Long-range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci.
Identifieur interne : 002A23 ( Ncbi/Merge ); précédent : 002A22; suivant : 002A24Long-range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci.
Auteurs : E Y Chen [États-Unis] ; M. Zollo ; R. Mazzarella ; A. Ciccodicola ; C N Chen ; L. Zuo ; C. Heiner ; F. Burough ; M. Repetto ; D. Schlessinger ; M. D'UrsoSource :
- Human molecular genetics [ 0964-6906 ] ; 1996.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Glucosephosphate Dehydrogenase.
- chemical : Cytidine, DNA, Guanosine.
- chemistry : Cosmids.
- genetics : Color Perception.
- Base Sequence, CpG Islands, Dinucleotide Repeats, Female, Humans, Introns, Molecular Sequence Data, Software, X Chromosome.
Abstract
DNA comprising 219 447 bp was sequenced in nine cosmids and verified at > 99.9% precision. Of the standard repetitive elements, 187 Alus make up 20.6% of the sequence, but there were only 27 MERs (2.9%) and 17 L1 fragments (1.6%). This may be characteristic of such high GC (57%) regions. The sequence also includes an 11.3 kb tract duplicated with 99.2% identity at a distance of 38 kb. The region is 80-90% transcribed and 12.5% translated. Thirteen known genes and their exon-intron borders are all accurately predicted at least in part by GRAIL programs, as are six additional genes. From centromere to telomere, the orientation of transcription varies among the first eight genes, then runs centromeric to telomeric for the next five, and is in the opposite sense for the last six. Eighteen of the 19 genes are associated with CpG islands. Two islands are exact copies in the 11.3 kb repeat units, and could thus give rise to double dosage levels of an X-linked gene. Another island is associated with two genes transcribed in opposite directions. From the sequence data, three genes and their exon structure are inferred. One of them, previously associated with HEX2, is shown to be a different gene unrelated to hexokinases; a second gene, previously known by an EST, is plexin, from its 65.5% identity with the Xenopus analog; and a third is a subunit of a vacuolar H-ATPase, and is named VATPS1.
DOI: 10.1093/hmg/5.5.659
PubMed: 8733135
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Long-range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci.</title><author><name sortKey="Chen, E Y" sort="Chen, E Y" uniqKey="Chen E" first="E Y" last="Chen">E Y Chen</name><affiliation wicri:level="2"><nlm:affiliation>Advanced Center for Genetic Technology, Applied Biosystems Division of Perkin Elmer Corp, Foster City, CA 94404, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Center for Genetic Technology, Applied Biosystems Division of Perkin Elmer Corp, Foster City, CA 94404</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zollo, M" sort="Zollo, M" uniqKey="Zollo M" first="M" last="Zollo">M. Zollo</name></author><author><name sortKey="Mazzarella, R" sort="Mazzarella, R" uniqKey="Mazzarella R" first="R" last="Mazzarella">R. Mazzarella</name></author><author><name sortKey="Ciccodicola, A" sort="Ciccodicola, A" uniqKey="Ciccodicola A" first="A" last="Ciccodicola">A. Ciccodicola</name></author><author><name sortKey="Chen, C N" sort="Chen, C N" uniqKey="Chen C" first="C N" last="Chen">C N Chen</name></author><author><name sortKey="Zuo, L" sort="Zuo, L" uniqKey="Zuo L" first="L" last="Zuo">L. Zuo</name></author><author><name sortKey="Heiner, C" sort="Heiner, C" uniqKey="Heiner C" first="C" last="Heiner">C. Heiner</name></author><author><name sortKey="Burough, F" sort="Burough, F" uniqKey="Burough F" first="F" last="Burough">F. Burough</name></author><author><name sortKey="Repetto, M" sort="Repetto, M" uniqKey="Repetto M" first="M" last="Repetto">M. Repetto</name></author><author><name sortKey="Schlessinger, D" sort="Schlessinger, D" uniqKey="Schlessinger D" first="D" last="Schlessinger">D. Schlessinger</name></author><author><name sortKey="D Urso, M" sort="D Urso, M" uniqKey="D Urso M" first="M" last="D'Urso">M. D'Urso</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1996">1996</date><idno type="RBID">pubmed:8733135</idno><idno type="pmid">8733135</idno><idno type="doi">10.1093/hmg/5.5.659</idno><idno type="wicri:Area/PubMed/Corpus">002776</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002776</idno><idno type="wicri:Area/PubMed/Curation">002776</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002776</idno><idno type="wicri:Area/PubMed/Checkpoint">002622</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002622</idno><idno type="wicri:Area/Ncbi/Merge">002A23</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Long-range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci.</title><author><name sortKey="Chen, E Y" sort="Chen, E Y" uniqKey="Chen E" first="E Y" last="Chen">E Y Chen</name><affiliation wicri:level="2"><nlm:affiliation>Advanced Center for Genetic Technology, Applied Biosystems Division of Perkin Elmer Corp, Foster City, CA 94404, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Center for Genetic Technology, Applied Biosystems Division of Perkin Elmer Corp, Foster City, CA 94404</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zollo, M" sort="Zollo, M" uniqKey="Zollo M" first="M" last="Zollo">M. Zollo</name></author><author><name sortKey="Mazzarella, R" sort="Mazzarella, R" uniqKey="Mazzarella R" first="R" last="Mazzarella">R. Mazzarella</name></author><author><name sortKey="Ciccodicola, A" sort="Ciccodicola, A" uniqKey="Ciccodicola A" first="A" last="Ciccodicola">A. Ciccodicola</name></author><author><name sortKey="Chen, C N" sort="Chen, C N" uniqKey="Chen C" first="C N" last="Chen">C N Chen</name></author><author><name sortKey="Zuo, L" sort="Zuo, L" uniqKey="Zuo L" first="L" last="Zuo">L. Zuo</name></author><author><name sortKey="Heiner, C" sort="Heiner, C" uniqKey="Heiner C" first="C" last="Heiner">C. Heiner</name></author><author><name sortKey="Burough, F" sort="Burough, F" uniqKey="Burough F" first="F" last="Burough">F. Burough</name></author><author><name sortKey="Repetto, M" sort="Repetto, M" uniqKey="Repetto M" first="M" last="Repetto">M. Repetto</name></author><author><name sortKey="Schlessinger, D" sort="Schlessinger, D" uniqKey="Schlessinger D" first="D" last="Schlessinger">D. Schlessinger</name></author><author><name sortKey="D Urso, M" sort="D Urso, M" uniqKey="D Urso M" first="M" last="D'Urso">M. D'Urso</name></author></analytic><series><title level="j">Human molecular genetics</title><idno type="ISSN">0964-6906</idno><imprint><date when="1996" type="published">1996</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Color Perception (genetics)</term><term>Cosmids (chemistry)</term><term>CpG Islands</term><term>Cytidine</term><term>DNA</term><term>Dinucleotide Repeats</term><term>Female</term><term>Glucosephosphate Dehydrogenase (genetics)</term><term>Guanosine</term><term>Humans</term><term>Introns</term><term>Molecular Sequence Data</term><term>Software</term><term>X Chromosome</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN</term><term>Chromosome X</term><term>Cosmides ()</term><term>Cytidine</term><term>Données de séquences moléculaires</term><term>Femelle</term><term>Glucose 6-phosphate dehydrogenase (génétique)</term><term>Guanosine</term><term>Humains</term><term>Ilots CpG</term><term>Introns</term><term>Logiciel</term><term>Perception des couleurs (génétique)</term><term>Répétitions de dinucléotides</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Glucosephosphate Dehydrogenase</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Cytidine</term><term>DNA</term><term>Guanosine</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Cosmids</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Color Perception</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glucose 6-phosphate dehydrogenase</term><term>Perception des couleurs</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>CpG Islands</term><term>Dinucleotide Repeats</term><term>Female</term><term>Humans</term><term>Introns</term><term>Molecular Sequence Data</term><term>Software</term><term>X Chromosome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Chromosome X</term><term>Cosmides</term><term>Cytidine</term><term>Données de séquences moléculaires</term><term>Femelle</term><term>Guanosine</term><term>Humains</term><term>Ilots CpG</term><term>Introns</term><term>Logiciel</term><term>Répétitions de dinucléotides</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA comprising 219 447 bp was sequenced in nine cosmids and verified at > 99.9% precision. Of the standard repetitive elements, 187 Alus make up 20.6% of the sequence, but there were only 27 MERs (2.9%) and 17 L1 fragments (1.6%). This may be characteristic of such high GC (57%) regions. The sequence also includes an 11.3 kb tract duplicated with 99.2% identity at a distance of 38 kb. The region is 80-90% transcribed and 12.5% translated. Thirteen known genes and their exon-intron borders are all accurately predicted at least in part by GRAIL programs, as are six additional genes. From centromere to telomere, the orientation of transcription varies among the first eight genes, then runs centromeric to telomeric for the next five, and is in the opposite sense for the last six. Eighteen of the 19 genes are associated with CpG islands. Two islands are exact copies in the 11.3 kb repeat units, and could thus give rise to double dosage levels of an X-linked gene. Another island is associated with two genes transcribed in opposite directions. From the sequence data, three genes and their exon structure are inferred. One of them, previously associated with HEX2, is shown to be a different gene unrelated to hexokinases; a second gene, previously known by an EST, is plexin, from its 65.5% identity with the Xenopus analog; and a third is a subunit of a vacuolar H-ATPase, and is named VATPS1.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">8733135</PMID><DateCompleted><Year>1997</Year><Month>06</Month><Day>04</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>12</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0964-6906</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><Issue>5</Issue><PubDate><Year>1996</Year><Month>May</Month></PubDate></JournalIssue><Title>Human molecular genetics</Title><ISOAbbreviation>Hum. Mol. Genet.</ISOAbbreviation></Journal><ArticleTitle>Long-range sequence analysis in Xq28: thirteen known and six candidate genes in 219.4 kb of high GC DNA between the RCP/GCP and G6PD loci.</ArticleTitle><Pagination><MedlinePgn>659-68</MedlinePgn></Pagination><Abstract><AbstractText>DNA comprising 219 447 bp was sequenced in nine cosmids and verified at > 99.9% precision. Of the standard repetitive elements, 187 Alus make up 20.6% of the sequence, but there were only 27 MERs (2.9%) and 17 L1 fragments (1.6%). This may be characteristic of such high GC (57%) regions. The sequence also includes an 11.3 kb tract duplicated with 99.2% identity at a distance of 38 kb. The region is 80-90% transcribed and 12.5% translated. Thirteen known genes and their exon-intron borders are all accurately predicted at least in part by GRAIL programs, as are six additional genes. From centromere to telomere, the orientation of transcription varies among the first eight genes, then runs centromeric to telomeric for the next five, and is in the opposite sense for the last six. Eighteen of the 19 genes are associated with CpG islands. Two islands are exact copies in the 11.3 kb repeat units, and could thus give rise to double dosage levels of an X-linked gene. Another island is associated with two genes transcribed in opposite directions. From the sequence data, three genes and their exon structure are inferred. One of them, previously associated with HEX2, is shown to be a different gene unrelated to hexokinases; a second gene, previously known by an EST, is plexin, from its 65.5% identity with the Xenopus analog; and a third is a subunit of a vacuolar H-ATPase, and is named VATPS1.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>E Y</ForeName><Initials>EY</Initials><AffiliationInfo><Affiliation>Advanced Center for Genetic Technology, Applied Biosystems Division of Perkin Elmer Corp, Foster City, CA 94404, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zollo</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Mazzarella</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Ciccodicola</LastName><ForeName>A</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>C N</ForeName><Initials>CN</Initials></Author><Author ValidYN="Y"><LastName>Zuo</LastName><ForeName>L</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Heiner</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Burough</LastName><ForeName>F</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Repetto</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Schlessinger</LastName><ForeName>D</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>D'Urso</LastName><ForeName>M</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>D16469</AccessionNumber><AccessionNumber>D45021</AccessionNumber><AccessionNumber>J03589</AccessionNumber><AccessionNumber>L40823</AccessionNumber><AccessionNumber>L44140</AccessionNumber><AccessionNumber>M73791</AccessionNumber><AccessionNumber>U10039</AccessionNumber><AccessionNumber>X12458</AccessionNumber><AccessionNumber>X53416</AccessionNumber><AccessionNumber>X55448</AccessionNumber><AccessionNumber>X74605</AccessionNumber><AccessionNumber>X74606</AccessionNumber><AccessionNumber>X74607</AccessionNumber><AccessionNumber>X74608</AccessionNumber><AccessionNumber>X74609</AccessionNumber><AccessionNumber>X74610</AccessionNumber><AccessionNumber>X82434</AccessionNumber><AccessionNumber>X87193</AccessionNumber><AccessionNumber>X87194</AccessionNumber><AccessionNumber>X87196</AccessionNumber><AccessionNumber>X87197</AccessionNumber><AccessionNumber>X87198</AccessionNumber><AccessionNumber>X87199</AccessionNumber><AccessionNumber>Z46376</AccessionNumber></AccessionNumberList></DataBank></DataBankList><GrantList CompleteYN="Y"><Grant><GrantID>417</GrantID><Agency>Telethon</Agency><Country>Italy</Country></Grant><Grant><GrantID>HG00201</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Hum Mol Genet</MedlineTA><NlmUniqueID>9208958</NlmUniqueID><ISSNLinking>0964-6906</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>12133JR80S</RegistryNumber><NameOfSubstance UI="D006151">Guanosine</NameOfSubstance></Chemical><Chemical><RegistryNumber>5CSZ8459RP</RegistryNumber><NameOfSubstance UI="D003562">Cytidine</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.1.1.49</RegistryNumber><NameOfSubstance UI="D005954">Glucosephosphate Dehydrogenase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003118" MajorTopicYN="N">Color Perception</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003360" MajorTopicYN="N">Cosmids</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018899" MajorTopicYN="N">CpG Islands</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003562" MajorTopicYN="Y">Cytidine</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018900" MajorTopicYN="N">Dinucleotide Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005954" MajorTopicYN="N">Glucosephosphate Dehydrogenase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006151" MajorTopicYN="Y">Guanosine</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007438" MajorTopicYN="N">Introns</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="N">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014960" MajorTopicYN="Y">X Chromosome</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1996</Year><Month>5</Month><Day>1</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1996</Year><Month>5</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1996</Year><Month>5</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">8733135</ArticleId><ArticleId IdType="pii">5w0361</ArticleId><ArticleId IdType="doi">10.1093/hmg/5.5.659</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li></region></list><tree><noCountry><name sortKey="Burough, F" sort="Burough, F" uniqKey="Burough F" first="F" last="Burough">F. Burough</name><name sortKey="Chen, C N" sort="Chen, C N" uniqKey="Chen C" first="C N" last="Chen">C N Chen</name><name sortKey="Ciccodicola, A" sort="Ciccodicola, A" uniqKey="Ciccodicola A" first="A" last="Ciccodicola">A. Ciccodicola</name><name sortKey="D Urso, M" sort="D Urso, M" uniqKey="D Urso M" first="M" last="D'Urso">M. D'Urso</name><name sortKey="Heiner, C" sort="Heiner, C" uniqKey="Heiner C" first="C" last="Heiner">C. Heiner</name><name sortKey="Mazzarella, R" sort="Mazzarella, R" uniqKey="Mazzarella R" first="R" last="Mazzarella">R. Mazzarella</name><name sortKey="Repetto, M" sort="Repetto, M" uniqKey="Repetto M" first="M" last="Repetto">M. Repetto</name><name sortKey="Schlessinger, D" sort="Schlessinger, D" uniqKey="Schlessinger D" first="D" last="Schlessinger">D. Schlessinger</name><name sortKey="Zollo, M" sort="Zollo, M" uniqKey="Zollo M" first="M" last="Zollo">M. Zollo</name><name sortKey="Zuo, L" sort="Zuo, L" uniqKey="Zuo L" first="L" last="Zuo">L. Zuo</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Chen, E Y" sort="Chen, E Y" uniqKey="Chen E" first="E Y" last="Chen">E Y Chen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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