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Zhou J, Ashouian N, Delepine M, Matsuda F, Chevillard C, Riblet R, Schildkraut CL, Birshtein BK. The origin of a developmentally regulated Igh replicon is located near the border of regulatory domains for Igh replication and expression. Proc Natl Acad Sci U S A 2002; 99:13693-8. [PMID: 12370427 PMCID: PMC129745 DOI: 10.1073/pnas.212392399] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2002] [Indexed: 11/18/2022] Open
Abstract
The 3' Ig heavy chain locus (Igh) regulatory region is the most downstream known element of the murine Igh gene cluster. We report here that the nearest non-Igh genes-Crip, Crp2, and Mta1-are located approximately 70 kb further downstream and are beyond the end of the domain of Igh transcriptional regulation. We have localized an origin of replication in MEL cells to a 3-kb segment located between the 3' Igh regulatory region and Crip. Sequences downstream of this origin are replicated by forks that move in both directions. Sequences upstream of this origin (Igh-C, -D, and -J) are replicated in a single direction through a 500-kb segment in which no active bidirectional origins can be detected. We propose that this origin may lie at or near the end of the Igh regulation domain.
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Affiliation(s)
- Jie Zhou
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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2
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de la Brousse FC, Birkenmeier EH, King DS, Rowe LB, McKnight SL. Molecular and genetic characterization of GABP beta. Genes Dev 1994; 8:1853-65. [PMID: 7958862 DOI: 10.1101/gad.8.15.1853] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This report outlines three observations relating to GABP beta, a polypeptide constituent of the heterotetrameric transcription factor GABP. Evidence is presented showing that the mouse genome encodes two highly related GABP beta polypeptides, designated GABP beta 1-1 and GABP beta 2-1. Genomic and cDNA copies of the newly defined Gabpb2 gene were cloned and characterized, providing the conceptually translated amino acid sequence of GABP beta 2-1. The genes encoding these two proteins, as well as GABP alpha, were mapped to three unlinked chromosomal loci. Although physically unlinked, the patterns of expression of the three genes were strikingly concordant. Finally, the molecular basis of GABP beta dimerization was resolved. Carboxy-terminal regions of the two GABP beta polypeptides, which mediate dimerization, bear highly related primary amino acid sequences. Both sequences are free of alpha-helix destabilizing residues and, when displayed on idealized alpha-helical projections, reveal marked amphipathy. Two observations indicate that these regions adopt an alpha-helical conformation and intertwine as coiled-coils. First, the dimer-forming region of GABP beta 2-1 can functionally replace the leucine zipper of a bZIP transcription factor. Second, a synthetic peptide corresponding to this region shows distinctive helical properties when examined by circular dichroism spectroscopy. Finally, evidence is presented showing that GABP beta 1-1 and GABP beta 2-1 can heterodimerize through this carboxy-terminal domain, but neither protein can heterodimerize via the dimer-forming region of the bZIP protein C/EBP beta.
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3
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de Meeus A, Alonso S, Demaille J, Bouvagnet P. A detailed linkage map of subtelomeric murine Chromosome 12 region including the situs inversus mutation locus IV. Mamm Genome 1992; 3:637-43. [PMID: 1360279 DOI: 10.1007/bf00352481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A mouse model is an invaluable tool to tackle genesis of human congenital diseases that have so far eluded human studies. Homozygote for the i.v. mutation, the murine Si/Col strain presents a left-right lateralization defect of thoracic and abdominal organs and heart defects very similar to human ones. This i.v. mutation has been mapped to the region between the Aat and Igh-C loci, suggesting the presence of an equivalent human gene in the human syntenic 14q3 region. A precise linkage map of the region is, therefore, of great interest since it will contribute to the genetic approach of the i.v. gene. Analysis of 242 back-cross progeny from Mus musculus (MAI) or spretus strains of mice and SI/Col mice has allowed mapping of the i.v. gene to a linkage group of eight markers. It includes four genes: Aat (alpha 1-antitrypsin), Ckb (creatine kinase, brain form), Crip (cysteine-rich intestinal protein), and Igh-C (immunoglobulin heavy chain constant region complex); three murine microsatellites: D12Mit6, D12Mit7, and D12Mit8; and one new marker, D12Mtp1, defined by a minisatellite human probe, pYNZ2. After analysis of the data by the LINKAGE program, the following multilocus map has been constructed: centromere-D12Mit6-6.9 cM-D12Mit7-1.7 cM-D12Mtp1-2.6 cM-Aat-5.0 cM-(Ckb, Igh-C)-0.4 cM-D12Mit8-0.4 cM-Crip-11.2 cM-i.v.-telomere. This map differs from the previous map in placing i.v. locus telomeric to Igh-C. D12Mit6 and D12Mit7 are now precisely mapped centromeric to the locus Aat. In addition, a new locus D12Mtp1 is located between Aat and D12Mit7.
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Affiliation(s)
- A de Meeus
- Centre de Recherche de Biochimie Macromoléculaire, CNRS UPR-9008 et INSERM U249, Montpellier, France
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4
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McGrath J, Horwich AL, Brueckner M. Duplication/deficiency mapping of situs inversus viscerum (iv), a gene that determines left-right asymmetry in the mouse. Genomics 1992; 14:643-8. [PMID: 1427890 DOI: 10.1016/s0888-7543(05)80163-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A recessive mutation in the mouse, situs inversus viscerum (iv), results in randomization of organ position along the left-right body axis: approximately 50% of the progeny of homozygous matings exhibit situs solitus and 50% exhibit situs inversus. Recent studies have established genetic linkage between iv and the immunoglobulin heavy chain gene complex (Igh-C), located on distal mouse chromosome 12. In the present study, we have refined the genetic map location of iv relative to the breakpoint of a reciprocal translocation, T(5;12)31H, involving the telomeric region of chromosome 12 distal to Igh-C and the proximal region of chromosome 5. The translocation results in a large 12(5) derivative chromosome and a small 5(12) derivative chromosome. Because mice with either monosomy or tertiary trisomy for the 5(12) chromosomal region are viable, duplication/deficiency mapping is possible. Deficiency mapping was performed by mating iv/iv homozygotes and T31H heterozygotes. Two animals monosomic for distal mouse chromosome 12 were produced. One of the animals with cytogenetically confirmed monosomy for distal chromosome 12 exhibited situs inversus, indicating that the iv mutation is located at or distal to the T31H breakpoint. For duplication analysis, matings were initially carried out between iv/iv homozygotes and unbalanced T31H animals trisomic for distal chromosome 12. Cytogenetically verified tertiary trisomic progeny were identified and backcrossed with iv/iv homozygotes. The resulting trisomic progeny, 50% of which are expected to carry the iv mutation on both cytogenetically normal copies of chromosome 12, were scored for phenotype.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510
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5
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Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky MR, Roderick TH. Comparative map for mice and humans. Mamm Genome 1992; 3:480-536. [PMID: 1392257 DOI: 10.1007/bf00778825] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J H Nadeau
- Jackson Laboratory, Bar Harbor, Maine 04609
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6
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Richards-Smith BA, Elliott RW. Mapping of the mouse ornithine decarboxylase-related sequence family. Mamm Genome 1992; 2:215-32. [PMID: 1347476 DOI: 10.1007/bf00355431] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A family of DNA sequences homologous to the mRNA encoding ornithine decarboxylase (ODC) and comprising approximately 12 members in the mouse genome has been analyzed genetically. The inheritance of variant DNA restriction fragments detected by ODC cDNA probes on Southern blots of DNA from inbred strain mice was determined in six sets of recombinant inbred (RI) mouse strains. The distributions of these variations among the RI strains were then compared with the RI strain distribution patterns (SDPs) of previously mapped loci. This allowed the identification of nine independent ODC-related loci, of which eight could be localized to specific regions of the mouse genome: Odc-rs1 near Lamb2 on Chromosome (Chr) 1; Odc-rs2 near Psp on Chr 2; Odc-rs5, a complex locus comprising at least 5-7 copies of the ODC sequence, associated with Igk on Chr 6; Odc-rs6 between Abpa and Tam-1 on proximal Chr 7; Odc-rs7 near Hbb on distal Chr 7; Odc-rs12 near Agt and Emv-2 on distal Chr 8; Odc-rs8 associated with the Igh complex on Chr 12; and Odc-rs9 near Otf-3f on Chr 14. The ODC-related sequence family thus comprises a set of genomically dispersed "marker" loci, and alleles for several of these loci can be analyzed simultaneously in DNA from mice or cell lines. DNA from mice of 70 inbred strains has been characterized for alleles at all nine Odc-rs loci.
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Affiliation(s)
- B A Richards-Smith
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
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7
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van Deursen J, Schepens J, Peters W, Meijer D, Grosveld G, Hendriks W, Wieringa B. Genetic variability of the murine creatine kinase B gene locus and related pseudogenes in different inbred strains of mice. Genomics 1992; 12:340-9. [PMID: 1740343 DOI: 10.1016/0888-7543(92)90383-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The role of genetic variation in isoenzyme gene families is often poorly appreciated. We report here on the determination of DNA sequences and typing of genetic variability in four creatine kinase B (CKB) gene loci in different inbred strains of mice. The unique functional murine CKB gene was found to be nearly identical to the previously characterised rat and human sequences in both size and exon-intron structure. In this gene, approximately 0.5% allelic nucleotide positions as well as the lengths of simple A-rich and [TG]n repetitive elements located at the 5' and 3' sides of the transcribed segment, differed between inbred strains of mice. Preliminary experiments suggest that this sequence divergence is of importance for design of gene targeting strategies involving homologous DNA recombination. The three additional CKB-like gene loci in mice all had the characteristics of processed pseudogenes. By Southern blot analysis we could demonstrate that both the type and number of pseudogenes differed between inbred strains. Analysis of the CKB gene sequences enabled us to speculate about the evolutionary history of this highly polymorphic subfamily of genes.
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Affiliation(s)
- J van Deursen
- Department of Cell Biology and Histology, University of Nijmegen, The Netherlands
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8
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Affiliation(s)
- R H Reeves
- Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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9
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Richards-Smith BA, Brodeur PH, Elliott RW. Deletion mapping of the mouse ornithine decarboxylase-related locus Odc-rs8 within Igh-V. Mamm Genome 1992; 3:568-74. [PMID: 1421765 DOI: 10.1007/bf00350623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Odc-rs8 locus belongs to a family of mouse DNA sequences related to the gene encoding ornithine decarboxylase (ODC). Odc-rs8 was mapped by recombinant inbred (RI) strain analysis to the region of Chromosome (Chr) 12 occupied by the variable region genes of the immunoglobulin heavy chain (Igh) complex. In the present study, alleles at Odc-rs8 were shown to cosegregate with those for Igh variable region (Igh-V or VH) genes among 37 inbred mouse strains that had been characterized previously for their haplotypes at Igh. For a more precise definition of the location of Odc-rs8 relative to Igh-V, DNAs from 17 Abelson murine leukemia virus (A-MuLV)-transformed pre-B cell lines cultured from mice heterozygous at Igh and Odc-rs8 were analyzed for the presence of DNA restriction fragments (RFs) derived from each parental Odc-rs8 allele. These cell lines, each of which has rearranged one or both Igh genes, previously were employed in mapping members of nine VH gene families by deletion analysis (Brodeur et al. 1988). Comparing the deletion profiles of the cell lines for Odc-rs8 with those for the VH gene families has located Odc-rs8b within the VHJ558/VH3609 gene cluster and Odc-rs8c either within or upstream of the 5'-most 9% of VHJ558, identifying Odc-rs8 as a potentially useful marker for the 5' end of the Igh complex.
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Affiliation(s)
- B A Richards-Smith
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
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10
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Ratty AK, Matsuda Y, Elliott RW, Chapman VM, Gross KW. Genetic mapping of two DNA markers, D16Ros1 and D16Ros2, flanking the mutation site in the chakragati mouse, a transgenic insertional mutant. Mamm Genome 1992; 3:5-10. [PMID: 1581634 DOI: 10.1007/bf00355834] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present here the genetic mapping of two novel loci, D16Ros1 and D16Ros2, to mouse Chromosome (Chr) 16. The probes for these loci were genomic fragments isolated from the chakragati mouse, a behavioral mutant resulting from insertional mutagenesis during the course of making transgenic mice. D16Ros1 and D16Ros2 were first mapped by recombinant inbred (RI) strain analysis and subsequently by the analysis of 145 progeny of two interspecific backcrosses between Mus domesticus and Mus spretus. These progeny had been typed for the centromere and this allowed mapping of D16Ros1 and D16Ros2 relative to the centromere. The other markers included in this study were Prm-1, Gap43 and Sod-1. The genetic map generated spanned 47.5 cM from the centromere to Sod-1, the most distal marker mapped here. The linkage data presented here should prove useful in mapping other loci relative to the centromere of Chr 16.
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Affiliation(s)
- A K Ratty
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263
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11
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Affiliation(s)
- P D'Eustachio
- Department of Biochemistry, Kaplan Cancer Center, New York University Medical Center, New York 10016
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12
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Affiliation(s)
- A M Buchberg
- Jefferson Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania 19107-5541
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13
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Abbott CM, Blank R, Eppig JT, Friedman JM, Huppi KE, Jackson I, Mock BA, Stoye J, Wiseman R. Mouse chromosome 4. Mamm Genome 1992; 3 Spec No:S55-64. [PMID: 1498443 DOI: 10.1007/bf00648422] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- C M Abbott
- Department of Genetics and Biochemistry, UCL, London, UK
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14
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Silver LM, Artzt K, Barlow D, Fischer-Lindahl K, Lyon MF, Klein J, Snyder L. Mouse chromosome 17. Mamm Genome 1992; 3 Spec No:S241-60. [PMID: 1498437 DOI: 10.1007/bf00648435] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- L M Silver
- Department of Molecular Biology, Princeton University, New Jersey 08544-1014
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15
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Moore SK, Appella E, Villar CJ, Kozak CA. Mapping of the mouse 86-kDa heat-shock protein expressed gene (Hsp86-1) on chromosome 12 and related genes on chromosomes 3, 4, 9, and 11. Genomics 1991; 10:1019-29. [PMID: 1916807 DOI: 10.1016/0888-7543(91)90193-i] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The HSP86 gene family in BALB/c, AKR/J, C58/J, and NFS/N inbred mice comprises an intron-containing expressed gene and, depending on the strain, two to four other HSP86-related members that are apparently processed pseudogenes. The expressed gene locus, Hsp86-1, was identified by its sequence identity with the mouse HSP86 cDNA coding region together with the presence of an intron at the same position as in the homologous human gene. Hsp86-1 was mapped 11.6 cM from the immunoglobulin heavy chain gene IgH on Chromosome 12 using an intersubspecies backcross. Two of the other loci that were common to all inbred strains tested, designated Hsp86-ps1 and Hsp86-ps2, were mapped to positions on Chromosomes 11 and 3, respectively. An HSP86-related locus specific to NFS/N and C58/J mice, designated Hsp86-ps3, was mapped on Chromosome 9. Also, an HSP86-related locus that was unique to NFS/N mice, designated Hsp86-ps4, was mapped to Chromosome 4.
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Affiliation(s)
- S K Moore
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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16
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Drivas G, Massey R, Chang HY, Rush MG, D'Eustachio P. Ras-like genes and gene families in the mouse. Mamm Genome 1991; 1:112-7. [PMID: 1686838 DOI: 10.1007/bf02443787] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Four human RAS-like cDNAs and a mouse genomic DNA fragment were used to define novel mouse Ras-like genes and gene families. Inheritance of DNA restriction fragment length variants associated with these genes in recombinant inbred and backcross mice allowed definition of 12 genetic loci, nine of which were mapped, to chromosomes (Chr) 2, 4, 7, 8, 9, and 17. Two possible clusters of Ras-like and/or G protein genes were identified, on Chrs 9 and 17.
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Affiliation(s)
- G Drivas
- Department of Biochemistry, New York University Medical Center, New York 10016
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17
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Blank R, Eppig J, Fiedorek FT, Frankel WN, Friedman JM, Huppi K, Jackson I, Mock B. Mouse chromosome 4. Mamm Genome 1991; 1 Spec No:S51-78. [PMID: 1799812 DOI: 10.1007/bf00656486] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R Blank
- Howard Hughes Medical Institute, Rockefeller University, New York, NY 10021
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18
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Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky M, Roderick TH. Comparative map for mice and humans. Mamm Genome 1991; 1 Spec No:S461-515. [PMID: 1799811 DOI: 10.1007/bf00656504] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- J H Nadeau
- Jackson Laboratory, Bar Harbor, ME 04609
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19
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Artzt K, Barlow D, Dove WF, Fischer-Lindahl K, Klein J, Lyon MF, Silver LM. Mouse chromosome 17. Mamm Genome 1991; 1 Spec No:S280-300. [PMID: 1799805 DOI: 10.1007/bf00656498] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- K Artzt
- Department of Molecular Biology, Princeton University, NJ 08544-1014
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20
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Affiliation(s)
- A M Buchberg
- Jefferson Cancer Institute, Department of Microbiology and Immunology, Philadelphia, PA 19107-5541
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21
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Affiliation(s)
- R H Reeves
- Developmental Genetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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22
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Affiliation(s)
- J H Nadeau
- Jackson Laboratory, Bar Harbor, ME 04609
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23
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Affiliation(s)
- P D'Eustachio
- Department of Biochemistry, New York University Medical Center, NY 10016
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