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Index of /release1/current_release/trna-ncrna

      Name                               Last modified       Size  Description

[DIR] Parent Directory 09-Dec-2008 10:03 - [TXT] dpulex1_gnomon_nodups.codonuse.txt 07-Aug-2007 12:33 2k [TXT] dpulex1_gnomon_dups.codonuse.txt 07-Aug-2007 12:33 2k [TXT] dpulex-tRNA_analysis2.gff 07-Aug-2007 11:39 375k [TXT] dpulex-tRNA_codonuse.txt 06-Aug-2007 15:22 68k [TXT] dpulex-tRNA_analysis2.txt 06-Aug-2007 13:50 220k

From: Way Sung <wsung@cisunix.unh.edu>
Subject: Daphnia tRNAs
Date: Fri, 27 Jul 2007 13:19:34 -0400

Similar to the drosophila tRNA analysis, we applied two separate
tRNA identification programs, Aragorn and tRNA-SE to the daphnia
assembly.

We located 3983 tRNAs from Aragorn, and 5440 tRNAs from tRNA-SE 
(there were 489 psuedo tRNAs in tRNA-SE).  We combined the analyses 
and determined that there was 3798 overlapping tRNAs from both 
programs.  These numbers are considerably greater than the number of 
tRNAs from other eukaryotes [170 to 570 *]

----------------------------------------------------------------------
Daphnia tRNAs:

             Predictor
        Aragorn tRNA-SE Both
Total   3983      5929  
Psuedo    0        489  
tRNA    3983      5440  3798
-----------------------------

Codon/Anticodon table for tRNA: dpulex-tRNA_codonuse.txt
Codon use table from genes: 
  dpulex1_gnomon_dups.codonuse.txt  = duplicated genes
  dpulex1_gnomon_nodups.codonuse.txt = non-duplicated genes
-----------------------------

tRNA locations: dpulex-tRNA_analysis2.gff, dpulex-tRNA_analysis2.txt
Map view: http://wfleabase.org/release1/gbrowse/dpulex_jgi060905/
          Search Landmark: tRNA:tRNA-*
-----------------------------

tRNA genes have about 50% tandem duplicates, using Anticodon
identity as duplicate. Of 3798 tRNAs, there are 1706 different
codon/scaffold genes, 473 are duplicates <= 3kb, another 400 <=
12kb, and another 1200 duplicates > 12kb / scaffold.  
Reverse duplicates ("rever") are less common in nearby tRNAs than
distant ones.

Tandy count of duplicate locations per group
Group           Stat    Same    Inside  Near3k  Near6k  Near9k  Near12k Far
all             count   1706    0       473     168     121     92      1232
all             freq    1.000   0.000   0.277   0.098   0.071   0.054   0.722
all             rever   0       0       19      19      10      7       266
-----------------------------

* See recent review of eukaryote tRNAs, who find 170 - 570 tRNA genes
in a range of eukaryotes from yeast to man:
Diversity of tRNA genes in eukaryotes, Jeffrey M. Goodenbour and Tao Pan
Nucleic Acids Research, 2006, Vol. 34, No. 21 61376146 doi:10.1093/nar/gkl725
-----------

Notes on tRNA clusters: these are some random observations
  on a few of the larger tRNA clusters seen on the genome map
  
scaffold_117:  many Ile-Leu duplicate pairs (~50), coincide with Bacterial-infection EST
  treatment, but no gene models, some Tiling expression
scaffold_122:  similar to scaffold_117, Ile-Leu (+Ser) coincide with Bacterial-infect EST
  Note: these Ile-Leu coincide with the *same* EST matches for bacteria: CBT01494, 
  not different ones at each location.
scaffold_126:  Thr repeated with some Leu, Ser
scaffold_136:  various ones repeated 
scaffold_12:   several repated clusters of 2-3 Asn-Val pairs with one Lys, some
  Tiling expression
scaffold_13:   Pro (only) repeated
scaffold_1456: Ala,Pro,Phe,Glu quartet repeated 4 times
scaffold_1470: Met,Arg,Lys,Ser,Gln repeated in Bacterial EST
scaffold_152: Ile-Leu repeated a bunch, some others, Tile expression
scaffold_153: Ile-Leu as scaffold_152
scaffold_161: Val-Lys pairs
scaffold_172: Glu,Phe,Pro,Ala, quartet repeated 4 times (like scaffold_1456)
scaffold_208: Ser repeated, around EST Microcytis fed
scaffold_227: Asp repeated ~ 30 times, in clusters of 4-7, coincident with EST Titan. nanopart.
scaffold_231: Gly-Trp repeated with WFes0004351, Tile expression
scaffold_238: Thr repeated , some Tile expression
scaffold_240: clusters of 5-6 repeats of Gly, Cys, 
scaffold_242: Ala, Cys with various EST stresses
scaffold_246: Ile-Leu and EST Bacterial infect
scaffold_256: Gln,Leu,Arg,Pro with EST Titan. nanopart. in 5 to 6 clusters, some Tile express.
scaffold_267: Lots of Ile-Leu and EST Bacterial infect clusters
  
  -- dgg