A region in T17A5 is also found in four other Arabidopsis genomic clones. Initial observations indicate the presence of A-rich tracts suggesting this repeat element is either a putative LINE element or a solo LTR. LINE elements terminate in a highly A-rich string, a remnant of a poly(A) tail of an mRNA, and are variable in length due to incomplete copying of that mRNA by a reverse transcriptase. Solo LTR elements, first described by Shepherd et al., 1984, are characterized by a 20-30 bp polypyrimidine tract and a region similar to a tRNA and are flanked by short inverted repeats.

Sequences from four BACs and a region upstream of the beta-fructosidase gene (X99111) are aligned. The genomic repeat extends for about 260 bp. The table lists the range in each clone where this repeat lies and on which strand. Potential poly(A) tracts are underlined; a polypyrimidine tract is noted; short inverted repeats are also noted. The polypyrimidine tract extends into the left IR.

        1                                               50
T13E15  ~TATCAAATACTTATTCTGTCAATATCAATACATTTTAGCCTAGTTAATC 
X99111  ~TATTTATTAATTGTTTATATTATTTTTAGTAAGAGAGTTTCTCAAAATT 
  F2N1  AAATATATTTAGAAAATTTCAAATCTGAGGCAAAGGCGCCGACGACCACG 
 F1N21  ~AAAAAATCATTATATTACTTTTGATAATTTTCTTATACAAACATTAAAA 
 T17A5  ~AAATAAGAATTGAATTTCTATGGATCTTGAGAATTAGTTGGAATACGGT 

        51                                             100
T13E15  AGTAATAAAAATAACATATACTCCCTCTATTTTTTTTTTTTTGATTGTTT 
X99111  GTAACTGATGCAATTAAATACTCCCTCTGTTCCTTTTTGTTTGATTGTTT 
  F2N1  TCTACTACAACTAAATTATACTCCC.CTGTTCATTTTTGTTTGATTGTTT 
 F1N21  TAAAACCAAAACTAATAGTACTCCCTTTGTTCCTTTTTGTTTGATTGTTT 
 T17A5  TTGGAGTTCCTTCGGTTATATTTTCTCTGTCTCTTTTTGTTTAATTTTCT

        101                                            150
T13E15  AGAAAAAAAAATTGTTTCTAAAAGATTGATTTTTTAAGTTTTCCATATAA 
X99111  AGAAAAAAAAATTGTTTCTAAAAGATTAATTTTTTAAGTTTTCTATGTAA 
  F2N1  AGAAAAAAAATTTGTTTCTAAAAGATTGATTTTTTAAGTTTTCCATGCAA 
 F1N21  AGAAAAAAAAATTGTTTCAAAAAGATTGATTTTTTAGATTTTCAATACAA 
 T17A5  AGAAATAAAATTTGTTTCAAAGAGATTGATTTTTTAGATTTTCTATACAA 

        151                                            200
T13E15  TATTTATTGGTTAGTATTGATAAATTGTAATTTTCAAGAAAAATAGTTAA 
X99111  TATTTATTGGTTAGTATTGGTGAATTGTAATTTTCAAGAAAAATAGTTAA 
  F2N1  TATTTATTGGTTAGTATTGGTAAATTGTAATTTTTAAGAAAAATAGTTAA 
 F1N21  TAGTTATTAGTTATAATTGATAAATTGTAAACTTCAATACAAATTAGTGA 
 T17A5  TATTTATTAGTTATTATTGATGAATTGTAAATTTTAATAAAAATAAGTAA 

        201                                            250
T13E15  TTATCATTGGTTTAAAGTTATAGAAAACTGTAAAACACTAAAAATAATAC 
X99111  CTATCATTGGTTTAGAGTTATAGAAAACTGTAAAACACTAAAAATAATAC 
  F2N1  TTATCATTGGTTTAGAGGTATAAAAAACTGTAAAACACTAAAAATAATAC 
 F1N21  ATATCATTGGTTTAAAGTTATTGAAAATTGTAAATCACAAAAAACAATAC 
 T17A5  ATATTATTGATTTAAAGTTATAGAAAATTATAAAACACAAAAAATAATAT 

        251                                            300
T13E15  ATTTATAATCAACATTTA..ATATCTTTTCTTAATATATGTG.TTTTTTC 
X99111  ATTTATAATCAACATTTA..ATATATTTTCTTAATATGTGTG.TTTTTTC 
  F2N1  ATTTATAATCAACATTTAATATATATTTTCTTAATATGTGTGTTTTTTTC 
 F1N21  ATTTAAAAGCAACATTTA..ATATGTTTTTTTAATATTTGTG.ATTTTTC 
 T17A5  ATATATAAAATCAACTTGATATGTCTACATT...AATATGTATGTTTTCC 

        301                                            350
T13E15  TAAACAATCAAATAAAAAGGTACAAATGGAGTACA..TATTAGTGATTTA 
X99111  TAAACAATCAAACAAAAAGGAACAGAGAGAGTATA..AGCTACCCACTTG 
  F2N1  TAAAAAATCAAACAAAAAATAACAGAGGGAGTATAAGAATTAGCCTGTGG 
 F1N21  TAAAAGATCAAACAAAAAGGAACAGAGAGAGTAGTATTTTACCGTACTAA 
 T17A5  TAAACAATCATATAAAAAGGAACAGAAAGAATATAAAAGAATGAGTTAAA 

        351                                               403
T13E15  GTACATCCTTTTCTTCAAACTAGTTCTATCTAGTTACCGGCAACCGCAATTAC
X99111  AAATAAGATATAACCCAACGTATATATATGGAGAAAAAACAATTCATAATAGG
  F2N1  GACATTTGTTTAAGTTCAACTATTGTATTTGAATCGTTATAAAGAAAGACT~~
 F1N21  TCTTTCTATTTTATTGTTAGAGATACCATGCTTGGGAAAACGACA~~~~~~~~ 
 T17A5  ATTTTAAGTACATAAGTAATACGTATTAATTCACTACTTATCAATTGATCT~~

written 1 Nov 97
Larry Parnell