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At least 1,153 records · Page 64Linked to original sources
PubMed1987

Mouse histone H2A and H2B genes: four functional genes and a pseudogene undergoing gene conversion with a closely linked functional gene.

The sequence of five mouse histone genes, two H2a and three H2b genes on chromosome 13 has been determined. The three H2b genes all code for different proteins, each differing in two amino acids from the others. The H2b specific elements present 5' to H2b genes from other species are present in all three mouse H2b genes. All three H2b genes are expressed in the same relative amounts in three different mouse cell lines and fetal mice. The H2b gene with the H2b specific sequence closest to the TATAA sequence is expressed in the highest amount. One of the H2a genes lacks the first 9 amino acids, the promoter region, the last 3 amino acids and contains an altered 3' end sequence. Despite these multiple defects, there is only one nucleotide change between the two H2a genes from codon 9 to 126. This indicates that a recent gene conversion has occurred between these two genes. The similarity of the nucleotide sequences in the coding regions of mouse histone genes is probably due to gene conversion events targeted precisely at the coding region.

Animals↗
PubMed1984

Rabbit class I MHC genes: cDNA clones define full-length transcripts of an expressed gene and a putative pseudogene.

The rabbit cell line RL-5 was recently found to express only a single detectable major histocompatibility complex class I protein, in contrast to the multiple class I proteins expressed in cells of the mouse (K, D, and L) and human (A, B, and C). To clarify this difference in the rabbit major histocompatibility complex, we have begun an investigation of the class I genes expressed in the RL-5 cell line and here report the construction of 31 class I cDNA clones derived from RL-5 mRNA. Restriction endonuclease mapping has allowed classification of these clones into five groups, apparently representing five distinct class I mRNA transcripts. The sequence of a full-length cDNA from the predominant group (representing 26 of the 31 clones) reveals a typical class I structure, with an amino terminus that exactly matches the 36 amino terminal residues previously determined for the class I protein immunoprecipitated from RL-5. Complete sequence of a second distinct class I mRNA transcript was deduced from cDNA clones of the second largest group (representing two of the 31 clones). Although this transcript corresponds to a complete class I sequence, an anomaly in initiation sequence may preclude its translation in the proper reading frame. Comparison of the rabbit class I sequences to those of mouse and human revealed significantly higher homologies between the rabbit and the human than between mouse and rabbit or mouse and human sequences.

Amino Acid Sequence↗
PubMed1982

Characterization of a rat tRNA gene cluster containing the genes for tRNAAsp, tRNAGly, and tRNAGlu, and pseudogenes.

Molecular cloning and sequence analysis of a rat DNA fragment hybridized to purified tRNAAsp revealed that the genes for tRNAAspGAU(C), tRNAGlyGGA(G), and tRNAGluGAG are in a cluster on the rat chromosome. These genes are arranged in this order and are regularly separated by DNA regions of about 450 bp. The cluster is reiterated about 10 times on the haploid DNA and is present exclusively in a 3.3 kb region cleaved by restriction endonuclease EcoRI. Five lambda clones each containing an independent repeating unit were isolated from a rat gene library. The clones revealed that the length of the repeating unit including the 3.3 kb EcoRI fragment was at least 13.5 kb. Nucleotide sequence analysis and in vitro transcription of the 3.3 kb DNA in the isolated lambda clones showed sequence variations among the repeating units and the presence of incomplete genes for tRNAGly and tRNAGlu within the clusters.

Animals↗
PubMed1997

Mutation pattern variation among regions of the primate genome.

We sequenced three argininosuccinate-synthetase-processed pseudogenes (PsiAS-A1, PsiAS-A3, PsiAS-3) and their noncoding flanking sequences in human, orangutan, baboon, and colobus. Our data showed that these pseudogenes were incorporated into the genome of the Old World monkeys after the divergence of the Old World and New World monkey lineages. These pseudogene flanking regions show variable mutation rates and patterns. The variation in the G/C to A/T mutation rate (u) can account for the unequal GC contents at equilibrium: 34.9, 36.9, and 41.7% in the pseudogene PsiAS-A1, PsiAS-A3, and PsiAS-3 flanking regions, respectively. The A/T to G/C mutation rate (v) seems stable and the u/v ratios equal 1.9, 1.7, and 1.4 in the flanking regions of PsiAS-A1, PsiAS-A3, and PsiAS-3, respectively. These "regional" variations of the mutation rate affect the evolution of the pseudogenes, too. The ratio u/v being greater than 1.0 in each case, the overall mutation rate in the GC-rich pseudogenes is, as expected, higher than in their GC-poor flanking regions. Moreover, a "sequence effect" has been found. In the three cases examined u and v are higher (at least 20%) in the pseudogene than in its flanking region-i.e., the pseudogene appears as mutation "hot" spots embedded in "cold" regions. This observation could be partly linked to the fact that the pseudogene flanking regions are long-standing unconstrained DNA sequences, whereas the pseudogenes were relieved of selection on their coding functions only around 30-40 million years ago. We suspect that relatively more mutable sites maintained unchanged during the evolution of the argininosuccinate gene are able to change in the pseudogenes, such sites being eliminated or rare in the flanking regions which have been void of strong selective constraints over a much longer period. Our results shed light on (1) the multiplicity of factors that tune the spontaneous mutation rate and (2) the impact of the genomic position of a sequence on its evolution.

Animals↗
PubMed1995

Two gene duplication events in the human and primate dopamine D5 receptor gene family.

The human dopamine D5 receptor (DRD5) gene family consists of the DRD5-encoding gene (DRD5) and the pseudogenes psi DRD5-1 and psi DRD5-2. Analysis of the 5' UTR of DRD5 and homologous regions in the pseudogenes revealed that the nucleotide identity (approx. 95%) extended for 1.9 kb and terminated at a monomeric Alu sequence in each of the pseudogenes. The presence of Alu sequences in the pseudogenes, at this point of divergence with DRD5, suggests that Alu sequences were involved in the evolution of the DRD5 family. This report is the first to describe a possible mechanism involved in the duplication of genes in the G-protein-coupled receptor (GPCR) family. The pseudogenes continue to share identity (approx. 98%) beyond this 5' UTR point of divergence with DRD5 for at least another 6 kb. Analysis of the 3' UTR of DRD5 and homologous regions in the pseudogenes revealed that the identity (approx. 95%) extends at least 14 kb, and the identity between the pseudogenes (approx. 98%) extends for at least 18 kb. Thus, the duplication unit that produced the first pseudogene was at least 16 kb, whereas the second pseudogene was at least 28 kb. We have also located two DRD5 pseudogenes in gorilla demonstrating that these closely related pseudogenes were present in a common ancestor of human and gorilla.

Animals↗
PubMed1987

Isolation and characterization of a processed gene for human ceruloplasmin.

A processed pseudogene for human ceruloplasmin has been isolated that contains DNA corresponding to the functional gene sequence encoding the carboxy-terminal 563 amino acid residues and the 3' untranslated region. The pseudogene appears to have arisen from a processed RNA species, since intervening sequences coincident with those of the functional gene have been removed, with the exception of a short segment of intronic sequence which denotes the 5' boundary of the pseudogene. The nucleotide sequence of the pseudogene is highly homologous (97% sequence identity) with that of the wild-type gene, suggesting that pseudogene formation was a relatively recent evolutionary event. In addition to single base substitutions, there is a large 213 base pair (bp) deletion in the pseudogene sequence which corresponds to the location of an intron-exon junction in the functional gene. A 4 bp duplication that occurs at amino acid residue 683 of the wild-type coding sequence results in a frameshift mutation and introduces a premature translational termination codon at this point. This is concordant with the inability to detect a human liver transcript corresponding to the pseudogene by nuclease S1 mapping analysis. The 3' end of the pseudogene is characterized by a 62 bp segment composed mainly of repeated TC dinucleotides. On the basis of genomic Southern blot analysis performed under high-stringency conditions, the pseudogene that we have identified seems to comprise the only sequence in the human genome that is closely related to the wild-type gene. Using somatic cell hybridization, we have mapped the pseudogene to human chromosome 8.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2004

Eleven daughters of NANOG.

Nanog is a recently discovered ANTP class homeobox gene. Mouse Nanog is expressed in the inner cell mass and in embryonic stem cells and has roles in self-renewal and maintenance of pluripotency. Here we describe the location, genomic organization, and relative ages of all human NANOG pseudogenes, comprising ten processed pseudogenes and one tandem duplicate. These are compared to the original, intact human NANOG gene. Eleven is an unusually high number of pseudogenes for a homeobox gene and must reflect expression in the human germ line. A pseudogene orthologous to NANOGP4 was found in chimpanzee and an expressed pseudogene in macaque. Examining pseudogenes of differing ages gives insight into pseudogene decay, which involves an excess of deletion mutations over insertions. The mouse genome has two processed pseudogenes, which are not clear orthologues of the primate pseudogenes.

Alternative Splicing↗