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)

SERPINF2		location ⇒	12:45426434-45426289		FP016227,CH242-99J5,12:45391979-45428198 (Clone quality: bE99J5 on chr=12; Num_of_Contigs=5; )
SERPING1		ENSSSCG00000013181	2:11329646-11344205		CU914175,CH242-140O21,2:11317953-11369705 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
SERPING1		location ⇒	2:11330145-11329676		CU914175,CH242-140O21,2:11317953-11369705 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
SERPING1		location ⇒	2:11331484-11331263		CU914175,CH242-140O21,2:11317953-11369705 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
SERPING1		location ⇒	2:11337948-11337741		CU914175,CH242-140O21,2:11317953-11369705 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
SERPING1		location ⇒	2:11342625-11342158		CU914175,CH242-140O21,2:11317953-11369705 (Clone quality: bE140O21 on chr=2; Num_of_Contigs=3; )
SERPINH1		ENSSSCG00000014859	9:9465586-9469980		CU467786,CH242-510E3,9:9464831-9473065 (Clone quality: bE510E3 on chr=9; Num_of_Contigs=17; )
SERPINH1		location ⇒	9:9465586-9465683		CU467786,CH242-510E3,9:9464831-9473065 (Clone quality: bE510E3 on chr=9; Num_of_Contigs=17; )
SERPINH1		location ⇒	9:9465782-9466017		CU467786,CH242-510E3,9:9464831-9473065 (Clone quality: bE510E3 on chr=9; Num_of_Contigs=17; )
SERPINH1		location ⇒	9:9469674-9470047		CU467786,CH242-510E3,9:9464831-9473065 (Clone quality: bE510E3 on chr=9; Num_of_Contigs=17; )
SERPINH1		location ⇒	9:9470602-9470669		CU467786,CH242-510E3,9:9464831-9473065 (Clone quality: bE510E3 on chr=9; Num_of_Contigs=17; )
SERPINI1		ENSSSCG00000011740	13:81597475-81675246
SERPINI1		location ⇒	13:81644164-81644435		CU469054,CH242-68P3,13:81627192-81650516 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
SERPINI1		location ⇒	13:81646015-81646248		CU469054,CH242-68P3,13:81627192-81650516 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
SERPINI1		location ⇒	13:81649868-81650075		CU469054,CH242-68P3,13:81627192-81650516 (Clone quality: bE68P3 on chr=13; Num_of_Contigs=4; )
SERPINI1		location ⇒	13:81674914-81675240		CU466302,CH242-510M3,13:81660153-81707876 (Clone quality: bE510M3 on chr=13; Num_of_Contigs=6; )
SERPINI2		ENSSSCG00000011737	13:81345516-81378018		CU582954,CH242-37M21,13:81344340-81513789 (Clone quality: bE37M21 on chr=13; Num_of_Contigs=1; )
SERPINI2		location ⇒	13:81353700-81353613		CU582954,CH242-37M21,13:81344340-81513789 (Clone quality: bE37M21 on chr=13; Num_of_Contigs=1; )
SERPINI2		location ⇒	13:81357876-81357778		CU582954,CH242-37M21,13:81344340-81513789 (Clone quality: bE37M21 on chr=13; Num_of_Contigs=1; )
SERTAD2		ENSSSCG00000008362	3:71232949-71233887		CU467929,CH242-297N18,3:71213957-71263753 (Clone quality: bE297N18 on chr=3; Num_of_Contigs=5; )
SERTAD4		ENSSSCG00000015608	9:125033703-125038575		CU466401,CH242-418L12,9:124954187-125041752 (Clone quality: bE418L12 on chr=9; Num_of_Contigs=2; )
SESN1		ENSSSCG00000004390	1:78676980-78690440		CU407267,CH242-470M3,1:78675645-78694783 (Clone quality: bE470M3 on chr=1; Num_of_Contigs=16; )
SESN2		ENSSSCG00000003624	6:61926695-61944977
SESN3		ENSSSCG00000014966	9:27644175-27668504		FP102840,CH242-43K12,9:27642367-27684877 (Clone quality: bE43K12 on chr=9; Num_of_Contigs=10; )
SESTD1		ENSSSCG00000016005	15:79859147-79957169
SET		ENSSSCG00000005656	1:283731663-283744686
SETBP1		ENSSSCG00000004490	1:98347915-98452067
SETD1A		ENSSSCG00000007782	3:16163499-16186521		FP102303,CH242-232B18,3:16147191-16217934 (Clone quality: bE232B18 on chr=3; Num_of_Contigs=7; )
SETD1B		ENSSSCG00000009806	14:30918308-30939205		CT737291,CH242-160P22,14:30791235-30951915 (Clone quality: bE160P22 on chr=14; Num_of_Contigs=1; )
SETD3		ENSSSCG00000002508	7:129696810-129770062	CT826393,CH242-246E17,7:129575311-129780704 (Clone quality: bE246E17 on chr=7; Num_of_Contigs=5; )
SETD5		ENSSSCG00000011540	13:54816916-55014949
SETD6		ENSSSCG00000002800	6:19327230-19331455		FP236673,CH242-274G15,6:19307220-19353552 (Clone quality: bE274G15 on chr=6; Num_of_Contigs=4; )
SETD8		ENSSSCG00000009777	14:29690784-29703678
SETDB1		ENSSSCG00000006645	4:102216132-102248007
SETDB2		ENSSSCG00000009395	11:18161967-18190937		CU633573,CH242-275C14,11:18094257-18194483 (Clone quality: bE275C14 on chr=11; Num_of_Contigs=2; )
SETX		ENSSSCG00000005724	1:287704636-287806356
SEZ6		ENSSSCG00000017780	12:42909116-42932113
SEZ6L		ENSSSCG00000009958	14:44545677-44621675		CU406993,CH242-439F22,14:44514038-44633678 (Clone quality: bE439F22 on chr=14; Num_of_Contigs=2; )
SF-1		ENSSSCG00000005588	1:279932203-279946880		CU633730,CH242-82E3,1:279932040-279989993 (Clone quality: bE82E3 on chr=1; Num_of_Contigs=5; )
SF-1		location ⇒	1:279940574-279939945		CU633730,CH242-82E3,1:279932040-279989993 (Clone quality: bE82E3 on chr=1; Num_of_Contigs=5; )
SF-1		location ⇒	1:279943565-279942845		CU633730,CH242-82E3,1:279932040-279989993 (Clone quality: bE82E3 on chr=1; Num_of_Contigs=5; )
SF-1		location ⇒	1:280125235-280124603		CU633730,CH242-82E3,1:280090425-280133791 (Clone quality: bE82E3 on chr=1; Num_of_Contigs=5; )
SF-1		location ⇒	1:280125534-280125271		CU633730,CH242-82E3,1:280090425-280133791 (Clone quality: bE82E3 on chr=1; Num_of_Contigs=5; )
SF1		ENSSSCG00000013021	2:5792161-5805583
SF1		location ⇒	2:5792039-5792191	FP101995,CH242-228D7,2:5787789-5792460 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
SF1		location ⇒	2:5793964-5794093	FP101995,CH242-228D7,2:5792561-5821026 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
SF1		location ⇒	2:5796785-5796864	FP101995,CH242-228D7,2:5792561-5821026 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
SF1		location ⇒	2:5799911-5800067	FP101995,CH242-228D7,2:5792561-5821026 (Clone quality: bE228D7 on chr=2; Num_of_Contigs=13; )
SF3A1		ENSSSCG00000010002	14:48124657-48144514
SF3A2		ENSSSCG00000013454	2:47046745-47056608

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).