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)

SMS1		location ⇒	14:103938560-103937801		CU468843,CH242-150G20,14:103910014-103941416 (Clone quality: bE150G20 on chr=14; Num_of_Contigs=6; )
SMS1		location ⇒	14:103939277-103939108		CU468843,CH242-150G20,14:103910014-103941416 (Clone quality: bE150G20 on chr=14; Num_of_Contigs=6; )
SMTN		ENSSSCG00000010017	14:48687103-48788249
SMTNL2		ENSSSCG00000017885	12:47829913-47849624		CU655858,CH242-208J3,12:47772347-47942311 (Clone quality: bE208J3 on chr=12; Num_of_Contigs=1; )
SMU1		ENSSSCG00000010999	10:31921639-31948532
SMURF1		ENSSSCG00000007608	3:5325538-5404998
SMYD1		ENSSSCG00000008215	3:52781440-52800380		CU856068,CH242-8G4,3:52762593-52803648 (Clone quality: bE8G4 on chr=3; Num_of_Contigs=15; )
SMYD2		ENSSSCG00000015583	9:121753523-121806995		CU929811,CH242-470E24,9:121749276-121811631 (Clone quality: bE470E24 on chr=9; Num_of_Contigs=2; )
SMYD3		ENSSSCG00000010880	10:18518392-18523729		CU466969,CH242-424N17,10:18508892-18527791 (Clone quality: bE424N17 on chr=10; Num_of_Contigs=7; )
SMYD4		ENSSSCG00000017819	12:45376926-45403142
SMYD5		ENSSSCG00000008305	3:63914359-63926774		FP089556,CH242-274G10,3:63904593-63934044 (Clone quality: bE274G10 on chr=3; Num_of_Contigs=6; )
SNAP23		ENSSSCG00000004727	1:135149948-135188452		CU929677,CH242-104I21,1:135136760-135189683 (Clone quality: bE104I21 on chr=1; Num_of_Contigs=5; )
SNAP29		ENSSSCG00000010094	14:51588223-51603171		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
SNAP47		ENSSSCG00000013984	2:66179919-66266917
SNAP91		ENSSSCG00000004453	1:86807843-86917184		CU407112,CH242-322O1,1:86776107-86939727 (Clone quality: bE322O1 on chr=1; Num_of_Contigs=4; )
SNAPAP		location ⇒	4:100132340-100132497		CU137691,CH242-31M11,4:100115756-100144233 (Clone quality: bE31M11 on chr=4; Num_of_Contigs=9; )
SNAPAP		location ⇒	4:100133665-100133849		CU137691,CH242-31M11,4:100115756-100144233 (Clone quality: bE31M11 on chr=4; Num_of_Contigs=9; )
SNAPAP		location ⇒	4:100248939-100248755		CU463867,CH242-10B5,4:100237775-100269080 (Clone quality: bE10B5 on chr=4; Num_of_Contigs=11; )
SNAPAP		location ⇒	4:100250264-100250107		CU463867,CH242-10B5,4:100237775-100269080 (Clone quality: bE10B5 on chr=4; Num_of_Contigs=11; )
SNAPC1		ENSSSCG00000005097	1:199839545-199866029
SNAPC1		location ⇒	1:188087536-188087484		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SNAPC1		location ⇒	1:199853236-199853293		FP236550,CH242-412M5,1:199846775-199861016 (Clone quality: bE412M5 on chr=1; Num_of_Contigs=6; )
SNAPC1		location ⇒	1:199862560-199862638		FP236550,CH242-412M5,1:199861117-199884977 (Clone quality: bE412M5 on chr=1; Num_of_Contigs=6; )
SNAPC1		location ⇒	1:228874404-228874347		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SNAPC2		ENSSSCG00000013589	2:51291895-51294543		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
SNAPC3		ENSSSCG00000005184	1:216382649-216544340
SNAPC5		ENSSSCG00000004944	1:171628672-171632256		CU407297,CH242-524I5,1:171627733-171632288 (Clone quality: bE524I5 on chr=1; Num_of_Contigs=20; )
SNCA		ENSSSCG00000009203	8:111089417-111113328
SNCA		location ⇒	8:111090672-111090527		FP102014,CH242-68K4,8:111073572-111112162 (Clone quality: bE68K4 on chr=8; Num_of_Contigs=5; )
SNCA		location ⇒	8:111110787-111110639		FP102014,CH242-68K4,8:111073572-111112162 (Clone quality: bE68K4 on chr=8; Num_of_Contigs=5; )
SNCA		location ⇒	8:111179459-111178969		FP102014,CH242-68K4,8:111174930-111193017 (Clone quality: bE68K4 on chr=8; Num_of_Contigs=5; )
SNCA		location ⇒	8:111182491-111182405		FP102014,CH242-68K4,8:111174930-111193017 (Clone quality: bE68K4 on chr=8; Num_of_Contigs=5; )
SNCAIP		ENSSSCG00000014235	2:113873708-113931640
SNCB		ENSSSCG00000014053	2:70306575-70316626	FP101981,CH242-191F5,2:70304317-70501298 (Clone quality: bE191F5 on chr=2; Num_of_Contigs=3; )
SND1		ENSSSCG00000016590	18:18475789-18778644
SNED1		ENSSSCG00000016381	15:132142482-132180843
SNN		ENSSSCG00000007897	3:28129411-28129674		FP089564,CH242-85K23,3:28125996-28132743 (Clone quality: bE85K23 on chr=3; Num_of_Contigs=5; )
snoR38		ENSSSCG00000019228	12:3273466-3273548		CU928356,CH242-33I18,12:3269827-3274400 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
snoR38		ENSSSCG00000019245	12:3271777-3271854		CU928356,CH242-33I18,12:3269827-3274400 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
snoR38		ENSSSCG00000019428	12:3274049-3274120		CU928356,CH242-33I18,12:3269827-3274400 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
SNORA1		ENSSSCG00000019016	11:15371931-15372046		CU633931,CH242-96K7,11:15370975-15394630 (Clone quality: bE96K7 on chr=11; Num_of_Contigs=6; )
SNORA1		ENSSSCG00000018819	2:37053215-37053342		CU468023,CH242-324O17,2:37014052-37127679 (Clone quality: bE324O17 on chr=2; Num_of_Contigs=7; )
SNORA1		ENSSSCG00000018374	11:15229204-15229319		CU468420,CH242-359D24,11:15228338-15241005 (Clone quality: bE359D24 on chr=11; Num_of_Contigs=8; )
SNORA1		ENSSSCG00000018329	9:26391142-26391277		CU694898,CH242-364L8,9:26386311-26391934 (Clone quality: bE364L8 on chr=9; Num_of_Contigs=25; )
SNORA11		ENSSSCG00000018121	12:22684979-22685108		CU928816,CH242-243D3,12:22676597-22697158 (Clone quality: bE243D3 on chr=12; Num_of_Contigs=4; )
SNORA11		ENSSSCG00000018148	5:78529023-78529139		CU856024,CH242-269P23,5:78524189-78529875 (Clone quality: bE269P23 on chr=5; Num_of_Contigs=12; )
SNORA11		ENSSSCG00000018149	12:36214783-36214910		CU694727,CH242-39G9,12:36193404-36216214 (Clone quality: bE39G9 on chr=12; Num_of_Contigs=15; )
SNORA11		ENSSSCG00000018191	7:120405570-120405697		CU468883,CH242-64J18,7:120405220-120417949 (Clone quality: bE64J18 on chr=7; Num_of_Contigs=16; )
SNORA11		ENSSSCG00000018305	X:44855215-44855343		CU639446,CH242-176C9,X:44847759-44857045 (Clone quality: bE176C9 on chr=X; Num_of_Contigs=6; )
SNORA11		ENSSSCG00000018322	7:20257271-20257399		CT737347,CH242-196L6,7:20166720-20328348 (Clone quality: bE196L6 on chr=7; Num_of_Contigs=1; )

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).