Sequence analysis of the 43 kb CRM1-YLM9-PET54-DIE2-SMI1-PHO81-YHB4-PFK1 region from the right arm of Saccharomyces cerevisiae chromosome VII

The nucleotide sequence of a 43 118 bp fragment from chromosome VII of Saccharomyces cerevisiae has been determined and analysed. The fragment originates from the right arm of chromosome VII. It starts approximately 11 kb centromere-proximal to the pet54 marker and ends in the middle of the PFK1 gene. The sequence contains a small nuclear RNA gene (SNR7) and 29 open reading frames (ORFs) larger than 100 amino acids. Six of these were completely internal to or partially overlapped other ORFs. Six previously described genes, YLM9/MRPL9, CRM1, DIE2, SMI1, PHO81 and YHB4, were mapped to this region in addition to pet54 and PFK1. Of the remaining 17 ORFs, four showed homology with other S. cerevisiae genes and four, including one of the partially overlapping ORFs, with genes from other organisms. Eight ORFs had no homology with any sequence in the databases. The actual sequences have been deposited in the EMBL database under Accession Number X87941.     

Sequencing and analysis of 51·6 kilobases on the left arm of chromosome XI from Saccharomyces cerevisiae reveals 23 open reading frames including the FAS1 gene

We have sequenced two segments containing a total of 51·6 kb of the left arm from chromosome XI of Saccharomyces cerevisiae. The first segment of 38·5 kb contains 18 open reading frames (ORFs) of more than 100 amino acid residues. Five ORFs encode known yeast genes, including the fatty acid synthase gene (FAS1). Three new yeast genes were discovered with homologies to non-yeast genes and ten new genes without homologies to any known sequences. The second segment of 13 kb contains five ORFs with two known yeast genes and three unknown genes. The sequences from cosmid pUKG041 were obtained entirely with the walking primer strategy resulting in a very low overall sequence redundancy of 2·8 and an average reading length of 443 bases.     

Sequencing of a 9·9 kb Segment on the Right Arm of Yeast Chromosome VII Reveals Four Open Reading Frames,including PFK1, the Gene Coding for Succinyl-CoA Synthetase (β-chain) and Two ORFs Sharing Homology with ORFs of the Yeast Chromosome VIII

A 9·9 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains four open reading frames (ORFs) longer than 100 amino acids. One gene, PFK1, has already been cloned and sequenced and the other one is the probable yeast gene coding for the β-subunit of the succinyl-CoA synthetase. The two remaining ORFs share homology with the deduced amino acid sequence (and their physical arrangement is similar to that) of the YHR161c and YHR162w ORFs from chromosome VIII. The sequence is in the EMBL data library under Accession Numbers Z73024, Z73025, Z73026, Z73028 and Z73029.©1997 John Wiley & Sons, Ltd.     

Sequence analysis of a 40·7 kb segment from the left arm of yeast chromosome X reveals 14 known genes and 13 new open reading frames including homologues of genes clustered on the right arm of chromosome XI

The complete nucleotide sequence of a 40·7 kb segment about 130 kb from the left end of chromosome X of Saccharomyces cerevisiae was determined from two overlapping cosmids. Computer analysis of that sequence revealed the presence of the previously known genes VPS35, INO1, SnR128, SnR190, MP12, YAK1, RPB4, YUR1, TIF2, MRS3 and URA2, three previously sequenced open reading frames (ORFs) of unknown function 5′ of the INO1, 5′ of the MP12 and 3′ of the URA2 genes and 13 newly identified ORFs. One of the new ORFs is homologous to mammalian glycogenin glycosyltransferases and another has similarities to the human phospholipase D. Some others contain potential transmembrane regions or leucine zipper motifs. The existence of yeast expressed sequence tags for some of the newly identified ORFs indicates that they are transcribed. A cluster of six genes within 10 kb (YUR1, TIF2, two new ORFs, an RSP25 homologue and MRS3) have homologues arranged similarly within 28·5 kb on the right arm of chromosome XI. The sequence has been deposited in the EMBL data library under Accession Number X87371.     

Sequence of a 39 411 bp DNA fragment covering the left end of chromosome VII of Saccharomyces cerevisiae

We have sequenced a DNA fragment of 39 411 bp which includes part of the left telomere of chromosome VII of Saccharomyces cerevisiae. We have identified 19 open reading frames (ORFs); six correspond to known yeast genes (ADH4, FZF1, HKB, RTG2, HFM1 and PDE1), nine have similarity with other genes and four exhibit no significant similarity with any known gene. The average size of these ORFs seems to be related to their location, the eight ORFs nearest the telomere being shorter than the 11 others. These two groups of genes are separated by a region of 4·5 kb devoid of significant ORFs. One ORF, NRF120, is a new member of the seripauperine family, represented once in all sequenced yeast chromosomes, in a subtelomeric location. This sequence has been entered in the EMBL data library under accession number X94357.     

Sequencing of a 40·5 kb Fragment Located on the Left Arm of Chromosome VII from Saccharomyces cerevisiae

The nucleotide sequence of a 40·5 kb DNA fragment from the left arm of chromosome VII of Saccharomyces cerevisiae was determined and analysed. Twenty-eight open reading frames (ORFs) longer than 300 nucleotides were identified. Eight of them correspond to the following known yeast genes: EMP24, GCN1, SPO8, COX13, CDC55, RPS26, COX4 and LSR1, also called GTS1. Twelve ORFs are new, among them eight show homology with other genes while four have no homology with any sequence in the databases. Eight additional ORFs are internal to or partially overlapping with other ORFs. The nucleotide sequence reported here is deposited in the EMBL database under the Accession Numbers X91837 and X91489. © 1997 by John Wiley & Sons, Ltd.     

XIV. Yeast sequencing reports. Twelve open reading frames revealed in the 23·6 kb segment flanking the centromere on the Saccharomyces cerevisiae chromosome XIV right arm

The nucleotide sequence of 23·6 kb of the right arm of chromosome XIV is described, starting from the centromeric region. Both strands were sequenced with an average redundancy of 4·87 per base pair. The overall G+C content is 38·8% (42·5% for putative coding regions versus 29·4% for non-coding regions). Twelve open reading frames (ORFs) greater than 100 amino acids were detected. Codon frequencies of the twelve ORFs agree with codon usage in Saccharomyces cerevisiae and all show the characteristics of low level expressed genes. Five ORFs (N2019, N2029, N2031, N2048 and N2050) are encoded by previously sequenced genes (the mitochondrial citrate synthase gene, FUN34, RPC34, PRP2 and URK1, respectively). ORF N2052 shows the characteristics of a transmembrane protein. Other elements in this region are a tRNA^Pro gene, a tRNA^Asn gene, a τ₃₄ and a truncated δ₃₄ element. Nucleotide sequence comparison results in relocation of the SIS1 gene to the left arm of the chromosome as confirmed by colinearity analysis. The nucleotide sequence data reported in this paper will appear in the EMBL, GenBank and DDBJ Nucleotide Sequence Databases under the accession number X77395.     

II. Yeast sequencing reports. Sequence analysis of a 78·6 kb segment of the left end of Saccharomyces cerevisiae chromosome II

We report the sequence analysis of a 78,601 bp DNA segment on the left arm of chromosome II of Saccharomyces cerevisiae. This 78·6 kb segment spans the region from the start of a subtelomeric Y′ element up to the ILS1 gene. It contains 49 open reading frames (ORFs) with more than 100 amino acids length including 14 internal and five overlapping ORFs. The gene density, excluding the internal ORFs, was calculated as one ORF per 2·2 kb. Eight ORFs (PKC1, TyA, TyB, ATP1, ROX3, RPL17a, PET112 and ILS1) correspond to previously characterized genes. ORF YBL0718 was identified as CDC27; YBL0706 as TEL1. Four other ORFs show strong similarities to already known genes. The gene product of YBL0838 is 60% identical to the ribosomal protein RPL32 from rat, mouse and man. YBL0701 encodes a protein with significant similarity to the initiation factor eIF2 associated p67 glycoprotein from rat. Eight ORFs were disrupted and the resulting yeast strains analysed with respect to their phenotype. The sequence has been deposited in the EMBL Nucleotide Sequence Database under the Accession Number X79489.     

Sequencing of a 17·6 kb segment on the right arm of yeast chromosome VII reveals 12 ORFs,including CCT,ADE3 and TR-I genes,homologues of the yeast PMT and EF1G genes,of the human and bacterial electron-transferring flavoproteins (β-chain) and of the Escherichia coli phosphoserine phosphohydrolase,and five new ORFs

A 17·6 kb DNA fragment from the right arm of chromosome VII of Saccharomyces cerevisiae has been sequenced and analysed. The sequence contains twelve open reading frames (ORFs) longer than 100 amino acids. Three genes had already been cloned and sequenced: CCT, ADE3 and TR-I. Two ORFs are similar to other yeast genes: G7722 with the YAL023 (PMT2) and PMT1 genes, encoding two integral membrane proteins, and G7727 with the first half of the genes encoding elongation factors 1γ, TEF3 and TEF4. Two other ORFs, G7742 and G7744, are most probably yeast orthologues of the human and Paracoccus denitrificans electron-transferring flavoproteins (β chain) and of the Escherichia coli phosphoserine phosphohydrolase. The five remaining identified ORFs do not show detectable homology with other protein sequences deposited in data banks. The sequence has been deposited in the EMBL data library under Accession Number Z49133.     

An 18·3 kb DNA Fragment from Yeast Chromosome VII Carries Four Unknown Open Reading Frames,the Gene for an Asn Synthetase,Remnants of Ty and Three tRNA Genes

An 18·3 kb DNA segment from yeast Saccharomyces cerevisiae chromosome VII encompasses the previously characterized MEP1, NUP57 and PPT1 genes as well as seven new open reading frames (ORFs) of at least 100 residues. G6358 is an ubiquitous glutamine-dependant asparagine synthase. G6362 is a membrane protein highly homologous to a protein of unknown function in the yeast Schizosaccharomyces pombe. Three ORFs (G6324, G6335 and G6365) have no significant homology with previously reported proteins or characteristic motifs. G6321 and G6359, enclosed in longer ORFs, are not likely to be coding. The segment also contains tRNA genes for Asn, Arg and Ile as well as a sigma element and two solo deltas. ORFs and genetic elements are named according to a preliminary working nomenclature. The sequence is recorded in GenBank^TM/EMBL under Accession Number X83099.©1997 John Wiley & Sons, Ltd.     

VI. Yeast sequencing reports. Sequencing of an 18·8 kb fragment from Saccharomyces cerevisiae chromosome VI

The nucleotide sequence of lambda phage clone 4121, which contains the 18·8 kb fragment of Saccharomyces cerevisiae chromosome VI left arm, was determined. This sequence had seven open reading frames (ORFs), four of which were identical to known genes (ACT1, YPT1, TUB2 and RPO41). Another three ORFs (4121orfR003, 4121orfR004 and 4121orfRN001) were highly homologous to FET3 multi-copper oxidase, glucose transport protein, and hypothetical protein of YIL106w on chromosome IX, respectively. 4121orfRN01 is suggested to contain an intron. The sequence has been submitted to DDBJ/EMBL/GenBank data library under Accession Number D44598.     

The complete sequence of a 9037 bp DNA fragment of the right arm of Saccharomyces cerevisiae chromosome VII

We report the sequence of a 9037 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete open reading frames (ORFs), namely G7572, G7576, G7579 and G7584. The first three corresponded, respectively, to the previously cloned genes: HIP1, coding for a high-affinity histidine-specific permease, TDH1, one of the known genes coding for glyceraldehyde-3-phosphate dehydrogenase and ODPX, which encodes a precursor of protein X, a component of the pyruvate dehydrogenase complex. The ORF G7584 showed 35·8% identity with a hypothetical protein of Caenorhabditis elegans chromosome 3. The reported sequence has been deposited in the EMBL data library under Accession Number X82408.     

X. Yeast sequencing reports. The sequence of 24·3 kb from chromosome X reveals five complete open reading frames,all of which correspond to new genes,and a tandem insertion of a ty1 transposon

We have determined the complete nucleotide sequence of a 24·3 kb segment from chromosome X carried by the cosmid pEJ103. The sequence encodes five complete open reading frames (ORFs), none of which correspond to previously described genes; however, four of these ORFs display interesting similarities with sequences present in the databanks. The sequence also contains a tandem insertion of a Ty1 element. An investigation of the Ty1 polymorphism in other strains has revealed that the original insertion occurred within an ORF. Finally, the structure of the Ty1 repeat suggests a mechanism by which it may have been generated. The sequence has been deposited in the EMBL data library under the Accession Number X87297 for the complete sequence and X87298 for the δty1 version.     

VII. Yeast sequencing reports. The sequence of an 11·1 kb fragment on the left arm of Saccharomyces cerevisiae chromosome VII reveals six open reading frames including NSP49, KEM1 and four putative new genes

We report the sequence of an 11·1 kb fragment located on the left arm of chromosome VII of Saccharomyces cerevisiae. By sequence analysis we have detected six open reading frames (ORFs) longer than 300 bp, which cover 87% of the entire sequence. ORF G1645 is 100% identical to the KEM1 gene, also identified as DST2, XRN1, SEP1 and RAR5, while G1648 is 100% identical to the NSP49 or NUP49 gene. ORF G1642 shares some identity with a hypothetical protein of Caenorhabditis elegans, while the other four ORFs show no significant homology to known proteins. The sequence has been submitted to the EMBL data library under Accession Number X84705.     

XIV. Yeast sequencing reports. The sequence of a 44 420 bp fragment located on the left arm of chromosome XIV from Saccharomyces cerevisiae

We have determined the complete nucleotide sequence of a 44 420 bp DNA fragment from chromosome XIV of Saccharomyces cerevisiae. The sequence data revealed 23 open reading frames (ORFs) larger than 300 bp, covering 73·5% of the sequence. The ORFs N2418, N2441, N2474 and N2480 correspond to previously sequenced S. cerevisiae genes coding respectively for the mitochondrial import protein Mas5, the nucleolar protein Nop2, the outer mitochondrial membrane porin Por1, the cytochrome c oxidase polypeptide VA precursor CoxA and the yeast protein tyrosine phosphatase Msg5. Translation products of three other ORFs N2406, N2411 and N2430 exhibit similarity to previously known S. cerevisiae proteins: the ribosomal protein YL9A, the protein Nca3 involved in the mitochondrial expression of subunits 6 and 8 of the ATP synthase and actin; in addition N2505 presents strong similarity to an ORF of chromosome IX. The predicted protein products of ORFs N2417 and N2403 present similarities with domains from proteins of other organisms: the Candida maltosa cycloheximide-resistance protein, the human interleukin enhancer-binding factor (ILF-2). The 12 remaining ORFs show no significant similarity to known proteins. In addition, we have detected a DNA region very similar to the yeast transposon Ty 1–15 of which insertion has disrupted a tRNA^Asp gene. The sequence has been deposited in the GenBank database with the Accession Number U12141.     

Sequencing of a 9·2 kb telomeric fragment from the right arm of Saccharomyces cerevisiae chromosome XIV

We report the complete sequence of a 9·2 kb fragment next to and including the right telomere of Saccharomyces cerevisiae chromosome XIV. Four open reading frames (ORFs) longer than 100 amino acids were observed in the sequenced segment. One ORF (378 codons) does not show any significant homology with proteins in the databases and corresponds to a putative new gene. Two ORFs are almost identical to the known YCR007/YKL219 and PAU1-like hypothetical protein families already identified on several S. cerevisiae chromosomes. These ORFs, whose function is unknown, are generally associated with sub-telomeric regions of chromosomes. The fourth one shows significant identities with bacterial mannitol dehydrogenases. It could be a yeast gene implicated in the metabolism of mannitol (or a related substrate). The sequence has been deposited in the EMBL data library under Accession Number X86790.     

Analysis of a 26 756 bp segment from the left arm of yeast chromosome IV

The nucleotide sequence of a 26·7 kb DNA segment from the left arm of Saccharomyces cerevisiae chromosome IV is presented. An analysis of this segment revealed 11 open reading frames (ORFs) longer than 300 bp and one split gene. These ORFs include the genes encoding the large subunit of RNA polymerase II, the biotin apo-protein ligase, an ADP-ribosylation factor (ARF 2), the ‘L35’-ribosomal protein, a rho GDP dissociation factor, and the sequence encoding the protein phosphatase 2A. Further sequence analysis revealed a short ORF encoding the ribosomal protein YL41B, an intron in a 5′ untranslated region and an extended homology with another cosmid (X83276) located on the same chromosome. The potential biological relevance of these findings is discussed. The sequence was submitted to the EMBL database under Accession Number X96876.     

The DNA Sequence of Cosmid 14–13b from Chromosome XIV of Saccharomyces cerevisiae Reveals an Unusually High Number of Overlapping Open Reading Frames

This work is part of the effort for sequencing chromosome XIV of Saccharomyces cerevisiae. Cosmid 14–13b contains a 37·8 kb insert derived from a partial Sau3A digestion of the genome, cloned into the BamHI site of the vector Pou6. The strategy used for sequencing is based on the fragmentation of the whole cosmid by sonication, followed by shotgun sequencing on an Applied Biosystem DNA sequencer. The clones with inserts corresponding to the vector were identified by dot-blot hybridization, without the need of sequencing. The analysis of the DNA sequence reveals 29 open reading frames (ORFs) longer than 300 bases. Nine ORFs are internal to some other ORFs. Similarity searches against DNA and protein data banks show that six ORFs correspond to already known yeast genes (OMP1, PSU1, MLS1, RPC19, DBP2, CYB5) and one ORF matches the sequence of a putative yeast gene (ESBP6). The cosmid sequence has been submitted to the EMBL data bank under Accession Number Z69382.©1997 John Wiley & Sons, Ltd.