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)

SHC1		location ⇒	4:98930772-98930893		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
SHC1		location ⇒	4:98931636-98931765		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
SHC3		ENSSSCG00000009581	14:768928-935245
SHC4		ENSSSCG00000004655	1:128073308-128235567
SHCBP1		ENSSSCG00000002849	6:25568892-25574749		CU929644,CH242-402M14,6:25566776-25575872 (Clone quality: bE402M14 on chr=6; Num_of_Contigs=6; )
SHD		ENSSSCG00000013503	2:48525453-48532030		CU929466,CH242-60A20,2:48517923-48541505 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
SHE		ENSSSCG00000006547	4:99352058-99370836	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
SHF		ENSSSCG00000004674	1:132310125-132319923		CU062525,CH242-125K20,1:132198699-132329693 (Clone quality: bE125K20 on chr=1; Num_of_Contigs=2; )
SHH		ENSSSCG00000016416	18:1734991-1744780
SHH		location ⇒	18:1735212-1735290		CU694860,CH242-251C18,18:1712405-1737044 (Clone quality: bE251C18 on chr=18; Num_of_Contigs=11; )
SHH		location ⇒	18:1740432-1740696		CU694860,CH242-251C18,18:1739566-1744004 (Clone quality: bE251C18 on chr=18; Num_of_Contigs=11; )
SHH		location ⇒	18:1743352-1743668		CU694860,CH242-251C18,18:1739566-1744004 (Clone quality: bE251C18 on chr=18; Num_of_Contigs=11; )
SHISA4		ENSSSCG00000010917	10:24304955-24307729		CU896694,CH242-111D22,10:24267978-24372745 (Clone quality: bE111D22 on chr=10; Num_of_Contigs=6; )
SHISA5		ENSSSCG00000011357	13:26216688-26219490		CU633242,CH242-208G16,13:26215590-26232481 (Clone quality: bE208G16 on chr=13; Num_of_Contigs=5; )
SHISA6		ENSSSCG00000018012	12:53032326-53038565		CU466970,CH242-427E16,12:52938106-53155314 (Clone quality: bE427E16 on chr=12; Num_of_Contigs=1; )
SHISA7		ENSSSCG00000003290	6:41295937-41300992		FP245423,CH242-507H20,6:41294163-41314943 (Clone quality: bE507H20 on chr=6; Num_of_Contigs=16; )
SHMT2		ENSSSCG00000000421	5:21377332-21382933		CU633428,CH242-524E23,5:21373043-21392203 (Clone quality: bE524E23 on chr=5; Num_of_Contigs=9; )
SHOC2		ENSSSCG00000010628	14:126999861-127046472		CT737336,CH242-143P15,14:126897173-127111088 (Clone quality: bE143P15 on chr=14; Num_of_Contigs=1; )
SHOX		ENSSSCG00000012090	X:320841-330067	FP015869,CH242-24N12,X:269256-460080 (Clone quality: bE24N12 on chr=X; Num_of_Contigs=2; )
SHPK		ENSSSCG00000017864	12:47008486-47026452		FP016040,CH242-164K7,12:47005177-47045855 (Clone quality: bE164K7 on chr=12; Num_of_Contigs=2; )
SHPRH		ENSSSCG00000004120	1:20526290-20598245
SHQ1		ENSSSCG00000011518	13:45868816-45929123
SHROOM1		ENSSSCG00000014287	2:123059461-123062918	CU407038,CH242-18J12,2:123020435-123138962 (Clone quality: bE18J12 on chr=2; Num_of_Contigs=6; )
SHROOM2		ENSSSCG00000012104	X:5267496-5381946
SHROOM3		ENSSSCG00000008984	8:61925599-61949828		FP015936,CH242-32L5,8:61911135-61952786 (Clone quality: bE32L5 on chr=8; Num_of_Contigs=3; )
SHROOM4		ENSSSCG00000012309	X:43619654-43727856
SI		ENSSSCG00000011735	13:80439804-80458590
SIAE		ENSSSCG00000015196	9:50340650-50378611
SIAH1		ENSSSCG00000002840	6:24469965-24470813		FP236250,CH242-471I10,6:24468893-24472087 (Clone quality: bE471I10 on chr=6; Num_of_Contigs=13; )
SIAH3		ENSSSCG00000009416	11:20788686-20823004
SIAT4A		ENSSSCG00000005943	4:6695726-6705795		CU179695,CH242-327C11,4:6638178-6710539 (Clone quality: bE327C11 on chr=4; Num_of_Contigs=5; )
SIAT7B		ENSSSCG00000017177	12:3277247-3285641		CU928356,CH242-33I18,12:3274501-3286837 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
SIAT7B		location ⇒	1:282707252-282707881		CU914182,CH242-198I10,1:282705323-282709428 (Clone quality: bE198I10 on chr=1; Num_of_Contigs=15; )
SIAT7B		location ⇒	1:282879786-282879157		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
SIAT7B		location ⇒	1:282883401-282882986		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
SIAT7B		location ⇒	1:282889655-282889485		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
SIDT1		ENSSSCG00000011919	13:109259617-109268135		CU915398,CH242-257L23,13:109145832-109269113 (Clone quality: bE257L23 on chr=13; Num_of_Contigs=2; )
SIDT2		ENSSSCG00000015074	9:43299519-43314366		CU633260,CH242-267D22,9:43263576-43314400 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
SIGLEC-2		ENSSSCG00000002894	6:30118885-30123429		CU694505,CH242-50N19,6:30118807-30135716 (Clone quality: bE50N19 on chr=6; Num_of_Contigs=14; )
SIGLEC-3		ENSSSCG00000003226	6:39295447-39301650		CU694842,CH242-204P3,6:39279332-39353368 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC1		ENSSSCG00000007146	17:33507033-33526629
SIGLEC1		location ⇒	17:33509270-33508968		FP236531,CH242-39P18,17:33501178-33513040 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
SIGLEC1		location ⇒	17:33514618-33514307		FP236531,CH242-39P18,17:33513141-33517824 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
SIGLEC1		location ⇒	17:33518689-33518354		FP236531,CH242-39P18,17:33517925-33525934 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
SIGLEC1		location ⇒	17:33521136-33520837		FP236531,CH242-39P18,17:33517925-33525934 (Clone quality: bE39P18 on chr=17; Num_of_Contigs=7; )
SIGLEC11		location ⇒	6:39270752-39270701		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC11		location ⇒	6:39426930-39426674		CU694842,CH242-204P3,6:39384038-39444131 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC11		location ⇒	6:39429064-39428940		CU694842,CH242-204P3,6:39384038-39444131 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )
SIGLEC11		location ⇒	6:39498922-39498872		CU019573,CH242-21M5,6:39444132-39502362 (Clone quality: bE21M5 on chr=6; Num_of_Contigs=9; )
SIGLEC12		location ⇒	6:39259971-39259745		CU694842,CH242-204P3,6:39249252-39279231 (Clone quality: bE204P3 on chr=6; Num_of_Contigs=6; )

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).