Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “pseudogene”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41Linked to original sources
PubMed1995

Isolation of CYP3A5P cDNA from human liver: a reflection of a novel cytochrome P-450 pseudogene.

We have isolated, from a human liver cDNA library, a 1627 bp CYP3A5 cDNA variant (CYP3A5P) that contains several large insertions, deletions, and in-frame termination codons. By comparison with the genomic structure of other CYP3A genes, the major insertions in CYP3A5P cDNA demarcate the inferred sites of several CYP3A5 exons. The segments inserted in CYP3A5P have no homology with splice donor acceptor sites. It is unlikely that CYP3A5P cDNA represents an artifact of the cloning procedures since Southern blot analysis of human genomic DNA disclosed that CYP3A5P cDNA hybridized with a DNA fragment distinct from fragments that hybridized with either CYP3A5, CYP3A3 or CYP3A4. Moreover, analysis of adult human liver RNA on Northern blots hybridized with a CYP3A5P cDNA fragment revealed the presence of an mRNA with the predicted size of CYP3A5P. We conclude that CYP3A5P cDNA was derived from a separate gene, CYP3A5P, most likely a pseudogene evolved from CYP3A5.

Base Sequence↗
PubMed1991

A preproinsulin-like pseudogene from Neurospora crassa.

A segment of DNA was amplified from the Neurospora crassa genome by the polymerase chain reaction using several oligonucleotides coding for highly conserved domains in proinsulin as primers and probe. A genomic clone corresponding to this segment was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of a part of this segment bears remarkable resemblance to preproinsulin, but lacks several requirements for transcription or translation and must therefore be considered to be a pseudogene.

Amino Acid Sequence↗
PubMed1987

Complete structure of the human transferrin gene. Comparison with analogous chicken gene and human pseudogene.

The complete structure of the human transferrin gene is presented. This gene has a total size of about 33.5 kb and is organized in 17 exons separated by 16 introns. The chicken ovotransferrin gene has a size of 10.5 kb and is also organized in 17 exons and 16 introns. The analysis of the structure of the two genes confirm, at the gene level, that transferrins originated by a gene duplication phenomenon. Finally, the existence of a new member of the transferrin family, a human transferrin non-processed pseudogene is demonstrated.

Amino Acid Sequence↗
PubMed1987

A variant gene and a pseudogene for human 5S RNA are transcriptionally active in vitro.

Screening of a human genomic DNA library with ribosomal 5S RNA yielded a variant 5S rRNA gene (pH5S1) and a pseudogene lacking the first 9 bp and the last 33 bp (pH5S2). Sequence analysis revealed that both genes contain several mutations in their coding region as compared to human 5S rRNA; however, their intragenic promoters are highly conserved. Both genes are transcribed in a homologous HeLa cell S100 extract. pH5S1 gives rise to a 5S-sized product, whereas the two pH5S2-derived RNAs are about 220 and 240 nucleotides long. pH5S1 is transcribed more efficiently than pH5S2; however, its ability to form a stable preinitiation complex is impaired.

Base Sequence↗
PubMed1987

Two bovine genes for cytochrome c oxidase subunit IV: a processed pseudogene and an expressed gene.

We have isolated and analyzed 17 clones from a bovine genomic library in phage lambda Charon28 probed with a bovine liver cDNA for cytochrome c oxidase subunit IV. Restriction enzyme mapping and Southern analysis indicated that these clones represent only two genomic regions. One region was shown by nucleotide sequencing to contain a subunit IV pseudogene of the processed type. The other class of clones contained the 5' region of a putative expressed gene; the region consists of two exons and two introns, with one exon encoding exclusively the domain representing the presequence present on newly synthesized subunit-IV polypeptides. Genomic Southern analysis indicated that these two clones probably represent the only sequences in the bovine nucleus that share nucleotide sequence identity with the liver subunit IV cDNA when utilizing moderately stringent hybridization conditions.

Amino Acid Sequence↗
PubMed1990

Human ornithine decarboxylase-encoding loci: nucleotide sequence of the expressed gene and characterization of a pseudogene.

Previous studies have shown that human ornithine decarboxylase (ODC)-encoding sequences map to two chromosome regions: 2pter-p23 and 7cen-qter. In the present work we have cloned the expressed human ODC gene from a genomic library of myeloma cells that overproduce ODC protein due to selective gene amplification and determined its entire nucleotide sequence. The gene comprises 12 exons and 11 introns and spans about 8 kb of chromosome 2 DNA. The organization of the human gene is very similar to that of the mouse and rat, with the major difference being the presence of longer intronic sequences in the human gene. Some of these differences can be accounted for by the insertion of four Alu sequences in the human gene. Several potential regulatory elements are present in the promoter region and in 5'-proximal introns, including a TATA box; GC boses; AP-1-, AP-2- and NF-1-binding sites; and a cAMP-responsive element. The 5'-untranslated sequence of ODC mRNA is extremely GC-rich, and computer predictions suggest a very stable secondary structure for this region, with an overall free energy of formation of -225.4 kcal/mol. In addition to the active ODC gene on chromosome 2, ODC gene-related sequences were isolated from human chromosome 7-specific libraries and shown to represent a processed ODC pseudogene.

Animals↗
PubMed1992

A pseudogene for human glutathione peroxidase.

Glutathione peroxidases (GPx) serve a bioprotective function in the reduction of peroxides to less toxic substances. Both cellular and secreted forms of the protein have been reported, as well a number of distinct cDNA sequences. Previous efforts have described three distinct loci on human chromosomes 3, 21 and X which hybridize to a GPX cDNA and these authors have speculated that only the chromosome 3 locus encodes a functional GPX gene. This conclusion was based on mapping studies showing a precise deletion of intron sequences in the GPX loci on chromosomes 21 and X despite strong conservation among these sequences in both the coding and 3'-untranslated regions. To pursue this issue, we have isolated the chromosome 21 GPX locus by molecular cloning and determined its nucleotide sequence. Consistent with the expectations of McBride et al. [Biofactors 4 (1988) 285-292], the sequence does reveal a highly conserved processed pseudogene. It is suggested that a retrotransposed copy of the GPX gene integrated into chromosome 21 and may have maintained activity prior to the accumulation of inactivating mutations.

Base Sequence↗
PubMed1992

Association of hY4 pseudogenes with Alu repeats and abundance of hY RNA-like sequences in the human genome.

Three loci having homology with the small human cytoplasmic RNA, hY4, were isolated from human genomic DNA libraries and sequenced. Each sequence contains dispersed mismatches as compared with hY4 RNA, is followed by an A-rich or A + T-rich sequence, and is bordered by direct repeats. Each of these loci, therefore, appears to constitute a small RNA class-III pseudogene. Surprisingly, two of the three loci are associated with Alu repeats. In the hY4.B7 locus, the hY4 sequence has integrated into the tail of an Alu element and in the hY4.F2 locus, an Alu sequence has inserted into the hY4 tail, confirming that A-rich tracts are preferential targets for retroposition. In addition, Southern blots with probes for each of the four hY RNAs indicate that hY RNA-like sequences are abundant in the human genome.

Base Sequence↗
PubMed1993

The human TYRO3 gene and pseudogene are located in chromosome 15q14-q25.

Partial cDNAs of the human TYRO3 gene, encoding a putative receptor tyrosine kinase, and its processed pseudogene (TYRO3P) were cloned from human teratocarcinoma cell, bone marrow and melanocyte cDNA libraries. The tyrosine kinase homologous domains of TYRO3 and TYRO3P were sequenced and compared with each other and with the mouse TYRO3 gene. Abundant levels of the 4.2-kb TYRO3 mRNA were detected in human brain, and lower levels in other human tissues. TYRO3 and TYRO3P were both assigned to human chromosome 15q14-q25 by analysis of DNAs from somatic cell hybrids.

Amino Acid Sequence↗
PubMed1995

Structure of the mouse thioredoxin-encoding gene and its processed pseudogene.

Thioredoxins (TXN) are small proteins with various biological functions, such as redox regulation, found in many species including bacteria, plants and animals. We previously reported the isolation of the TXN-encoding cDNAs from human and mouse. In order to elucidate the functions of the mammalian TXN system, we planned to generate Txn knockout mice, and cloned the genomic DNA fragments using the Txn cDNA as a probe. The Txn gene extends over 12 kb and consists of five exons separated by four introns. Detailed Southern analyses revealed that the mouse genome contains only one active Txn gene and one processed pseudogene (Txn-ps1), in contrast to some species which have families of active TXN-encoding genes. These findings should help to understand Txn itself, and provide a basis for transgenic experiments by gene targeting.

Amino Acid Sequence↗
PubMed1995

An aromatase pseudogene is transcribed in the bovine placenta.

The present investigation is focused on a new, truncated bovine aromatase cytochrome P-450-encoding transcript (bCyp19) which was repeatedly isolated from a placental lambda gt10 cDNA library. Different cDNA probes derived from bCyp19 were used during screenings. The deviant transcript contains areas of considerable sequence homology (89-98%) corresponding to exons II, III, V, VIII and IX of bCyp19. Exons VI and VII are missing. Exon IV is replaced by a bovine repeat sequence motif. Numerous translation stop codons occur within all reading frames, thus suggesting that the transcript does not encode a functional protein. The gene was detected by PCR in the genomes of all animals investigated (n = 38). The experiments demonstrate that the bovine genome contains a non-functional copy (pseudogene, Cyp19 phi) of bCyp19 that is transcribed together with the bCyp19 messenger in the bovine post-parturition placenta.

Animals↗
PubMed1994

Genomic analysis of a NF1-related pseudogene on human chromosome 21.

A neurofibromatosis type-1 (NF1)-related locus on human chromosome 21 has been characterized. A detailed genomic mapping performed by yeast artificial chromosome (YAC) dot-hybridization revealed that the NF1-related locus is close to the sequence-tagged site (STS), D21S329 (G52E12), which is located on the proximal region of 21q11.2. Sequence analysis showed that this locus seemed to be conserved to the NF1 gene only in several partial regions. Two exon-like segments corresponding to exons 8 and 9 of NF1 were found, in addition to two previously found fragments corresponding to exons 7 and 11. Other exon-like segments were not found in the region so far sequenced. Comparing these homologous segments with the NF1 cDNA, a 2-bp deletion appeared in exon 8 of the locus, resulting in the existence of stop codons in all reading frames. In addition, there were no amplified fragments derived from the related locus by reverse transcription-PCR. Thus, our results suggest that the NF1-related locus on chromosome 21 is a nonprocessed pseudogene.

Animals↗
PubMed1994

Structural organisation of the rat genes encoding liver- and heart-type of cytochrome c oxidase subunit VIa and a pseudogene related to the COXVIa-L cDNA.

To study the tissue-specific expression of the heart(H)- and liver(L)-type of rat cytochrome-c oxidase subunit VIa (rCOXVIa), we have screened and sequenced the genes for the two isoforms. Both genes contain three exons and two introns, spanning 880 bp (rCOXVIa-H) and 3089 bp (rCOXVIa-L), respectively. In both genes, exon I codes for the whole leader sequence comprising 12 (rCOXVIa-H) or 26 (rCOXVIa-L) amino acids and for 12 (rCOXVIa-H) or 10 (rCOXVIa-L) amino acids of the corresponding mature protein, while the remaining amino acids for the mature proteins are encoded by exons II and III. The 5' region of the genes lack both TATA and CAAT boxes, but show a high G+C content in the early 5'-upstream region. We have identified in upstream regions and in the introns of both genes several putative binding sites associated with respiratory function, muscle gene activation and housekeeping function. In rCOXVIa-H, we identified a CCAC/Myo-D motif, known to be required for muscle-specific expression of the human myoglobin-encoding gene, which is not present in rCOXVIa-L. In addition, we have analyzed a pseudogene, showing 84% homology to the COXVIa-L cDNA sequence.

Amino Acid Sequence↗
PubMed1994

A growth hormone pseudogene in the salmon genome.

Representatives of the fish family Salmonidae were reported to possess two nonallelic growth hormone (GH)-encoding genes. In addition to those, we found a third GH-like sequence in a chum salmon genomic DNA library. A number of point mutations and large deletions abolished the possibility of expressing this sequence, showing that the chum salmon genomic DNA contains a GH pseudogene besides functional GH genes.

Amino Acid Sequence↗
PubMed1995

Characterization of a processed pseudogene of human FAU1 on chromosome 18.

A member of the human FAU (Finkel-Biskis-Reilly murine sarcoma virus-associated ubiquitously expressed) gene subfamily, encoding the ribosomal protein S30 fused in frame to an ubiquitin-like protein, was cloned, sequenced and analysed. This clone, FAU1P, is a processed pseudogene with a completely intact, although transcriptionally silent, open reading frame of 137 codons. FAU1P exhibits an amplification of the (AAG) triplet repeat present in the S30 coding part of FAU. FAU1P is integrated in an antisense orientation within a sequence homologous to the promoter of the islet amyloid polypeptide (IAPP or amylin)-encoding gene. By means of PCR hybrid panel mapping, FAU1P was assigned to chromosome 18.

Amyloid↗
PubMed1995

Cloning and sequence of a processed p53 pseudogene from rat: a potential source of false 'mutations' in PCR fragments of tumor DNA.

We describe here the nucleotide (nt) sequence of a p53 processed pseudogene (psi-gene) from the normal F344 rat genome. Exon-derived primers were utilized to amplify and clone a 1447-bp polymerase chain reaction (PCR) product corresponding to the coding regions of exons 2-11 of the functional gene. This psi-gene is a cDNA-like sequence possessing 87% homology with the functional rat p53. We have also partially characterized two additional and distinctly different putative rat p53 psi-genes, focussing on the sequences surrounding the reported rat p53 mutational hot spots of codons 202R and 211R within exon 6/7. Each of these three psi-gene sequences contained various single- and/or double-nt substitutions, small deletions and insertions that distinguish them from p53. One substitution, 211R CGG-->CAG, found both in the cloned psi-gene and in one of the partially characterized, putative psi-genes, corresponded precisely with the sequence that has been reported as a mutation at one of the hot spots. Co-amplification of one or more of the p53 psi-genes with portions of the functional p53 is likely, if exon-based primers are utilized for PCR amplification of rat p53. Consequently, psi-gene sequences are potential sources of sequence variations that can be misidentified as somatic cell mutations by direct sequencing of inappropriately generated PCR products.

Animals↗