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)

SF3A3		ENSSSCG00000003643	6:63527912-63552618	CR956649,PigE-92E11,6:63451761-63579213 (No clone quality info on bT92E11)
SF3B1		ENSSSCG00000012957	2:4652181-4666757		CU694743,CH242-58A13,2:4546810-4689644 (Clone quality: bE58A13 on chr=2; Num_of_Contigs=2; )
SF3B1		ENSSSCG00000016075	15:94815655-94859645
SF3B1		location ⇒	15:94816148-94815660		CU468160,CH242-67M21,15:94814817-94851976 (Clone quality: bE67M21 on chr=15; Num_of_Contigs=2; )
SF3B1		location ⇒	15:94819325-94819052		CU468160,CH242-67M21,15:94814817-94851976 (Clone quality: bE67M21 on chr=15; Num_of_Contigs=2; )
SF3B1		location ⇒	15:94823753-94823529		CU468160,CH242-67M21,15:94814817-94851976 (Clone quality: bE67M21 on chr=15; Num_of_Contigs=2; )
SF3B1		location ⇒	15:94825423-94825149		CU468160,CH242-67M21,15:94814817-94851976 (Clone quality: bE67M21 on chr=15; Num_of_Contigs=2; )
SF3B2		ENSSSCG00000012957	2:4652181-4666757		CU694743,CH242-58A13,2:4546810-4689644 (Clone quality: bE58A13 on chr=2; Num_of_Contigs=2; )
SF3B3		ENSSSCG00000002725	6:9757914-9818204
SF3B4		ENSSSCG00000006665	4:103134532-103140148		CU468464,CH242-21F2,4:103092969-103158703 (Clone quality: bE21F2 on chr=4; Num_of_Contigs=8; )
SF3B5		ENSSSCG00000004126	1:22211394-22211651		CU861515,CH242-118D7,1:22209109-22355773 (Clone quality: bE118D7 on chr=1; Num_of_Contigs=2; )
SFI1		ENSSSCG00000010031	14:49115036-49188468	CU459044,CH242-171L17,14:49086749-49222812 (Clone quality: bE171L17 on chr=14; Num_of_Contigs=2; )
SFMBT1		ENSSSCG00000011454	13:29619637-29678437
SFMBT2		ENSSSCG00000011130	10:60238222-60251025		CU469192,CH242-181F13,10:60192784-60307541 (Clone quality: bE181F13 on chr=10; Num_of_Contigs=5; )
SFN		ENSSSCG00000003562	6:57857031-57858334		FP015947,CH242-485K18,6:57822585-57995160 (Clone quality: bE485K18 on chr=6; Num_of_Contigs=2; )
SFRP1		ENSSSCG00000007012	17:10336026-10341656		CU606957,CH242-166M5,17:10309456-10351106 (Clone quality: bE166M5 on chr=17; Num_of_Contigs=4; )
SFRP2		ENSSSCG00000009005	8:64588167-64596072
SFRP5		ENSSSCG00000010529	14:113963369-113968675		CT867982,CH242-512F14,14:113912716-114011979 (Clone quality: bE512F14 on chr=14; Num_of_Contigs=2; )
SFRS1		ENSSSCG00000017626	12:32016578-32018530		CU915688,CH242-107O9,12:31998190-32036239 (Clone quality: bE107O9 on chr=12; Num_of_Contigs=9; )
SFRS11		ENSSSCG00000003791	6:100388163-100434901		CU694928,CH242-516C13,6:100384679-100527084 (Clone quality: bE516C13 on chr=6; Num_of_Contigs=2; )
SFRS12		ENSSSCG00000016955	16:41954655-41992636
SFRS12		location ⇒	16:41954606-41954815		CU466255,CH242-441J5,16:41944128-41962705 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
SFRS12		location ⇒	16:41974751-41974915		CU466255,CH242-441J5,16:41962806-41989288 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
SFRS12		location ⇒	16:41975055-41975235		CU466255,CH242-441J5,16:41962806-41989288 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
SFRS12		location ⇒	16:41976705-41976835		CU466255,CH242-441J5,16:41962806-41989288 (Clone quality: bE441J5 on chr=16; Num_of_Contigs=10; )
SFRS13B		ENSSSCG00000004313	1:59919170-59936319
SFRS14		ENSSSCG00000013926	2:63157740-63157877		CU640483,CH242-64G8,2:63053243-63184458 (Clone quality: bE64G8 on chr=2; Num_of_Contigs=8; )
SFRS17A		ENSSSCG00000012627	X:96844445-96851850
SFRS18		ENSSSCG00000004350	1:69726121-69731796		CU062571,CH242-40C6,1:69725907-69732699 (Clone quality: bE40C6 on chr=1; Num_of_Contigs=11; )
SFRS2		ENSSSCG00000012212	X:29970351-29970656		CU468189,CH242-117I7,X:29969775-29980153 (Clone quality: bE117I7 on chr=X; Num_of_Contigs=7; )
SFRS2IP		ENSSSCG00000000806	5:72563316-72609975		CU694768,CH242-151M22,5:72545575-72628205 (Clone quality: bE151M22 on chr=5; Num_of_Contigs=3; )
SFRS3		ENSSSCG00000001564	7:36921152-36928125		CU633682,CH242-258O13,7:36904430-36964313 (Clone quality: bE258O13 on chr=7; Num_of_Contigs=5; )
SFRS4		ENSSSCG00000003588	6:58948735-58976610		FP236541,CH242-213E6,6:58932388-58988177 (Clone quality: bE213E6 on chr=6; Num_of_Contigs=2; )
SFRS5		ENSSSCG00000002312	7:101789066-101793654	CT737423,CH242-28F9,7:101687301-101874212 (Clone quality: bE28F9 on chr=7; Num_of_Contigs=2; )
SFRS6		ENSSSCG00000007362	17:47904855-47907901
SFRS7		ENSSSCG00000008484	3:94671951-94677044		FP102731,CH242-53K21,3:94641943-94727749 (Clone quality: bE53K21 on chr=3; Num_of_Contigs=3; )
SFRS8		ENSSSCG00000009744	14:23411936-23489599		CU655912,CH242-233J4,14:23387657-23491194 (Clone quality: bE233J4 on chr=14; Num_of_Contigs=3; )
SFRS8		location ⇒	14:23430294-23430389		CU655912,CH242-233J4,14:23387657-23491194 (Clone quality: bE233J4 on chr=14; Num_of_Contigs=3; )
SFRS8		location ⇒	14:23442266-23442460		CU655912,CH242-233J4,14:23387657-23491194 (Clone quality: bE233J4 on chr=14; Num_of_Contigs=3; )
SFRS8		location ⇒	14:23443600-23443832		CU655912,CH242-233J4,14:23387657-23491194 (Clone quality: bE233J4 on chr=14; Num_of_Contigs=3; )
SFRS9		ENSSSCG00000009906	14:40530686-40539834		CU468509,CH242-66D17,14:40518945-40544778 (Clone quality: bE66D17 on chr=14; Num_of_Contigs=12; )
SFT2D1		ENSSSCG00000004020	1:2631480-2674321
SFT2D2		ENSSSCG00000006300	4:86006413-86022699	CU151849,CH242-198O5,4:85931827-86135389 (Clone quality: bE198O5 on chr=4; Num_of_Contigs=5; )
SFT2D3		ENSSSCG00000015860	15:55700216-55700875		CU855997,CH242-197O1,15:55665561-55713521 (Clone quality: bE197O1 on chr=15; Num_of_Contigs=4; )
SFTA2		ENSSSCG00000001385	7:27377788-27378770	CT971577,CH242-239H1,7:27216113-27394697 (Clone quality: bE239H1 on chr=7; Num_of_Contigs=1; )
SFTPA1		ENSSSCG00000010336	14:85572641-85576858		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPA1		location ⇒	14:85574078-85573570		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPA1		location ⇒	14:85574612-85574532		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPA1		location ⇒	14:85575492-85575369		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPA1		location ⇒	14:85575944-85575748		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )

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).