Path: utzoo!utgpu!watserv1!watmath!uunet!bionet!root From: GenBank-Updates@genbank.bio.net Newsgroups: bionet.molbio.genbank.updates Subject: O.fallax micronuclear (81-MAC family, version C) DNA, regions Message-ID: Date: 16 Mar 91 13:00:26 GMT Sender: root@genbank.bio.net Distribution: bionet Lines: 104 Approved: lear@genbank.bio.net Checksum: 03521 6 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JOURNAL Cell 43, 759-768 (1985) STANDARD full staff_review REFERENCE 2 (bases 1 to 591) AUTHORS Herrick,G. JOURNAL Unpublished (1987) Univ.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 //