Worm Breeder's Gazette 14(4): 16 (October 1, 1996)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Tc1 Sequence Tagged Sites, An Update

Hendrik C. Korswagen1, Richard M. Durbin2, Miriam T. Smits1, Ronald H.A. Plasterk1

1 Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
2 The Sanger Centre, Hinxton Hall, Hinxton, Cambridge CB10 1RQ, United Kingdom

In an effort to establish a high density Tc1 STS map as an extension of
the mapping strategy developed by Williams et al. (1), we shotgun
sequenced Tc1 insertion sites present in the high Tc1 copy number
strains RW7000, CB4000 and KR1787 (2). To map these Tc1 insertion sites,
flanking sequences were compared to the genomic sequence. In principle,
all Tc1 insertion sites will fall in place when the complete genomic
sequence of C. elegans becomes available. So far, we mapped 151
polymorphic Tc1 insertion sites in 40 Mbp of genomic sequence; a density
of about one insertion in every 265 kb. Information on these mapped Tc1
insertion sites is available through ACeDB. These Tc1 insertions can be
used as polymorphic markers, but can also be used for deletion
mutatgenesis when a Tc1 insertion is located in or close to a gene of
interest.

(1) Williams, B. D. (1995) in Caenorhabditis elegans: Modern biological
analysis of an organism, eds. Epstein, H. F. & Shakes, D. C. (Academic
Press, San Diego), pp. 81-96. (2) Korswagen et al. (1995) Worm Breeder's
Gazette 13(5): 90.

Mapped polymorphic Tc1 insertion sites:

(Indicated are approximate position on the genetic map, the cosmid the
Tc1 is inserted in and the position of that Tc1 insertion in the cosmid
sequence. Strain designations are A. RW7000, B. CB4000 and C. KR1787)


Chromosome I
pkP5319   0.00      C09D4     14218     A
pkP5422   0.04      F55F8     15300     A
pkP5242   1.25      T23B3     1135      A
pkP5383   2.22      F27D4     683       A
pkP550    2.26      D2005     17254     A
pkP652    2.43      T28B8     6269      B
pkP596    2.43      T28B8     20095     A
pkP979    2.54      T01G9     3827      A
pkP5459   2.80      K02B12    12868     A

Chromosome II
pkP5453   -4.60     W06A11    4604      A
pkP5030   -4.53     F31D5     25916     A
pkP5235   -4.53     F31D5     25984     A
pkP682    -4.53     B0286     31305     B
pkP632    -4.52     T12C9     9085      A
pkP908    -4.52     T05C1     11339     A
pkP5167   -3.32     R05F9     11496     B
pkP617    -3.32     R05F9     12719     A
pkP5017   -2.07     F07F6     25039     C
pkP557    -1.40     C17C3     19067     A
pkP727    -1.40     C17C3     27303     B
pkP597    -0.84     B0034     10606     A
pkP738    -0.50     F13H8     12107     C
pkP5091   0.23      T02G5     14855     B
pkP5162   0.29      C27H5     20352     B
pkP416    0.30      E04F6     31057     A
pkP5179   0.32      C30G12    9985      B
pkP504    0.45      F35D2     6363      B
pkP5391   0.48      F18A1     3056      A
pkP5241   0.67      T05H10    19209     A
pkP5009   0.79      F49E12    4748      C
pkP5184   0.79      F14E5     17096     B
pkP605    0.85      F46C5     9487      A
pkP955    1.20      D2013     909       A
pkP5187   1.25      C06C3     18716     B
pkP746    1.41      T19H5     8754      C
pkP5170   1.45      AH6       10404     B
pkP515    1.48      F35H8     19105     C
pkP5299   1.52      E02H1     1150      A
pkP735    1.70      C08H9     11316     C
pkP758    1.70      C08H9     11489     C
pkP613    2.89      C09G5     23572     A
pkP5144   3.21      B0491     8802      B
pkP5260   3.36      C05D12    24325     A
pkP645    3.53      B0334     34659     B
pkP5190   3.73      F07A11    32699     B
pkP683    3.82      C47D12    28460     B

Chromosome III
pkP417    -26.3     F42G9     1945      A
pkP583    -4.84     C36A4     22793     A
pkP753    -4.13     E03A3     31006     C
pkP409    -4.04     C03C10    25246     A
pkP406    -3.70     R07E5     3225      A
pkP524    -3.47     T23F11    13007     C
pkP689    -3.40     T04A8     12234     B
pkP410    -2.56     C35D10    22392     A
pkP644    -2.56     C35D10    23225     B
pkP5174   -1.75     F48E8     30331     B
pkP601    -0.92     C56G2     39105     A
pkP402    -0.80     C06E8     22591     A
pkP415    -0.75     R151      13226     A
pkP403    -0.66     C07H6     54473     A
pkP400    -0.52     ZK652     14661     A
pkP405    -0.48     C29E4     39173     A
pkP411    -0.27     R05D3     2352      C
pkP729    2.31      R01H10    23395     B

Chromosome IV
pkP701    3.12      C01G5     19492     B
pkP5024   3.38      B0496     17856     A
pkP664    3.59      C26B2     24688     B
pkP672    3.67      B0218     3876      B
pkP512    3,92      C09G4     26221     C
pkP5151   4.58      K07F5     37251     B
pkP614    4.58      C47E12    24453     A
pkP528    4.61      R09E10    13343     C
pkP576    4.63      F13B12    13504     A
pkP5392   4.73      R102      21118     A
pkP756    5.53      K08E4     3577      C
pkP5333   5.94      F08G5     10566     A
pkP570    6.02      F53B2     3686      A

Chromosome V
pkP5306   -5.51     C52D10    37203     A
pkP5223   -1.69     F08F3     16667     A
pkP5475   -1.69     F08F3     16447     A
pkP585    0.62      C33G8     28366     A
pkP5401   0.62      C33G8     28416     A
pkP5132   0.79      C37C3     17798     B
pkP5056   0.84      F58G4     11837     A
pkP520    1.88      F21C10    30979     C
pkP5168   2.24      R07B5     4346      B
pkP5309   2.33      T07C12    23165     A
pkP5337   2.42      F57A8     21726     A
pkP5385   2.42      F57A8     24331     A
pkP710    2.45      C08B6     2290      B
pkP5175   2.70      C35A5     6704      B
pkP534    3.43      T11F9     36422     C
pkP554    3.44      F38B7     12234     A
pkP5181   3.85      F55C5     20402     B
pkP5393   4.04      K01D12    22580     A
pkP667    5.31      C56A3     6919      B
pkP945    5.70      R10D12    4086      A

Chromosome X
pkP5165   -19.0     C02H7     5126      B
pkP670    -14.3     F48B9     6937      B
pkP706    -14.0     F47G3     15263     B
pkP5020   -13.1     M02F4     17362     A
pkP687    -13.1     M02F4     30478     B
pkP5386   -12.7     ZK816     25592     A
pkP744    -9.52     C01C4     7940      C
pkP5335   -8.93     F47B7     2364      A
pkP733    -7.46     F15A8     14142     C
pkP538    -6.11     F43C9     7107      C
pkP526    -5.92     M03F4     8930      C
pkP754    -5.68     C42D8     4187      C
pkP743    -5.02     F55D1     592       C
pkP511    -3.99     F49E10    37400     C
pkP943    -3.64     C09B8     19591     A
pkP507    -2.87     C15B12    13        B
pkP5058   -2.84     C25B8     13152     B
pkP5382   -2.15     C16E9     17742     A
pkP618    -1.97     K03A1     26302     A
pkP532    -0.65     C18A11    4886      C
pkP5116   -0.59     C47D2     11528     A
pkP5285   -0.58     R09F10    23808     A
pkP960    -0.02     K01A12    3152      A
pkP5037   0.06      F12D9     20611     B
pkP588    0.78      F47E1     13960     A
pkP704    1.01      F18G5     13626     B
pkP643    1.51      R07B1     21127     B
pkP668    1.58      F19C6     10958     B
pkP976    1.64      ZC373     9484      A
pkP5331   1.78      F41E7     18069     A
pkP503    1.93      ZC504     21481     B
pkP720    2.03      F59F5     19347     B
pkP5495   4.86      C35C5     38107     A
pkP5028   8.57      R09A8     24734     A
pkP757    9.55      C52G5     11870     C
pkP514    10.6      F11C1     21686     C
pkP980    11.7      K09A11    19736     A
pkP649    11.8      R04D3     2050      B
pkP5348   14.9      F48F7     28800     A
pkP966    16.3      T24C2     24299     A
pkP5154   18.7      C27C12    25078     B
pkP5149   21.0      F47C8     15566     B
pkP573    22.9      T27A8     13387     A
pkP521    24.1      T21F2     16242     C
pkP5302   24.1      C30G4     8866      A
pkP651    24.1      C33E10    6646      B
pkP834    24.1      C33E10    17338     A
pkP933    24.3      F20B4     16665     A