Worm Breeder's Gazette 15(1): 24 (October 1, 1997)

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.

The C. elegans Genome Sequencing Project: Update

The C. elegans Genome Sequencing Consortium

The Genome Sequencing Center, Washington University, St. Louis, MO, USA and The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

There are now over 70 megabases of finished C. elegans sequence and 3.2
megabases of C. briggsae sequence (see J. Schein this issue).  The
breakdown for C. elegans by chromosome is as follows:

I. 8.8 MB  II.11.9 MB  III. 8.8 MB  IV. 10.4 MB  V. 14.5 MB  X.  15.9

The small gaps in the cosmid- and gene-rich central regions of the
autosomes are being resolved by screening fosmids or long range PCR.
Numerous YACs are in various stages of production and finishing as the
primary method of resolving the larger gaps in the autosomal arms.
        There are now nearly 12,000 predicted proteins in the finished
sequence with 43% having significant similarity to proteins from other
organisms.  In the recent data release of AECDB (WS 4-20) some of the
more numerous kinds of proteins are; protein kinases (255), collagens
and phosphatases (119), peptidases/proteases (113), channel proteins
(93), homeobox proteins (71), G-protein coupled receptors (73),
ribosomal proteins (68), transposable elements (59), EGF-like proteins
(43) and zinc finger proteins (34).
        We are annotating new sequence as quickly as possible and hope
to be caught up with the finished sequence soon.  Updating the
annotation of older sequence is a continuous process as new information
is made available to us or errors are brought to our attention.  We are
committed to making the sequence as useful as possible, and since
accurate annotation is a large part of that we eagerly solicit and
always appreciate any contributions.  Assigning proper locus
designations to the appropriate sequence is sometimes problematic,
therefore the worm community's input can be particularly helpful.  The
following table shows each locus and the corresponding gene where
Any additions or corrections, or information concerning annotation in
general, should be directed to Steve Jones (sjj@sanger.ac.uk) or John
Spieth (jspieth@watson.wustl.edu).
        All sequences are made available after completing the initial
"shotgun" phase by anonymous FTP and the World Wide Web.  The latter
offers on-line search capabilities.  For information regarding the C.
elegans database ACEDB contact either Richard Durbin (rd@sanger.ac.uk)
or Jean Thierry-Meig (meig@kaa.cnrs-mop.fr).  Requests for cosmids
should be sent to Alan Coulson (alan@sanger.ac.uk).

FTP and WWW sites:
        Sanger Center:
                        directory: /pub/databases/C.elegans_sequences
                WWW: http://www.sanger.ace.uk
        Genome Sequencing Center:
                        directory: /pub/gscl/gschmpg.html
                WWW: http://genome.wustl.edu/gsc/gschmpg.html
ACEDB data releases can be retrieved from:
                USA: ncbi.nlm.nih.gov ( in
                UK: ftp.sanger.ac.uk ( in pub/acedb
                France: lirmm.lirmm.fr ( in genome/acedb

abl-1      M79.1
ace-1      F01G12.4
ace-1      W09B12.1
acr-2      K11G12.2
acr-3      K11G12.7
act-4      M03F4.2
ama-1      F36A4.7
aph-2      ZC434
arg-1      F31A9.3
bli-4      K04F10.4d
bli-4      K04F10.4a
bli-4B     K04F10.4b
bli-4C     K04F10.4e
bli-4D     K04F10.4c
cap-1      D2024.6
cct-6      F01F1.8
ced-4      C35D10.9
ced-11     ZK512.3
ceh-1      F16H11.4
ceh-6      K02B12.1
ceh-7      C34C6.8
ceh-8      ZK265.4
ceh-10     W03A3.1
ceh-13     R13A5.5
ceh-14     F46C8.5
ceh-16     C13G5.1
ceh-18     ZC64.3
ceh-20     F31E3.1
ceh-21     T26C11.6
ceh-22     F29F11.5
ceh-23     ZK652.5
ceh-26     K12H4.1
ceh-30     C33D12.7
ceh-31     C33D12.1
ceh-32     W05E10.3
ceh-33     C10G8.7
ceh-34     C10G8.6
ceh-35     F56A12
ceh-36     C37E2.4
ceh-37     C37E2.5
cej-1      C07G2.1
clk-1      ZC395.2
cnr-14     F44A6.2
col-2      W01B6.7
col-6      ZK1290.3
col-8      F11H8.3
col-36     C27H5.5
cpr-4      F44C4.3
cpr-6      C25B8.3
cul-1      D2045.6
cut-1      C47G2.1
cwn-2      W01B6.1
daf-4      C05D2.1
daf-7      B0412.2
deg-1      C47C12.1
dif-1      F49E8.5
dom-3      F54C1.2
dpy-2      T14B4.6
dpy-7      F46C8.6
dpy-1      T14B4.7
dpy-19     F22B7.10
dpy-20     T22B3.1
dpy-26     C25G4.5
dpy-30     ZK863.6
eat-6      B0365.3
eft-1      ZK328.2
eft-3      F31E3.5
egl-5      C08C3.1
egl-10     F28C1.2
egl-15     F58A3.2
egl-43     R53.3a
egl-43     R53.3b
egl-45     C27D11.1
emb-5      T04A8.14
emb-9      K04H4.1
fem-1      F35D6.1
fem-2      T19C3.8
fem-3      C01F6.4
gap-1      T24C12.2
gba-3      E02C12.5
gld-1      T23G11.3
glh-1      C55B7.1
glh-1      T21G5.3
glp-1      F02A9.6
gpa-2      F38E1.5
gpa-3      E02C12.5
gpd-2      K10B3.8
gpd-3      K10B3.7
gst-1      R107.7
ham-2      C07A12.1
her-1      ZK287.8
him-14     ZK1127.11
his-9      F17E9.10
his-10     C50F4.7
his-10     K03A1.6
his-11     F17E9.9
his-12     C50F4.13
his-12     F35H10.1
hlh-1      B0304.1
hsp-1      F26D10.3
hsp-2      K09C4.3
hsp-3      C15H9.6
hsp-16A    T27E4.2
hsp-16A    T27E4.8
hum-4      F46C3.3
inf-1      F57B9.6
kin-2      R07E4.6
kin-11     E01H11.1
kin-13     F10C2.1
kin-13     F57F5.5
kup-1      F10C2.2
lag-1      M03D4.2
let-2      F01G12.5a
let-2      F01G12.5b
let-23     ZK1067.1
let-70     M7.1
let-653    C29E6.1
let-721    C05D11.12
let-756    C05D11.4
lim-4      ZC64.4
lim-6      K03E6.1
lin-2      F17E5.1a
lin-2      F17E5.1b
lin-3      F36H1.4
lin-4      F59G1.6
lin-9      ZK637.7
lin-10     T01G9.2
lin-11     ZC247.3
lin-12     R107.8
lin-14     T25C12.1a
lin-14     T25C12.1b
lin-15     ZK662.4
lin-15     ZK678.1
lin-19     D2045.6
lin-25     F56H9.5
lin-26     F18A1.2
lin-32     T14F9.5
lin-36     F44B9.6
lin-39     C07H6.7
lir-1      F18A1.3
lon-1      F43C9.3
mab-5      C08C3.3
mai-1      K10B3.9
mec-2      F14D12.4
mec-4      T01C8.7
mec-7      ZK154.3
mec-8      C17E4.11
mec-9      C50H2.3
mec-10     F16F9.5
mei-1      T01G9.5
mel-32     C05D11.11
mes-3      F54C1.3
mig-10     F10E9.6
msp-19     F36H12.7
msp-31     R05F9.13
msp-32     R05F9.3
msp-33     R05F9.8
msp-37     K08F4.10
msp-38     K08F4.8
msp-40     C33F10.9
msp-51     ZK354.5
msp-52     F36H12.6
msp-53     R13H9.4
msp-57     R13H9.2
msp-58     ZK354.10
msp-59     ZK354.11
msp-65     ZK354.1
msp-113    ZK354.4
msp-142    K05F1.2
mua-1      F54H5.4
myo-1      T18D3.4
ncc-1      T05G5.3
ncs-2      F10G8.5
nhr-2      C32F10.6
nhr-6      C48D5.1
nhr-9      ZK418.1
nhr-10     B0280.8
nhr-17     C02B4.2
nhr-19     E02H1.7
nhr-20     F43C1.4
nhr-22     K06A1.4
odc-1      K11C4.4
osm-3      M02B7.3
ost-1      C44B12.7
pal-1      C38D4.6
pat-3      ZK1058.2
pat-3      ZK1058.7
pes-1      T28H11.4
pgp-3      ZK455.7
rol-6      T01B7.7
rop-1      C12D8.11
sdc-1      F52E10.1
sem-5      C14F5.5
skn-1      T19E7.2
snt-1      F31E8.2
spe-4      ZK524.1
spe-11     F48C1.7
spe-27     C06E7.6
sqt-1      B0491.2
sra-1      AH6.4
sra-2      AH6.6
sra-3      AH6.7
sra-4      AH6.8
sra-5      AH6.9
sra-6      AH6.10
sra-7      AH6.11
sra-8      AH6.12
sra-9      AH6.14
sra-10     F44F4.5
sra-11     F44F4.13
sra-12     F44F4.7
srb-1      C27D6.10
srb-2      C27D6.9
srb-3      C27D6.8
srb-4      C27D6.7
srb-5      C27D6.6
srb-6      R05H5.6
srb-7      F37C12.17
srb-8      F37C12.15
srb-9      F37C12.16
srb-10     F23F12.11
srb-11     F23F12.10
srd-1      F33H1.5
srd-2      R05H5.1
sre-1      B0495.1
sre-2      C41C4.2
srg-1      C18F10.4
srg-3      C18F10.6
srg-4      T12A2.12
srg-5      T12A2.11
srg-6      T12A2.13
srg-7      C18F10.8
srg-8      T12A2.9
srg-9      T12A2.10
srg-10     T04A8.1
srg-11     T04A8.2
srg-12     R13F6.3
srg-13     T23F11.5
sro-1      D1022.6
sup-7      C03B1.t1
tba-2      F26E4.8
tbg-1      F58A4.8
toc-1      ZC395.3
ubq-1      F25B5.4
unc-1      K03E6.5
unc-2      T02C5.5
unc-4      F26C11.2
unc-6      F41C6.1
unc-7      R07D5.1
unc-13     ZK524.2
unc-18     F27D9.1
unc-22     ZK617.1a
unc-30     B0564.10
unc-31     ZK897.1
unc-36     C50C3.11
unc-43     K11E8.1
unc-44     B0350.2a
unc-44     B0350.2b
unc-44     B0350.2c
unc-44     B0350.2d
unc-68     K11C4.5
unc-76     C01G10.11
unc-86     C30A5.7a
unc-86     C30A5.7b
unc-93     C46F11.1
unc-103    C30D11.1
unc-104    C52E12.2
unc-116    R05D3.7
vab-1      M03A1.1
vab-7      M142.4
vit-1      K09F5.2
vit-2      C42D8.2
vit-3      T27A10.4
vit-4      F56B6.a
vit-5      C04F6.1
xol-1      C18A11.5
zyg-11     C08B11.1