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At least 919 records · Page 51Linked to original sources
PubMed1985

Isolation of a rat immune response gene identical to an alleged mouse a class II beta-chain pseudogene.

A human HLA-DQ beta-chain cDNA was used as a probe to identify and isolate a rat major histocompatibility antigen beta-chain gene from a genomic library constructed in the vector lambda Charon 28 using Wistar rat DNA (RT1u). The isolated exon of the rat gene (RT1.B beta 2) encoding a beta-chain second domain was found to share 93% nucleotide homology with a mouse A beta 2 exon. Although the genomic organization of this gene is consistent with the hypothesis that it represents a pseudogene, the remarkable preservation of a specific sequence favors the view that this class II antigen beta-chain gene has retained its coding function.

Amino Acid Sequence↗
PubMed1985

Assignment of human dihydrofolate reductase gene to band q23 of chromosome 5 and of related pseudogene psi HD1 to chromosome 3.

The chromosomal location of the human dihydrofolate reductase (DHFR; EC 1.5.1.3) gene that is amplified in a methotrexate-resistant human cell line has been investigated by screening a number of human-Chinese hamster ovary cell hybrids containing terminal and interstitial deletions in human chromosome 5. A correlation of genomic blotting data with the chromosome 5 constitution of the individual hybrids has allowed the assignment of the human DHFR gene to 5q23. The present work also establishes the location of the related intronless pseudogene psi HD1 in chromosome 3.

Animals↗
PubMed1984

Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications.

We have obtained a revised estimate of the pattern of point mutation by considering more pseudogene sequences. Compared with our previous estimate, it agrees better with expectations based on the double-strand structure of DNA. The revised pattern, like the previous one, indicates that mutation occurs nonrandomly among the four nucleotides. In particular, the proportion of transitional mutations (59%) is almost twice as high as the value (33%) expected under random mutation. The same high proportion of transitions is observed in synonymous substitutions in genes. The proportion of transitional changes observed among electrophoretic variants of human hemoglobin is about the same as that predicted by the revised pattern of mutation. We also show that nonrandom mutation increases, by about 15%, the proportion of synonymous mutations due to single-nucleotide changes in the codon table, and increases, from 10% to 50%, the rate of synonymous mutation in the seven genes studied. However, nonrandom mutation reduces (by about 10%) the proportion of polar changes among nonsynonymous mutations in a gene. As far as single-nucleotide changes (in the codon table) are concerned, nonrandom mutation only slightly favors relatively conservative amino acid interchanges, and has virtually no effect on the proportions of radical changes and nonsense mutations.

Amino Acid Sequence↗
PubMed1996

Characterisation of a human serine hydroxymethyltransferase pseudogene and its localisation to 1p32.3-33.

The conversion of serine and tetrahydrofolate to glycine and 5,10 methylene tetrahydrofolate by serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is the major route for the provision of one-carbon units for biosynthetic reactions. SHMT cDNAs have been cloned from both rabbit and man, and a human mitochondrial SHMT gene sequence has recently been reported. We have isolated phage clones containing human genomic sequences homologous to cytosolic SHMT and have found these to contain a processed pseudogene (SHMT-ps1) with a 90% identity to cloned SHMT cDNAs. SHMT-ps1 contains 2335 nt that are homologous to SHMT but it has an additional leader sequence of 203 nt of unknown origin. The complete SHMT-ps1 sequence of 2538 nt is bounded by two 16 nt direct repeats that are characteristic of retroelement insertion sites. Two phage clones containing SHMT-ps1 have been mapped by fluorescence in situ hybridisation to 1p32.3-33. In addition, an SHMT CDNA clone hybridized to the same region and to 17p11.2-12. The latter is consistent with a previous localisation of the gene for cytosolic SHMT.

Base Sequence↗
PubMed1996

Integration of four genes, a pseudogene, thirty-one STSs, and a highly polymorphic STRP into the 7-10 Mb YAC contig of 5q34-q35.

Thirty-one sequence tagged sites and a highly polymorphic short tandem repeat polymorphism have been isolated from 5q34-q35 and integrated into the yeast artificial chromosome (YAC) contig of 5q34-q35. In addition, four genes (MSX2, CSX, DRD1, and CL100) and a pseudogene (GLUT6) were localized on this map. The high density of new markers in the region allowed further refinement of the YAC contig of distal 5q. This is a prerequisite for the conversion of this YAC into a cosmid contig.

Base Sequence↗
PubMed1983

Isolation and characterization of the mouse corticotropin-beta-lipotropin precursor gene and a related pseudogene.

Two mouse genomic DNA sequences homologous with human corticotropin-beta-lipotropin precursor gene sequences have been cloned. One of them represents the functional corticotropin-beta-lipotropin precursor gene, which exhibits a structural organization similar to those of its bovine and human counterparts. The other represents a pseudogene that corresponds to the functional mouse gene sequence encoding the carboxy-terminal 143 amino acid residues (including corticotropin and beta-lipotropin) and the 3'-untranslated region.

Animals↗
PubMed1995

Assignment to chromosome 11 of mouse p68 RNA helicase gene (Hlr1) and pseudogene (Hlr1-ps1).

The gene encoding murine p68 RNA helicase (Hlr1) was mapped to the distal portion of mouse chromosome 11 by linkage analysis of DNA restriction length polymorphisms using an interspecific genetic backcross between (C57BL/6J x SPRET/Ei) F1 hybrids and SPRET/Ei mice. A closely related gene (Hlr1-ps1) was identified, isolated, and mapped to the proximal part of the same chromosome. Sequence analysis and PCR results suggest that Hlr1-ps1 is a pseudogene, flanked by DNA stretches similar to mouse insertion element IE118.

Animals↗
PubMed1984

Isolation and nucleotide sequence analysis of the beta-type globin pseudogene from human, gorilla and chimpanzee.

The beta-globin gene cluster of human, gorilla and chimpanzee contain the same number and organization of beta-type globin genes: 5'-epsilon (embryonic)-G gamma and A gamma (fetal)-psi beta (inactive)-delta and beta (adult)-3'. We have isolated the psi beta-globin gene regions from the three species and determined their nucleotide sequences. These three pseudogenes each share the same substitutions in the initiator codon (ATG----GTA), a substitution in codon 15 which generates a termination signal TGG----TGA, nucleotide deletion in codon 20 and the resulting frame shift which yields many termination signals in exons 2 and 3. The basic structure of these psi beta-globin genes, however, remains consistent with that found for functional beta-globin genes: their coding regions are split by two introns, IVS 1 (which splits codon 30, 121 base-pairs in length) and IVS 2 (which splits codon 104, 840 to 844 base-pairs in length). These introns retain the normal splice junctions found in other eukaryotic split genes. The three hominoid psi beta-globin genes show a high degree of sequence correspondence, with the number of differences found among them being only about one-third of that predicted for DNA sites evolving at the neutral rate (i.e. for sites evolving in the absence of purifying selection). Thus, there appears to be a deceleration in the rate of evolution of the psi beta-globin locus in higher primates.

Animals↗
PubMed1985

Genes and pseudogenes for rat U3A and U3B small nuclear RNA.

We report here the isolation and primary structure of two genes encoding rat U3 small nuclear RNA. One of the genes encodes U3B RNA; the other encodes an RNA which is almost identical to U3A RNA. Both genes are expressed after microinjection into the nuclei of Xenopus laevis oocytes and can direct the accumulation of mature U3 RNA as well as longer transcripts which may be the U3 precursors. We have also isolated and sequenced four other regions of the rat genome homologous to U3 RNA. One of these almost certainly represents a second U3B gene; the other three are pseudogenes which appear to have been generated by the reverse flow of genetic information from U3 RNA back into the genome. Using genomic blotting techniques, we show that the rat U3 genes are present in only a few copies per haploid genome and are probably not closely linked to one another.

Animals↗
PubMed1985

Structural relationship of human interferon alpha genes and pseudogenes.

We have isolated and characterized DNA segments containing IFN-alpha-related sequences from human lambda and cosmid clone banks. We describe six linkage groups comprising 18 distinct IFN-alpha-related loci, and report the nucleotide sequences of nine chromosomal IFN-alpha-genes with intact reading frames, as well as of five pseudogenes. Taking into account as yet unsequenced genes as well as clones described by others, there are now seven linkage groups and 23 loci, of which 15 correspond to potentially functional genes and six to non-functional genes; two loci remain unsequenced. Eighteen additional sequences are likely to be allelic to the above. The finding that at least two IFN-alpha genes appear to be natural hybrids of other IFN-alpha genes, and that two distinct IFN-alpha loci have completely identical coding sequences, although their flanking regions are different, is evidence for information exchange between the individual genes.

Amino Acid Sequence↗
PubMed1980

The nucleotide sequence of a rabbit beta-globin pseudogene.

We report the nucleotide sequence of a rabbit beta-globin pseudogene, psi beta 2. A comparison the psi beta 2 sequence with that of the rabbit adult beta-globin gene, beta 1, reveals the presence of frameshift mutations and premature termination codons in the protein coding sequence which render pse beta 2 unable to encode a functional beta-globin polypeptide. psi beta 2 contains two intervening sequences at the same locations in the globin protein coding sequence as beta 1 and all other sequenced beta-globin genes. An examination of the DNA sequences at the intron/exon junctions suggests that a putative pse beta 2 precursor mRNA could not be spliced normally. We compare the flanking and noncoding sequences of pse beta 2 and beta 1 and discuss the evolutionary relationship between these two genes.

Animals↗
PubMed1982

The structure of the human zeta-globin gene and a closely linked, nearly identical pseudogene.

DNA sequencing studies indicate that only one of two closely linked human embryonic alpha-like globin genes, zeta (zeta), encodes a functional polypeptide. The other is a pseudogene (psi zeta) that differs by only 3 bp in the protein coding sequence, one of which converts the codon for amino acid 6 into a chain termination codon. Both zeta-globin genes differ from all other alpha-like genes thus far reported in that they contain large introns consisting, in part, of simple repeat sequences. Intron 1 of each gene contains a variation of the repeat sequence ACAGTGGGGAGGGG, while intron 2 contains the repeat sequence CGGGG. Comparison of the human zeta- and alpha-globin gene sequences reveals that the embryonic and adult alpha-like genes began to diverge from each other relatively early in vertebrate evolution (400 million years ago). In contrast, the beta-like embryonic globin gene, epsilon (epsilon), is the product of a much more recent evolutionary event (200 million years ago). Thus, even though the temporal and quantitative expression of zeta- and epsilon-globin genes must be coordinately controlled during development, their evolutionary histories are clearly distinct.

Amino Acid Sequence↗
PubMed1985

P31, a mammalian housekeeping protein encoded by a multigene family containing a high proportion of pseudogenes.

The primary structure of P31, a 13.300 kDa mammalian 'housekeeping' protein, was deduced from the nucleotide sequence of a rat recombinant cDNA clone. The P31 mRNA has 950 nucleotides and codes for a protein of 121 amino acids. This mRNA is present in several mouse tissues and in other mammals. Nuclei of rapidly growing cells contain mature P31 mRNA and a distinctive set of larger transcripts. P31 is encoded by a multigene family. Five members of the family were isolated from a mouse genomic library and restriction mapping and S1 nuclease analysis of four of them (P31-4, P31-12, P31-13 and P31-14) suggest that they are processed genes. The very low homology of the fifth (P31-8) with respect to the corresponding cDNA sequence indicates that it is a pseudogene. Although the features of the mRNA and the genes encoding P31 exhibit extensive similarity with those of ribosomal proteins, neither the identity nor the biological function of the protein has yet been determined.

Amino Acid Sequence↗
PubMed1984

The coding region of the human c-mos pseudogene contains Alu repeat insertions.

We have determined the nucleotide sequence of an 841-bp fragment derived from a segment of the human genome previously cloned by Chumakov et al. [Gene 17 (1982) 19-26] and Zabarovsky et al. [Gene 23 (1983) 379-384] and containing regions homologous to the viral mos gene probe. This sequence displays homology with part of the coding region of the human and murine c-mos genes, contains several termination codons, and is interrupted by two Alu-family elements flanked by short direct repeats. Probably, the progenitor of the human c-mos gene was duplicated approximately at the time of mammalian divergence, was converted to a pseudogene, and acquired insertions of two Alu elements.

Base Sequence↗
PubMedDate not supplied

Isolation and characterization of four mouse ribosomal-protein-L18 genes that appear to be processed pseudogenes.

We describe the isolation and initial characterization of six independent lambda Charon 4A recombinant phages which carry four mouse genes for ribosomal protein L18 (L18-15, L18-17, L18-18, L18-30). Structural analysis indicates that these L18 genes contain the entire coding sequence (approx. 600 bp), but lack introns and differ both in their flanking and coding sequences. Based on these features we propose that these are processed pseudogenes. However, we have no indications whether these genes are expressed at either the transcriptional or translational levels. Quantitative estimation of sequence divergence of these genes suggest that the order of their evolutionary emergence (integration) is: first L18-17 and L18-18, then L18-15 and finally L18-30. We discuss the implication of the high proportion of L18 processed genes in this multigene family with respect to the coordinate regulation of r-proteins.

Animals↗
PubMed2002

The third myrosinase gene TGG3 in Arabidopsis thaliana is a pseudogene specifically expressed in stamen and petal.

Genomic clones and full-length cDNA for the myrosinase gene TGG3 from Arabidopsis thaliana ecotype Columbia were sequenced. The TGG3 gene was similar with the earlier described myrosinase genes and shared the conserved intron/exon splice sites but had an insertion of one nucleotide in exon 5, a deletion of two nucleotides in exon 6 and a deletion of approximately 210 nucleotides in exon 12. These mutations shifted the open reading frame in exon 5 and resulted in a truncated protein. Analysis of the TGG3 DNA sequence from five other Arabidopsis ecotypes showed polymorphisms, but in no case did a functional TGG3 gene appear to be present. Although TGG3 apparently is a pseudogene, it was expressed specifically in stamen and petal according to RT-PCR analysis, while TGG1 and TGG2 transcripts were present in most of the tested tissues. Western blot analysis showed only one myrosinase band of 68 kDa corresponding to TGG1 and TGG2 in flower samples, while no band corresponding to TGG3 was encountered. Apparently only two functional myrosinases are present in this gene family in Arabidopsis.

Journal Article↗
PubMed1980

Human immunoglobulin variable region genes--DNA sequences of two V kappa genes and a pseudogene.

The study of immunoglobulin genes at the molecular level can allow us to elucidate the origin of antibody diversity. Investigations of immunoglobulin gene structure in the mouse have shown that light chains are encoded by three gene segments: the C gene encoding the constant region and the V and J genes encoding the variable region. In antibody-producing cells the V and J genes join together to create a complete immunoglobulin gene. No data are available on the structure of human light chain variable region genes, but the variable regions of over 150 human kappa light chain proteins have been sequenced and they comprise four distinct subgroups. Here we report the complete DNA sequences of three human kappa variable region (V kappa) genes isolated from fetal liver DNA. The sequences demonstrate that two non-allelic genes encoding subgroup I proteins have more than 90% nucleotide homology in both proteins coding and non-coding regions. Comparison of these human genes with two complete DNA sequences of mouse V kappa genes shows that V kappa gene structure is highly conserved between the two species, which suggests that V kappa genes rearrange during the differentiation of human lymphocytes by a very similar mechanism to that in the mouse. The sequence of a defective V kappa gene is also described--this gene is unable to code for a functional immunoglobulin due to substitutions, deletions and insertions in its sequence. It is analogous to the pseudogenes of globin and Xenopus 5S RNA.

Animals↗