 locus at 17q12-21. Using the cDNA of the EDH17B2 gene as a probe, we screened a human genomic cosmid library. Positive cosmid clones were aligned and a contig around the EDH17B2 gene was established, expanding the previously reported map. In order to identify genes located in this region, we used the cosmid inserts to select cDNAs from a human ovarian cDNA library. Among the clones identified, cDNA OV-1 corresponds to a human homologue of a rat PRL-1 tyrosine phosphatase gene that shows enhanced expression during hepatic regeneration and in some tumour cell lines. Neither the OV-1 nor the PRL-1 protein shares strong homology with any previously characterised phosphotyrosine phosphatase, suggesting that they probably belong to a new phosphatase family. In an attempt to characterise the OV-1 gene, we found that the genomic sequence present on chromosome 17 probably corresponds to a nonfunctional copy of the gene, as it contains several sequence changes that disrupt the potential coding information of the gene. Three other cDNAs, corresponding to unrelated genes, were also identified and characterised. They did not reveal striking homologies in database sequence comparison and therefore represent new genes localised on chromosome 17q, in a region that frequently shows loss of heterozigosity in sporadic breast and ovarian cancers.

Amino Acid Sequence↗
PubMed1994

A rearrangement on chromosome 5 of an expressed human beta-glucuronidase pseudogene.

A novel transcript containing homology to exons 5, 9, 10, and 11 of the beta-glucuronidase gene has been shown to be derived from Chromosome (Chr) 5. In situ hybridization analysis has shown that this transcript is homologous to four loci on Chr 5 (5p13.3, 5p15.1, 5q13.1, and 5q15), two loci on Chr 6 (6p11.2 and 6p21.3), and one on Chr 22 at 22q11.2. Analysis of cosmid clones from Chr 5 has defined three distinct contigs in which there are tandem genomic repeats of a unit containing sequences homologous to exons 5, 9, and 10 but not 11. Pulsed-field gel electrophoresis (PFGE) analysis has shown that the length of these repeats is highly variable between unrelated individuals, indicating that these regions of Chr 5 are prone to rearrangement. These sequences may be important with respect to stability around the Chr 5 centromere.

Base Sequence↗
PubMed1992

A mouse Y chromosome pseudogene is related to human ubiquitin activating enzyme E1.

A 2041 bp DNA fragment isolated from the Sxr (sex reversed) region of the mouse Y Chromosome (Chr) was sequenced and characterized. The sequence, pY8/b, contains four exons that are highly similar to 525 contiguous bases from the cDNA of human ubiquitin activating enzyme E1. Two of the exons contain stop codons, indicating that pY8/b is not part of a functional gene. Sequences related to pY8/b were amplified from the Y Chr of the inbred mouse strain, C57BL/6J. These sequences may be portions of the recently discovered functional equivalent of pY8/b. Despite a high degree of similarity with the human E1 gene, the functional equivalent of pY8/b is not the mouse E1 gene, because unlike E1, the functional equivalent of pY8/b is expressed in a tissue-specific manner. These data are discussed with respect to theory on the evolution of the mammalian Y Chr, and in particular, to the prediction that functional genes on the Y Chr have a male-specific function.

Amino Acid Sequence↗
PubMed1989

DNA sequence of a class I pseudogene from the Tla region of the murine MHC: recombination at a B2 alu repetitive sequence.

We have determined the DNA sequence of a BALB/c Tla region class I gene from the major histocompatibility complex (MHC) that had been identified previously as encoding a murine antigen by DNA-mediated gene transfer. Analysis of the DNA sequence shows, however, that this gene, the T1c gene from the Tlac genotype, could not encode a TL antigen or any other functional class I molecule due to the presence of numerous stop codons and frameshift mutations in the coding regions. This result suggests that the earlier transformation data may have been incorrect or perhaps that the clone containing the T1c gene contains sequences that induced expression of a serologically reactive Tla gene in the genome of the recipient L cell. The T1c gene is structurally related to the previously sequenced T13c gene that encodes a serologically defined TL antigen. The 3' half of the T1c gene including exons 4, 5, 6, and the 3' untranslated region has about 85% nucleotide similarity (including introns) with the corresponding parts of the T13c gene; however, the 5' half of the T1c gene has little homology with the T13c gene. There is a sharp line of demarcation between the homologous and nonhomologous regions, and this border occurs precisely at a B2 Alu repeat sequence present in the T13c gene. This suggests that a recombination event took place here and that an Alu repeat sequence that is known to have characteristics of transposable elements played some role in a recombination or gene conversion event.

Animals↗
PubMed1997

Segmented gene conversion as a mechanism of correction of 18S rRNA pseudogene located outside of rDNA cluster in D. melanogaster.

The peculiarities of the sequences of 18S rDNA included in a 90-kb DNA segment cloned in YAC vector are described. This heterochromatic segment is situated on the X chromosome distal to the main rDNA cluster. The pseudo 18S rDNA sequence comprised undamaged stretches of rDNA interspersed with segments characterized by high density of nucleotide substitutions and insertions/deletions. The observed patchwork arrangement of unaltered rDNA sequences was considered as evidence of segmented gene conversion events between the normal and damaged genes which are thought to constitute one of the mechanisms of rDNA array homogenization. The 18S rDNA fragment (510 bp) located nearby, homologous to the internal, undamaged part of pseudo 18S rDNA, carries comparable density of randomly distributed nucleotide substitutions with no evidence of correction.

Animals↗
PubMed2007

Unusual origin of a nuclear pseudogene in the Italian wall lizard: intergenomic and interspecific transfer of a large section of the mitochondrial genome in the genus Podarcis (Lacertidae).

Two distinct cytochrome b-like sequences were discovered in the genome of Podarcis sicula. One of them represents a nuclear copy of a mitochondrial sequence (numt-sic) differing by 14.3% from the authentic mitochondrial (mt) sequence obtained from the same individual. This numt, however, differs by only 2.7% from the mt sequence found in one population of Podarcis muralis, a related species in which no corresponding numt was detected. The numt-sic sequence extends over at least 7637 bp and is homologous to a section of the mt genome spanning from the tRNA-Lys to the tRNA-Pro gene. Premature mt stop codons were detected in two of the nine protein coding genes of numt-sic. The distribution of substitutions among the three codon positions and the transition/transversion ratio of the numt-sic sequence resemble, with few exceptions, those of functional mt genes, indicating a rather recent transfer to the nucleus. Phylogenetic analyses performed on the data set including P. sicula numt-cytb sequences as well as mt-cytb sequences from the same individuals and mt sequences of various P. muralis populations suggest that numt-sic originated in P. muralis. In a geographic survey, P. sicula populations belonging to different mt lineages, covering most of the distribution area, were screened for the presence of numt-sic and for a 15-bp duplication polymorphism in the numt-nd5 sequence. Our results suggest that numt-sic has spread rapidly through the species range via sexual transmission, thereby being transferred to populations belonging to well-separated mt lineages that diverged 1-3 Mya.

Animals↗
PubMed2001

Truncated and dispersed rpl2 and rps19 pseudogenes are co-transcribed with neighbouring downstream genes in wheat mitochondria.

The wheat mitochondrial genome contains only partial coding sequences for the L2 and S19 ribosomal proteins, unlike in rice or liverwort mitochondria, where these genes are functional and have a bacterial-type linkage. A single-copy stretch corresponding to the extreme 3' terminus of the wheat rpl2 gene is co-transcribed with the trans-splicing nad1 exon 4; and, at another unique location, the rps19 segment lacking the 5' coding region is co-transcribed with the downstream nad4L gene. In both cases, the 5' termini of these transcripts map to promoter consensus motifs acquired through genomic reorganization, enabling continued expression of essential downstream genes. In both wheat and rice, the rpl2 and rps19 genomic regions differ in their RNA profiles between germinating embryos and seedlings. The absence of intact rpl2 and rps19 genes in wheat mitochondria is consistent with their inactivation through DNA rearrangement/deletion after the successful transfer of functional copies to the nucleus.

Amino Acid Sequence↗