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)

SIGLEC12		location ⇒	6:39272415-39272134		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC12		location ⇒	6:39272943-39272576		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC12		location ⇒	6:39296073-39296354		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC14		ENSSSCG00000003236	6:39481730-39501436		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC15		ENSSSCG00000004493	1:99284559-99290281		CU694902,CH242-378G17,1:99170632-99336108 (Clone quality: bE378G17 on chr=1; Num_of_Contigs=1; )
SIGLEC2		ENSSSCG00000002894	6:30118885-30123429		CU694505,CH242-50N19,6:30118807-30135716 (Clone quality: bE50N19 on chr=6; Num_of_Contigs=14; )
SIGLEC5		ENSSSCG00000003236	6:39481730-39501436		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC5		location ⇒	6:39260292-39260214		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC5		location ⇒	6:39295748-39295831		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC5		location ⇒	6:39500614-39500333		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC5		location ⇒	6:39501181-39500800		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC6		location ⇒	6:39271089-39270924		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC6		location ⇒	6:39272415-39272312		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC6		location ⇒	6:39296073-39296176		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC6		location ⇒	6:39499256-39499095		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC7		location ⇒	6:39260379-39260133		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC7		location ⇒	6:39295520-39295912		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC7		location ⇒	6:39500967-39500884		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC7		location ⇒	6:39511633-39511550		CU019573,CH242-21M5,6:39502463-39511670 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC8		location ⇒	8:35666765-35666817		FP015961,CH242-68J9,8:35666593-35707684 (Clone quality: bE68J9 on chr=8; Num_of_Contigs=5; )
SIGLEC9		location ⇒	6:39295912-39295520		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC9		location ⇒	6:39296127-39296073		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC9		location ⇒	6:39500884-39500967		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC9		location ⇒	6:39511550-39511633		CU019573,CH242-21M5,6:39502463-39511670 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIK3		ENSSSCG00000015071	9:43020364-43127211
SIKE1		ENSSSCG00000006751	4:110083894-110091056		CU151855,CH242-234C5,4:110062473-110097642 (Clone quality: bE234C5 on chr=4; Num_of_Contigs=10; )
SIL		location ⇒	6:117617290-117616954		CU694906,CH242-407D16,6:117591962-117641359 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
SIL		location ⇒	6:117626825-117626574		CU694906,CH242-407D16,6:117591962-117641359 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
SIL		location ⇒	6:117628851-117628640		CU694906,CH242-407D16,6:117591962-117641359 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
SIL		location ⇒	6:117631079-117631011		CU694906,CH242-407D16,6:117591962-117641359 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
SIL1		ENSSSCG00000014342	2:128004581-128183929
SILV		ENSSSCG00000000371	5:20308141-20314195
SILV		location ⇒	5:20308351-20308141	CU606916,CH242-141C7,5:20252909-20311092 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
SILV		location ⇒	5:20309356-20309148	CU606916,CH242-141C7,5:20252909-20311092 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
SILV		location ⇒	5:20311551-20310904	CU606916,CH242-141C7,5:20252909-20311092 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )	CU457395,CH242-13B13,5:20311093-20314968 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
SILV		location ⇒	5:20311959-20311797		CU457395,CH242-13B13,5:20311093-20314968 (Clone quality: bE13B13 on chr=5; Num_of_Contigs=23; )
SIM1		ENSSSCG00000004357	1:70627001-70709897
SIN3A		ENSSSCG00000001880	7:63452446-63501381
SIN3B		ENSSSCG00000013867	2:61364629-61404605
SIP1		ENSSSCG00000004985	1:177600571-177625325
SIPA1		ENSSSCG00000010169	14:60001127-60116044
SIPA1		ENSSSCG00000012982	2:5005234-5013225
SIPA1		ENSSSCG00000002332	7:103362224-103506697
SIPA1		location ⇒	2:4989053-4989168		CU856129,CH242-95H3,2:4988912-5001366 (Clone quality: bE95H3 on chr=2; Num_of_Contigs=5; )
SIPA1		location ⇒	2:4989256-4989467		CU856129,CH242-95H3,2:4988912-5001366 (Clone quality: bE95H3 on chr=2; Num_of_Contigs=5; )
SIPA1		location ⇒	2:5005423-5005217		CU914305,CH242-95H15,2:5005118-5007050 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
SIPA1L1		ENSSSCG00000002332	7:103362224-103506697
SIPA1L2		ENSSSCG00000010169	14:60001127-60116044
SIPA1L3		ENSSSCG00000002950	6:32313415-32345884
SIRPA		ENSSSCG00000007181	17:35100996-35142659		CU076083,CH242-165N9,17:35094633-35142680 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).