C. elegans Cosmid and YAC Info.
Ordering
Please submit all requests for C.elegans genomic clones via this request portal.
Nomenclature
There are seven different types of "Clone" objects in WormBase:
| Type
|
Nomenclature
|
| Cosmid
|
A*, B*, C*, D*, F*,J*,K*,M*,R*,T*,W*,Z*
|
| Fosmid
|
H* WRM*
|
| YAC
|
Y*
|
| cDNA
|
yk*, EC*, EB*, OST*, CK*, EF*, CEE*, CEM*, CES*, CB*, CN*, cm*
|
| Plasmid: PCR clones
|
V*,EGAP*
|
| Other
|
telo clones, 1 BAC, plasmid
|
Most Cosmids, Fosmids, YACs can be requested from Sanger via the form at the top of the page,
cDNA (yk*) from Dr. Yuji Kohara.
The EGAP* plasmids can be obtained from........
WRM Vancouver_fosmid
The V* plasmids are no longer available.
The EC* ESTs were distributesd by Exelixis but are no longer available.
Vector Sequences
| Clone series |
Vector Sequence |
Comment |
Vector publication |
NCBI/DB Accession
|
| A |
Lambda 2001? |
Sau3A1 partial |
Gene. 1984 Dec;32(1-2):217-24. |
Vector db
|
| ZL |
Lambda 2001? |
Sau3A1 partial, probe selected |
Gene. 1984 Dec;32(1-2):217-24. |
Vector db
|
| YSL |
Lambda 2001? |
Sau3A1 partial, YAC subclones |
Gene. 1984 Dec;32(1-2):217-24. |
Vector db
|
| B |
pJB8 |
Sau3A1 partial |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| C |
pJB8 |
Sau3A1 partial, microtitre array |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| D |
pJB8 |
Sau3A1 partial, filter gridded |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| E |
pJB8 |
Sau3A1 partial, EcoK- host |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| R |
pJB8 |
EcoR1 partial |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| M |
pJB8 |
Mbo1 partial |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| ZC |
pJB8 |
EcoR1 partial, probe selected |
Nucleic Acids Res. 1981 Jul 10;9(13):2989-98. |
X98612
|
| K |
loristB |
Sau3A1 partial |
Gene. 1986;49(1):9-22. |
X98613
|
| T |
lorist2 |
Sau3A1 partial |
Gene. 1987;53(2-3):275-81. |
X98409
|
| W |
lorist6 |
NotI complete, Sau3A1 partial |
Gene. 1987;53(2-3):283-6. |
X98450
|
| F 1-28 |
lorist2 |
Sau3A1 partial |
Gene. 1987;53(2-3):275-81. |
X98409
|
| F 29 on |
lorist6 |
Sau3A1 partial |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 15-56 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 57-130 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK131-164 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 165-177 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 178-192 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 193-344 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 345-354 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 355-514 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 515-552 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 553-596 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 597-616 |
lorist |
Sau3A1 partial, probe selected |
|
|
| ZK 617-626 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 627-692 |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| ZK 693-756 |
lorist2 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):275-81. |
X98409
|
| ZK 757 on |
lorist6 |
Sau3A1 partial, probe selected |
Gene. 1987;53(2-3):283-6. |
X98450
|
| Y |
pYAC4 |
|
Gene. 1994 Apr 8;141(1):125-7. |
XXU01086 Vector db
|
Protocols and Methods
The Protocols and methods used when generating the Physical Map of C. elegans and the Genome Sequencing Project can be found in this book chapter [Methods in cell biology, Volume 48
YAC clone Information
Specific YAC information can be found in these publications:
Nature. 1988 Sep 8;335(6186):184-6. Genome linking with yeast artificial chromosomes. Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y.
science 1987 May 15;236(806-812) Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. DT Burke, GF Carle, and MV Olson
Note When ordering YAC clones.
Suffixes appended to YAC names (e.g. Y73B3A, Y73B3B) indicate sequenced segments of the YAC that have been used to bridge gaps between finished Cosmids
They do not exist as subclones so you will be sent the whole YAC.
Clone ends within wormbase
The set of clone ends is dumped as part of the gff files:
http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/GFF_files.shtml
This is the source for the extents displayed in WormBase.
The caveat with this is that the 'true' end is not marked up for all clones. The early cosmids do not have such annotations because nobody thought about marking them up. Later cosmids do have clone left and right ends as this became part of the standard procedure. Finally, many of the YACs do not have clone ends because the segment submitted to GenBank/EMBL is much smaller than the full clone, and hence the true ends lie within sequences already finished at that stage of the sequencing (i.e. we never went back to update clone ends in sequence already finished).
