Pig genome annotation: A Gene Wish List

A Wish List of Genes for Annotation (version 3.26)

(Matches to BACs by their Genome Locations Based on Pig Genome Build v.9 (Data Downloads as of Mar. 7, 2010 )

Info:

Purpose: Help users to find where to go from gene names to their genome locations/BACs in order to locate a starting spot in the pig genome to bring into Otterlace for annotations.
Methods: The gene locations are determined in 2 ways: Ensembl predictions and Blasts. Clones are sought based on their overlapping genome locations with that of your gene.
Terms: Finished BACs: A total of 811 "finished" clones that met the "golden standard" of finished sequencing quality. Unfinished clones: Out of 15,837 clones on the "unfinished clones" list, only 1,769 have been processed to have genome locations. FPC clones: 254K+ of those clones in the sequencing pipeline
Related links:

HINTS:

Owner/Status info: : Someone has this gene on their wish-list to annotate. : This gene is to be annotated. : This gene has been annotated (click to check for details - maybe only a gene variant is annotated. The ultimate annotator list is from Otterlace entries; This list only provides a working reference).
Additional info: : have orthologous gene information. : have refseq information. : details (click for more)
Ensembl Gene ID, Genome Locations, and BAC names are all hyper-linked to Ensembl database

( Go to genes whose symbol start with: 1, 5, 7, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z )
Search results:	Show Finished BAC Show unFinished BAC

User Gene List			Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)
Symbol	Owner/ Status	Ensembl Gene ID	Genome Location (Chr.:start-end)	Fell within Finished BACs (Contig, BACname, Chr.:Start-End)	Fell within Unfinished Clones (SeqName, Chr.:Start-End)

TYROBP		location ⇒	6:30468720-30468584		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
TYROBP		location ⇒	6:30469346-30469268		CU466979,CH242-510C11,6:30452219-30481257 (Clone quality: bE510C11 on chr=6; Num_of_Contigs=10; )
TYRP1		ENSSSCG00000005193	1:219103973-219121975		CU302437,CH242-341J3,1:219022894-219162934 (Clone quality: bE341J3 on chr=1; Num_of_Contigs=2; )
TYSND1		location ⇒	14:76020349-76019427		CU468481,CH242-304F15,14:76010785-76046069 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
TYSND1		location ⇒	14:76024357-76024169		CU468481,CH242-304F15,14:76010785-76046069 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
TYSND1		location ⇒	14:76025422-76025288		CU468481,CH242-304F15,14:76010785-76046069 (Clone quality: bE304F15 on chr=14; Num_of_Contigs=5; )
TYSND1		location ⇒	14:76124096-76124230		CU633580,CH242-307B6,14:76121419-76124498 (Clone quality: bE307B6 on chr=14; Num_of_Contigs=16; )
TYW3		ENSSSCG00000003779	6:97005715-97021496

Go to records:
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$version: 3.26; Updates: Mar. 6, 2010; Apr. 20, 2010; Aug 21, 2010

Related publications:

Martien Groenen, Alan Archibald, Hirohide Uenishi, Christopher Tuggle, Yasuhiro Takeuchi, Max Rothschild, Claire Rogel-Gaillard, ... Denis Milan, Hendrik-Jan Megens, ... Zhi-Liang Hu, Sean J. Humphray, ... James M. Reecy, ..., Gary A. Rohrer, ... Shuhong Zhao, Jane Rogers, Carol Churcher & Lawrence B. Schook. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491, 393-398 (15 November 2012).