GenBank-Updates@genbank.bio.net (03/16/91)
LOCUS OFA81MAC1 92 bp ds-DNA INV 16-MAR-1991 DEFINITION O.fallax micronuclear (81-MAC family, version A) DNA, region SRRHGKH-a (partial). ACCESSION M15836 M13033 KEYWORDS 81-MAC chromosome family; alternative DNA processing; homolog of mitochondrial solute carriers. SEGMENT 1 of 3 SOURCE O.fallax (subkaryonide 3.5) micronuclear DNA, region SRRHGKH-a, clone L47-mic21. ORGANISM Oxytricha fallax Eukaryota; Animalia; Metazoa; Ciliophora; Polyhymenophora; Spirotricha; Hypotrichida; Sporadotrichina; Oxytrichidae. REFERENCE 1 (bases 1 to 92) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ. of Utah, Salt Lake City, Utah 84132 STANDARD full staff_entry REFERENCE 2 (bases 1 to 92) AUTHORS Herrick,G., Hunter,D., Williams,K. and Kotter,K. TITLE Alternative processing during development of a macronuclear chromosomal family in Oxytricha fallax JOURNAL Genes Dev. 1, 1047-1058 (1987) STANDARD full staff_entry REFERENCE 3 (bases 1 to 92) AUTHORS Herrick,G., Cartinhour,S.W., Williams,K.R. and Kotter,K.P. TITLE Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family JOURNAL J. Protozool. 34, 429-434 (1987) STANDARD full staff_review COMMENT Draft entry and computer-readable sequence for [J. Protozool. 34, 429-434 (1987)] kindly provided by G.Herrick, 12-DEC-1986. This sequence is the first 92 bp of that referred to as SRRHGKH-a in [J. Protozool. 34, 429-434 (1987)]. It also could be referred to as mic-SR-a by the conventions in [J. Protozool. 34, 429-434 (1987)] The 81-MAC chromosome family is created by alternative processing of the micronuclear DNA. The 81-MAC family consists of three sizes of macronuclear chromosomes: 4.9 kb (MACI), 2.9 kb (MACII), and 1.6 kb (MACIII). Alternative processing results from alternative choice of chromosome break/telomere-addition sites. The 1.6 kb region in common between the three chromosomes bears a transcribed open reading frame, the conceptual translation product of which is homologous to solute carrier proteins from plants and metazoans. There are three distinct micronuclear loci (sequence versions),vA, vB, and vC. Alternative processing of each micronuclear version independently gives rise to a I+II+III family of macronuclear chromosomes. The open reading frame is conserved in all three versions. Little is known about the structure of vB micronuclear DNA (no clones), but vA and vC micronuclear DNAs bear micronucleus-limited sequences called internal eliminated sequences (IESs). vA and vC have small IESs in common, but in addition, vC bears two large transposons, TBE1-1 and -2, which also are IESs. IESs are precisely excised, leaving one short flanking direct repeat in macronuclear DNA. Only one copy of the tandem repeat (positions 56-69) is found in vB and vC. FEATURES Location/Qualifiers repeat_region 56..62 /note="direct tandem repeat tgatata copy A" repeat_region 63..69 /note="direct tandem repeat tgatata copy B" BASE COUNT 39 a 6 c 15 g 32 t ORIGIN 1 aaaaagcgag aggtattatt gaatgaataa tcaagagttt atcaaagatt tagaatgata 61 tatgatataa tgctttataa tgtactttat ca //
GenBank-Updates@genbank.bio.net (03/16/91)
LOCUS OFA81MAC3 353 bp ds-DNA INV 16-MAR-1991 DEFINITION O.fallax micronuclear (81-MAC family, version A) DNA, region mic-KH-a. ACCESSION M13042 KEYWORDS 81-MAC chromosome family; alternative DNA processing; homolog of mitochondrial solute carriers. SEGMENT 3 of 3 SOURCE O.fallax (subkaryonide 3.5) micronuclear DNA, region mic-KH-a, clone L47-mic21. ORGANISM Oxytricha fallax Eukaryota; Animalia; Metazoa; Ciliophora; Polyhymenophora; Spirotricha; Hypotrichida; Sporadotrichina; Oxytrichidae. REFERENCE 1 (bases 1 to 353) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ. of Utah, Salt Lake City, Utah 84132 STANDARD full staff_entry REFERENCE 2 (bases 1 to 353) AUTHORS Herrick,G., Cartinhour,S.W., Williams,K.R. and Kotter,K.P. TITLE Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family JOURNAL J. Protozool. 34, 429-434 (1987) STANDARD full staff_review COMMENT Draft entry and computer-readable sequence for [J. Protozool. 34, 429-434 (1987)] kindly provided by G.Herrick, 12-DEC-1986. The 81-MAC chromosome family is created by alternative processing of the micronuclear DNA. The 81-MAC family consists of three sizes of macronuclear chromosomes: 4.9 kb (MACI), 2.9 kb (MACII), and 1.6 kb (MACIII). Alternative processing results from alternative choice of chromosome break/telomere-addition sites. The 1.6 kb region in common between the three chromosomes bears a transcribed open reading frame, the conceptual translation product of which is homologous to solute carrier proteins from plants and metazoans. There are three distinct micronuclear loci (sequence versions),vA, vB, and vC. Alternative processing of each micronuclear version independently gives rise to a I+II+III family of macronuclear chromosomes. The open reading frame is conserved in all three versions. Little is known about the structure of vB micronuclear DNA (no clones), but vA and vC micronuclear DNAs bear micronucleus-limited sequences called internal eliminated sequences (IESs). vA and vC have small IESs in common, but in addition, vC bears two large transposons, TBE1-1 and -2, which also are IESs. IESs are precisely excised, leaving one short flanking direct repeat in macronuclear DNA. When the IES is excised the 5' imperfectly duplicated sequence 'atta' remains in the macronuclear DNA. The sequence of the homologous macronuclear DNA can be found in a separate entry: M15835. FEATURES Location/Qualifiers repeat_region 138..141 /note="5' imperfectly duplicated sequence" iDNA 142..210 /note="IES" repeat_region 207..210 /note="3' imperfectly duplicated sequence" BASE COUNT 125 a 56 c 27 g 145 t ORIGIN 5 bp upstream of KpnI site; about 0.9 kb after segment 2. 1 ggtaccttct tctccagtac tcaactaaaa ataaatttta taaatcgatg attcgatatt 61 ttattgataa atttaccttc catttaagta ggcatctttc ttgattgctt attttaaaat 121 aattttaata actttatatt attgtaatca cattaagatt tatagtataa tttcaaagaa 181 tcattttaat ttccttatat tcaagcaata attatgttta ttacaaatta tttcaattaa 241 gttcattcaa aaataaatct ctgccacctt taaaatctat atttaggtta actcaagtct 301 tcaaacaaca cttctctgtg aagaatcact tcttaaaaca ccagttttct act //
GenBank-Updates@genbank.bio.net (03/16/91)
LOCUS OFA81MCA1 846 bp ds-DNA INV 16-MAR-1991 DEFINITION O.fallax micronuclear (81-MAC family, version C) DNA, region mic-BSRRHG-c. ACCESSION M13035 M13029 M13036 KEYWORDS 81-MAC chromosome family; TBE1 telomere bearing element; alternative DNA processing; homolog of mitochondrial solute carriers; transposon. SEGMENT 1 of 3 SOURCE O.fallax (subkaryonide 3.5) micronuclear DNA, regions SRRHG-c, mic-RR-c and mic-Rg-c, clones L47-mic[10,20]. ORGANISM Oxytricha fallax Eukaryota; Animalia; Metazoa; Ciliophora; Polyhymenophora; Spirotricha; Hypotrichida; Sporadotrichina; Oxytrichidae. REFERENCE 1 (sites) AUTHORS Herrick,G., Cartinhour,S., Dawson,D., Ang,D., Sheets,R., Lee,A. and Williams,K. TITLE Mobile elements bounded by C-4-A-4 telomeric repeats in Oxytricha fallax JOURNAL Cell 43, 759-768 (1985) STANDARD full staff_review REFERENCE 2 (bases 1 to 846) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ. of Utah, Salt Lake City, Utah 84132 STANDARD full staff_entry REFERENCE 3 (bases 1 to 846) AUTHORS Herrick,G., Cartinhour,S.W., Williams,K.R. and Kotter,K.P. TITLE Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family JOURNAL J. Protozool. 34, 429-434 (1987) STANDARD full staff_review COMMENT [Cell 43, 759-768 (1985)] sites; telomere-bearing element description. Draft entry and computer-readable sequence for [J. Protozool. 34, 429-434 (1987)] kindly provided by G.Herrick, 12-DEC-1986. This sequence would be named 'mic-SRRg-c' by the conventions in [J. Protozool. 34, 429-434 (1987)]. Bases 1-494 come from region SRRHG-c, 372-617 from mic-RR-c, and 612-846 from mic-Rg-c as referred to in [J. Protozool. 34, 429-434 (1987)]. The 81-MAC chromosome family is created by alternative processing of the micronuclear DNA. The 81-MAC family consists of three sizes of macronuclear chromosomes: 4.9 kb (MACI), 2.9 kb (MACII), and 1.6 kb (MACIII). Alternative processing results from alternative choice of chromosome break/telomere-addition sites. The 1.6 kb region in common between the three chromosomes bears a transcribed open reading frame, the conceptual translation product of which is homologous to solute carrier proteins from plants and metazoans. There are three distinct micronuclear loci (sequence versions),vA, vB, and vC. Alternative processing of each micronuclear version independently gives rise to a I+II+III family of macronuclear chromosomes. The open reading frame is conserved in all three versions. Little is known about the structure of vB micronuclear DNA (no clones), but vA and vC micronuclear DNAs bear micronucleus-limited sequences called internal eliminated sequences (IESs). vA and vC have small IESs in common, but in addition, vC bears two large transposons, TBE1-1 and -2, which also are IESs. IESs are precisely excised, leaving one short flanking direct repeat in macronuclear DNA. When TBE1-1 is excised one flanking 'aat' probably remains in macronuclear DNA, as judged from oligomer hybridization experiments. FEATURES Location/Qualifiers repeat_region 490..494 /note="5' IES duplicated sequence" iDNA 495..566 /note="IES" repeat_region 562..566 /note="3' IES duplicated sequence" repeat_region 715..717 /note="5' TBE1-1 duplicated insertion target sequence" repeat_region 718..734 /note="telomere sequence of TBE1-1" repeat_region 718..795 /note="5' TBE1-1 inverted terminal repeat" transposon 718..>846 /note="TBE1-1 insertion element" BASE COUNT 293 a 100 c 155 g 298 t ORIGIN 86 bp upstream of SphI site. 1 agagacggag gaatgattga atgtgcaaaa tatatcttta agaatgaaca tgggtttatg 61 ggattttgga gagggttctc agcatgcagt gcaagagcag tatttgctaa ttctttcatg 121 tttgtggctt atgaatatgc ttagaaaaaa gcgagaggta ttattgaatg aatgatcgtg 181 gatttatcaa agtttttgaa tgatataatg ctttataatg tactttatca aagtaactta 241 agactgtgat attaatatga actaagatta tatataaatt taatattttt aaataggttt 301 aaataacaaa taaatctcta ctttaacaca aagcatgtga taatacttta tgttagagac 361 aatttatttc tgaattctca gataattgcg agattttctt ttcctgaagg atgagcagct 421 cccatacctc cagtagctgt agtataagta gcaactaatt ttttattgaa ggcatctgtg 481 tatggatcat gaatcataac gatttataaa attttggaaa aaatcataat ctaaaatttc 541 tgcttcatta taataagtta ttgaatatcg taatcgatac cactttgata gtggaatctc 601 tgtggttgcc agaattcttg atcatagtag ttttcgttat agtagtctac caagaattga 661 gaaagataac aaatcaagaa caatctgagg aagtaggctt cacctcctgc atagaatcaa 721 aaccccaaaa ccccttaagt agatggttta gtgtattgat ttgtagagaa tttgttaggg 781 gttggggtta ttaatagttt ttaatgtgga aatttatagt aaatgtattt aatttaatca 841 ctcaaa //
GenBank-Updates@genbank.bio.net (03/16/91)
LOCUS OFA81MCA2 1232 bp ds-DNA INV 16-MAR-1991 DEFINITION O.fallax micronuclear (81-MAC family, version C) DNA, regions SRRHG-c (partial), mic-gH-c and GKH-c (partial). ACCESSION M13037 M13029 M13038 N00056 KEYWORDS 81-MAC chromosome family; TBE1 telomere bearing element; alternative DNA processing; homolog of mitochondrial solute carriers; transposon. SEGMENT 2 of 3 SOURCE O.fallax (subkaryonide 3.5) micronuclear DNA, regions mic-gH-c and SRRHG-c, clones L47-mic[2,8,10,20,22,26]. ORGANISM Oxytricha fallax Eukaryota; Animalia; Metazoa; Ciliophora; Polyhymenophora; Spirotricha; Hypotrichida; Sporadotrichina; Oxytrichidae. REFERENCE 1 (sites) AUTHORS Herrick,G., Cartinhour,S., Dawson,D., Ang,D., Sheets,R., Lee,A. and Williams,K. TITLE Mobile elements bounded by C-4-A-4 telomeric repeats in Oxytricha fallax JOURNAL Cell 43, 759-768 (1985) STANDARD full staff_review REFERENCE 2 (bases 1 to 1232) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ. of Utah, Salt Lake City, Utah 84132 STANDARD full staff_entry REFERENCE 3 (bases 1 to 827) AUTHORS Herrick,G., Cartinhour,S.W., Williams,K.R. and Kotter,K.P. TITLE Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family JOURNAL J. Protozool. 34, 429-434 (1987) STANDARD full staff_review REFERENCE 4 (bases 828 to 1232) AUTHORS Hunter,D.J., Williams,K., Cartinhour,S. and Herrick,G. TITLE Precise excision of telomere-bearing transposons during Oxytricha fallax macronuclear development JOURNAL Genes Dev. 3, 2101-2112 (1989) STANDARD full staff_entry COMMENT [Cell 43, 759-768 (1985)] sites; telomere-bearing element description. Draft entry and computer-readable sequence for [J. Protozool. 34, 429-434 (1987)] kindly provided by G.Herrick, 12-DEC-1986. Bases 1-398 are from region mic-gH-c and 118-827 from SRRHG-c as referred to in [J. Protozool. 34, 429-434 (1987)]. This sequence would be named 'mic-gHGh-c' by the convention in [J. Protozool. 34, 429-434 (1987)]. The 81-MAC chromosome family is created by alternative processing of the micronuclear DNA. The 81-MAC family consists of three sizes of macronuclear chromosomes: 4.9 kb (MACI), 2.9 kb (MACII), and 1.6 kb (MACIII). Alternative processing results from alternative choice of chromosome break/telomere-addition sites. The 1.6 kb region in common between the three chromosomes bears a transcribed open reading frame, the conceptual translation product of which is homologous to solute carrier proteins from plants and metazoans. There are three distinct micronuclear loci (sequence versions),vA, vB, and vC. Alternative processing of each micronuclear version independently gives rise to a I+II+III family of macronuclear chromosomes. The open reading frame is conserved in all three versions. Little is known about the structure of vB micronuclear DNA (no clones), but vA and vC micronuclear DNAs bear micronucleus-limited sequences called internal eliminated sequences (IESs). vA and vC have small IESs in common, but in addition, vC bears two large transposons, TBE1-1 and -2, which also are IESs. IESs are precisely excised, leaving one short flanking direct repeat in macronuclear DNA. When TBE1-1 is excised one flanking 'aat' probably remains in macronuclear DNA, as judged from oligomer hybridization experiments. When TBE1-2 is excised one flanking 'aat' remains in macronuclear DNA; the sequence of the resulting macronuclear DNA can be found in a separate entry, accession number M25391. FEATURES Location/Qualifiers transposon <1..114 /note="TBE1-1 insertion element" repeat_region 38..114 /note="3' TBE1-1 inverted terminal repeat" repeat_region 98..114 /note="telomere sequence of TBE1-1" repeat_region 115..117 /note="3' TBE1-1 duplicated insertion target sequence" repeat_region 1048..1050 /note="5' TBE1-2 duplicated insertion target sequence" repeat_region 1051..1067 /note="telomere sequence of TBE1-2" repeat_region 1051..1128 /note="5' TBE1-2 inverted terminal repeat" transposon 1051..>1232 /note="TBE1-2 insertion element" BASE COUNT 379 a 232 c 224 g 394 t 3 others ORIGIN About 3.2 kb after segment 1. 1 agaccccgga tagcttgtaa tttttgtctc gcatttaatt aataacccaa cccctaacaa 61 attccctaca aatcaataca ctaaaccatc tacttaaggg gttttggggt tttgaatgat 121 ccaaagttag acatccactt tgagttacac tcgtacttta tgatcttgtt gaagcaatca 181 atcatgccgt tatatggcat ttgaccgttt ggtagtggtc tcatggtgtg tagtcttgtt 241 ctgatcatat cgaaaggcat acttacagca gttcctatag caacagctac ggcagtaccc 301 cacaatctat taatccaatg aggaccaaag aagaagtagg agttttcctt gcaccaatcg 361 tagatgtttg tcattgatga acaaatagct gcaagcttaa aaccgttggc accagcacct 421 ctgaagagag caccttcttc agcaactttg gcaagtcctt aaattgtatt tgagtaattt 481 cttctggcag cttgtggata aagctcatca acttgcattc tattgtagac gatatcgatt 541 ggatttgtca ctacaccagc aataaatcct ccgagtactc ctgctgctac caagaagtct 601 ggacgagcaa ctcttctggg atctttattt accttatcgt agaaataacc gaaggctgtt 661 actctggcag tagtgtaaca aacagttctg aagaagaatg tgtcgaaact ataccaatat 721 aaattagcta aatttattgc aattcctcaa ttataatgtt gagagagaac tttatataag 781 ccaaattttg tttatacact tacgcagaat agaatttttt gagtccacct cctgctgcat 841 aaatctcttc cataatttag aatggatacc aacccttttg ataaccaagg cctgagaagg 901 tcttgccctc ttacagcatt tgagatctga ttctaaccat atcgagtggt taagtctata 961 ttacatttag aatatgatta atcattgcta ataagataga aaatgtgcta tagaatacta 1021 acttacagca gcatgagtta tgagagcaat caaaacccca aaacccctta agtagatggt 1081 ttagtgtatt gatttgtagg gaatttgtta ggggttgggg ttattaatag gttttaatgt 1141 gaaatttaaa gtatatmtat ttaactttaa tcactcaaaa tmtacttttg gatcgtgtgg 1201 gagnggtctg aaggtttatc ttacttaacc ac //
GenBank-Updates@genbank.bio.net (03/16/91)
LOCUS OFA81MCA3 591 bp ds-DNA INV 16-MAR-1991 DEFINITION O.fallax micronuclear (81-MAC family, version C) DNA, regions mic-rK-c, GKH-c (partial), and mic-KH-c. ACCESSION M13039 M13030 M13040 KEYWORDS 81-MAC chromosome family; TBE1 telomere bearing element; alternative DNA processing; homolog of mitochondrial solute carriers; transposon. SEGMENT 3 of 3 SOURCE O.fallax (subkaryonide 3.5) micronuclear DNA, regions mic-rK-c, GKH-c and mic-KH-c, clone L47-mic22. ORGANISM Oxytricha fallax Eukaryota; Animalia; Metazoa; Ciliophora; Polyhymenophora; Spirotricha; Hypotrichida; Sporadotrichina; Oxytrichidae. REFERENCE 1 (sites) AUTHORS Herrick,G., Cartinhour,S., Dawson,D., Ang,D., Sheets,R., Lee,A. and Williams,K. TITLE Mobile elements bounded by C-4-A-4 telomeric repeats in Oxytricha fallax JOURNAL Cell 43, 759-768 (1985) STANDARD full staff_review REFERENCE 2 (bases 1 to 591) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ. of Utah, Salt Lake City, Utah 84132 STANDARD full staff_entry REFERENCE 3 (bases 1 to 591) AUTHORS Herrick,G., Hunter,D., Williams,K. and Kotter,K. TITLE Alternative processing during development of a macronuclear chromosomal family in Oxytricha fallax JOURNAL Genes Dev. 1, 1047-1058 (1987) STANDARD full staff_entry REFERENCE 4 (bases 1 to 591) AUTHORS Herrick,G., Cartinhour,S.W., Williams,K.R. and Kotter,K.P. TITLE Multiple sequence versions of the Oxytricha fallax 81-MAC alternate processing family JOURNAL J. Protozool. 34, 429-434 (1987) STANDARD full staff_review COMMENT [Cell 43, 759-768 (1985)] sites; telomere-bearing element description. Draft entry and computer-readable sequence for [J. Protozool. 34, 429-434 (1987)] kindly provided by G.Herrick, 12-DEC-1986. Bases 1-237 are from region mic-rK-c; 194-372 and 443-591 from GKH-c; and 232-591 from mic-KH-c as referred to in [J. Protozool. 34, 429-434 (1987)]. This sequence would be named 'mic-rKH-c' by the conventions in [J. Protozool. 34, 429-434 (1987)]. The 81-MAC chromosome family is created by alternative processing of the micronuclear DNA. The 81-MAC family consists of three sizes of macronuclear chromosomes: 4.9 kb (MACI), 2.9 kb (MACII), and 1.6 kb (MACIII). Alternative processing results from alternative choice of chromosome break/telomere-addition sites. The 1.6 kb region in common between the three chromosomes bears a transcribed open reading frame, the conceptual translation product of which is homologous to solute carrier proteins from plants and metazoans. There are three distinct micronuclear loci (sequence versions),vA, vB, and vC. Alternative processing of each micronuclear version independently gives rise to a I+II+III family of macronuclear chromosomes. The open reading frame is conserved in all three versions. Little is known about the structure of vB micronuclear DNA (no clones), but vA and vC micronuclear DNAs bear micronucleus-limited sequences called internal eliminated sequences (IESs). vA and vC have small IESs in common, but in addition, vC bears two large transposons, TBE1-1 and -2, which also are IESs. IESs are precisely excised, leaving one short flanking direct repeat in macronuclear DNA. When the short IES is excised the 5' imperfectly duplicated sequence 'atta' remains in the macronuclear DNA. Similarly, when TBE1-2 is excised one flanking 'aat' remains in macronuclear DNA. The sequence of the homologous macronuclear DNA can be found in a separate entry, accession number M25391. FEATURES Location/Qualifiers transposon <1..190 /note="TBE1-2 insertion element" repeat_region 114..190 /note="3' TBE1-2 inverted terminal repeat" repeat_region 174..190 /note="telomere sequence of TBE1-2" repeat_region 191..193 /note="3' TBE1-2 duplicated insertion target sequence" repeat_region 369..372 /note="5' IES imperfectly duplicated sequence" iDNA 373..442 /note="IES" repeat_region 439..442 /note="3' IES imperfectly duplicated sequence" BASE COUNT 209 a 106 c 55 g 221 t ORIGIN About 3 kb after segment 2. 1 ggtttgactt agtcactata tatatcacat ccatatcgca gtttaaacac taaatctata 61 tactcttcat cataaataga ccccaatagc ttgtaatttt tgtctcgcat ttaattaata 121 acccaacccc taacaaattc cctacaaatc aatacactaa accatctact taaggggttt 181 tggggttttg aatgacatta gcagcagcaa atctttcata gttcatgcgt tggtaccttc 241 ttctccagta ctcaactaaa acgaaatttt agaaatcaat gattcgatat tttattgata 301 aatttacctt ccatttaagt aggcatcttt cttgattgct tattttaaaa taattataat 361 aactttatat tattgcaata acattaagat ttaatagttt ataatgacga tttcatttta 421 atttcattat attcaagcaa taattatgtt tattacaaat tatttcaatt aagttcatta 481 aaaaacatta atctctctac caatttaaaa atttatatgt aagttaactc aagtcttcaa 541 acaacacttc tctgtgaaga atcacttctt aaaacaccag tcttctacta a //