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)

VSTM2L		ENSSSCG00000007338	17:43354373-43368453
VSX2		ENSSSCG00000002363	7:105786902-105805784
VTA1		ENSSSCG00000004140	1:24052003-24081804
VTCN1		ENSSSCG00000006731	4:107621872-107690212		CU207228,CH242-366F10,4:107617782-107740116 (Clone quality: bE366F10 on chr=4; Num_of_Contigs=2; )
VTI1A		ENSSSCG00000010634	14:128418173-128655869
VTI1B		ENSSSCG00000002295	7:99791949-99820058
VWA1		ENSSSCG00000003344	6:42968001-42972028		FP102593,CH242-171J19,6:42966854-42985611 (Clone quality: bE171J19 on chr=6; Num_of_Contigs=11; )
VWA2		ENSSSCG00000010649	14:130459743-130496019		CU019667,CH242-264H11,14:130338198-130508081 (Clone quality: bE264H11 on chr=14; Num_of_Contigs=1; )
VWA3A		ENSSSCG00000007841	3:21705989-21909298
VWA5A		ENSSSCG00000015175	9:49708124-49738570		CU856234,CH242-6B11,9:49662749-49762584 (Clone quality: bE6B11 on chr=9; Num_of_Contigs=3; )
VWA5A		location ⇒	9:49710777-49710984		CU856234,CH242-6B11,9:49662749-49762584 (Clone quality: bE6B11 on chr=9; Num_of_Contigs=3; )
VWA5A		location ⇒	9:49711299-49711515		CU856234,CH242-6B11,9:49662749-49762584 (Clone quality: bE6B11 on chr=9; Num_of_Contigs=3; )
VWA5A		location ⇒	9:49724331-49724450		CU856234,CH242-6B11,9:49662749-49762584 (Clone quality: bE6B11 on chr=9; Num_of_Contigs=3; )
VWA5A		location ⇒	9:49725221-49725343		CU856234,CH242-6B11,9:49662749-49762584 (Clone quality: bE6B11 on chr=9; Num_of_Contigs=3; )
VWA5B1		ENSSSCG00000003503	6:54093440-54265862
VWA5B2		ENSSSCG00000003500	6:53929608-53992626
VWC2		ENSSSCG00000015626	9:127901957-128001667		CU855634,CH242-192A14,9:127900231-128025034 (Clone quality: bE192A14 on chr=9; Num_of_Contigs=4; )
VWC2L		ENSSSCG00000016168	15:109837042-109838168		CU915370,CH242-57E3,15:109835672-109859298 (Clone quality: bE57E3 on chr=15; Num_of_Contigs=4; )
VWCE		ENSSSCG00000013093	2:8606712-8638394
VWF		ENSSSCG00000000712	5:60531222-60603781
vWF		location ⇒	5:60567425-60567622		FP102760,CH242-92K19,5:60530360-60588038 (Clone quality: bE92K19 on chr=5; Num_of_Contigs=2; )
vWF		location ⇒	5:60568322-60568537		FP102760,CH242-92K19,5:60530360-60588038 (Clone quality: bE92K19 on chr=5; Num_of_Contigs=2; )
vWF		location ⇒	5:60572966-60573207		FP102760,CH242-92K19,5:60530360-60588038 (Clone quality: bE92K19 on chr=5; Num_of_Contigs=2; )
vWF		location ⇒	5:60602403-60603767		FP102760,CH242-92K19,5:60588139-60603955 (Clone quality: bE92K19 on chr=5; Num_of_Contigs=2; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-24

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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).