Cosmids/YACs

From WormBaseWiki
Jump to: navigation, search

C. elegans Cosmid and YAC Info.

Ordering

Please submit all requests for C.elegans genomic clones via this request portal.

Clone Requests


Note: The resources aren't listed on the landing page but are on the actual order page.

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).