Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal tohis5

Xiang, Zheng; Moore, Karen; Wood, Valerie; Rajandream, Maire‐Adèle; Barrell, Barclay G.; Skelton, Jason; Churcher, Carol; Lyne, M.; Devlin, K.; Gwilliam, Rhian; Rutherford, Kim; Aves, Stephen J.

doi:10.1002/1097-0061(200011)16:15<1405::aid-yea625>3.0.co;2-h

Cited by 6 publications

(5 citation statements)

References 32 publications

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“…The ORFs, considering YlVI-104c, occupy 69.5% of the complete sequence, a value slightly lower than the 72% described for S. cerevisiae (Dujon, 1996) but higher than those obtained for Sz. pombe (54-59%; Sanchez et al, 1999;Xiang et al, 2000). The sequence region has an overall G+C content of 48.5%, in good agreement with previously reported data (49.6-51.7%; Nakase and Komagata, 1971;Kü rtzman and Fell, 1998;Kü ck et al, 1980).…”

Section: Resultssupporting

confidence: 88%

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Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species

Sánchez

Domínguez

2001

Yeast

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We have determined the sequence of a 10275 bp DNA segment of Yarrowia lipolytica located on chromosome VI. The sequence contains six complete open reading frames (ORFs) longer than 100 amino acids and two more partial ORFs at both ends. Two of the ORFs encode for the well-characterized genes YlURA5 (orotate phosphoribosyltransferase) and YlSEC65 (encoding a subunit of the signal recognition particle). These two genes show an identical organization-located on opposite strands and in opposite orientations-in four yeast species: Saccharomyces cerevisiae, Kluyveromyces lactis, Candida albicans and Y. lipolytica. One ORF and the two partial ORFs code for putative proteins showing significant homology with proteins from other organisms. YlVI-108w (partial) and YlVI-103w show 39% and 54% identity, respectively, with YDR430c and YHR088w from S. cerevisiae. YlVI-102c (partial) shows significant homology with a matrix protein, lustrin A from Haliotis rufescens, and with the PGRS subfamily (Gly-rich proteins) of Mycobacterium tuberculosis. The three remaining ORFs show weak or nonsignificant homology with previously sequenced genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AI006754.

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Section: Resultssupporting

confidence: 88%

“…pombe (7.8 Mb, 13.6r55%;Sanchez et al, 1999;Xiang et al, 2000). Only a few Y. lipolytica genes have introns (Barth and Gaillardin, The URA5-SEC65 region of ascomycetous yeasts 811 1996) and to date no chromosomal duplications have been described.…”

Section: Orfs and Orf Productsmentioning

confidence: 99%

Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species

Sánchez

Domínguez

2001

Yeast

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“…The analysis methods used for the Sz. pombe genome combine ab initio gene prediction algorithms and homology search results with rigorous manual inspection of biological context (Xiang et al, 2000). In addition, consistency checks using available cDNAs and ESTs have been routinely performed, and new experimental data from the fission yeast community immediately incorporated into the dataset.…”

Section: Aimsmentioning

confidence: 99%

“…pombe genome) (Xiang et al, 2000). Searches were performed against public databases (SWISS-PROT and TrEMBL (Bairoch and Apweiler, 1999), EMBL (Stoesser et al, 1999), Pfam (Bateman et al, 1999), and PROSITE (Bairoch, 1994)) using standard software (BLAST (Altschul et al, 1990), MSPcrunch (Sonnhammer and Durbin, 1994), tRNAscan (Lowe and Eddy, 1997), FASTA (Pearson and Lipman, 1988) and Genewise (Birney et al, 1996)), to complete a series of automated analyses.…”

Section: Analysis Proceduresmentioning

confidence: 99%

A Re‐annotation of the Saccharomyces cerevisiae Genome

et al. 2001

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Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described. 370 ORFs are defined as totally spurious ORFs which should be disregarded. At least a further 193 genes could be described as very hypothetical, based on a number of criteria. It was found that disparate genes with sequence overlaps over ten amino acids (especially at the N-terminus) are rare in both S. cerevisiae and Sz. pombe. A new S. cerevisiae gene number estimate with an upper limit of 5804 is proposed, but after the removal of very hypothetical genes and pseudogenes this is reduced to 5570. Although this is likely to be closer to the true upper limit, it is still predicted to be an overestimate of gene number. A complete list of revised gene coordinates is available from the Sanger Centre (S. cerevisiae reannotation: ftp://ftp/pub/yeast/SCreannotation).

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“…pombe cosmids (Sá nchez et al, 1999;Lucas et al, 2000;Xiang et al, 2000). However, the 16 coding sequences cover 67.5% of the total sequence, a value higher than those reported for other cosmids located on chromosome II (54.1% cosmid c32F12, Sá nchez et al, 1999; and 59% cosmids c16H5, c12D12, c24C6 and c19G7, Xiang et al, 2000). Seven of the ORFs have introns.…”

Section: Sequence Analysismentioning

confidence: 75%

Analysis of 41 kb of the DNA sequence from the right arm of chromosome II of Schizosaccharomyces pombe

Sánchez

Revuelta

Rey

et al. 2001

Yeast

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We report the complete sequence of cosmid c18A7 (41 046 bp insert), located on the right arm of chromosome II of the Schizosaccharomyces pombe genome. The sequence, which partially overlaps with cosmids SPBC4F6 and SPBC336, contains 16 open reading frames (ORFs) capable of coding for proteins of at least 100 amino acid residues in length (one partial) and one small nucleolar RNA (snoRNA). Four known genes were found: swi10 (encoding a mating-type switching protein also involved in nucleotide excision repair); dim1 (encoding a dimethyladenosine transferase); arf1 (encoding ADP-ribosylation factor 1); and pol3 (cdc6) the partial fragment, encoding the 125 kDa catalytic subunit of the DNA polymerase type B. Six ORFs similar to known proteins were found. They include a transporter of the major facilitator superfamily class, a vacuolar sorting protein, an asparagine synthase, a nuclear protein, a reticulum oxidoreductin and a heat shock protein.Each protein product of the other six ORFs has conserved domains and can be assigned a molecular, but not a biological, function. The sequence has been submitted to the EMBL database under Accession No. AL080287.

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Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal tohis5

Cited by 6 publications

References 32 publications

Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species

Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species

A Re‐annotation of the Saccharomyces cerevisiae Genome

Analysis of 41 kb of the DNA sequence from the right arm of chromosome II of Schizosaccharomyces pombe

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