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)

SIRPB1		location ⇒	17:35117528-35117210		CU076083,CH242-165N9,17:35094633-35142680 (Clone quality: bE165N9 on chr=17; Num_of_Contigs=11; )
SIRPB1		location ⇒	17:35223250-35222932		CU407174,CH242-240D14,17:35216522-35282296 (Clone quality: bE240D14 on chr=17; Num_of_Contigs=11; )
SIRPB1		location ⇒	17:35248982-35248664		CU407174,CH242-240D14,17:35216522-35282296 (Clone quality: bE240D14 on chr=17; Num_of_Contigs=11; )
SIRPB1		location ⇒	17:35480164-35479846		CU855972,CH242-152H19,17:35476390-35490184 (Clone quality: bE152H19 on chr=17; Num_of_Contigs=30; )
SIRPB2		ENSSSCG00000007185	17:35425579-35435570
SIRPB2		ENSSSCG00000007185	17:35425579-35435570
SIRPD		ENSSSCG00000007182	17:35200771-35208882		CU407174,CH242-240D14,17:35171298-35216421 (Clone quality: bE240D14 on chr=17; Num_of_Contigs=11; )
SIRPD		ENSSSCG00000007182	17:35200771-35208882		CU407174,CH242-240D14,17:35171298-35216421 (Clone quality: bE240D14 on chr=17; Num_of_Contigs=11; )
SIRPG		location ⇒	17:35479885-35479846		CU855972,CH242-152H19,17:35476390-35490184 (Clone quality: bE152H19 on chr=17; Num_of_Contigs=30; )
SIRT1		ENSSSCG00000010235	14:74220079-74245927		CT997807,CH242-507P18,14:74104999-74249590 (Clone quality: bE507P18 on chr=14; Num_of_Contigs=4; )
SIRT3		ENSSSCG00000014558	2:139842569-139858659		CU928488,CH242-163I11,2:139819049-139956868 (Clone quality: bE163I11 on chr=2; Num_of_Contigs=2; )
SIRT4		ENSSSCG00000009901	14:40430181-40439002
SIRT5		ENSSSCG00000001055	7:9985118-10185983
SIRT6		ENSSSCG00000013502	2:48514141-48515720		CU929466,CH242-60A20,2:48498879-48517822 (Clone quality: bE60A20 on chr=2; Num_of_Contigs=5; )
SIT1		ENSSSCG00000005312	1:247464276-247465700		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
SIT1		location ⇒	1:247464862-247464443		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
SIT1		location ⇒	1:247465004-247464939		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
SIT1		location ⇒	1:247465383-247465245		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
SIT1		location ⇒	1:247465698-247465490		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
SIVA		location ⇒	2:60014956-60015394		CU915718,CH242-156C19,2:60006607-60065169 (Clone quality: bE156C19 on chr=2; Num_of_Contigs=6; )
SIX1		ENSSSCG00000005087	1:198366654-198369555		CU462967,CH242-442C15,1:198336966-198395017 (Clone quality: bE442C15 on chr=1; Num_of_Contigs=2; )
SIX2		ENSSSCG00000008446	3:88812052-88815064		FP067345,CH242-458A5,3:88804366-88815138 (Clone quality: bE458A5 on chr=3; Num_of_Contigs=6; )
SIX4		ENSSSCG00000005089	1:198419169-198427593		CU855869,CH242-339M6,1:198395018-198475768 (Clone quality: bE339M6 on chr=1; Num_of_Contigs=4; )
SIX6		ENSSSCG00000005086	1:198242930-198245057		CU462967,CH242-442C15,1:198238711-198336865 (Clone quality: bE442C15 on chr=1; Num_of_Contigs=2; )
SKAP1		ENSSSCG00000017527	12:21831008-21883082		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SKAP1		location ⇒	12:21840609-21840743		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SKAP1		location ⇒	12:21859140-21859243		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SKAP1		location ⇒	12:21880793-21880904		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SKAP1		location ⇒	12:21882987-21883082		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SKAP2		ENSSSCG00000016708	18:44439045-44669864
SKIIP		location ⇒	8:67034638-67034604		FP016091,CH242-139K9,8:67021247-67035165 (Clone quality: bE139K9 on chr=8; Num_of_Contigs=7; )
SKIL		ENSSSCG00000011746	13:83042624-83098074
SKIV2L		ENSSSCG00000001424	7:27869040-27879647	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
SKIV2L2		ENSSSCG00000016911	16:32052023-32232504
SKP2		ENSSSCG00000016835	16:18868174-18905906	CU856110,CH242-36H10,16:18824515-19007053 (Clone quality: bE36H10 on chr=16; Num_of_Contigs=2; )
SLA		ENSSSCG00000001396	7:27580187-27583921
SLA		ENSSSCG00000001228	7:24434481-24435039		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA		ENSSSCG00000001231	7:24498283-24532919
SLA		ENSSSCG00000001341	7:26558428-26569310	CU498826,CH242-119D24,7:26553813-26728014 (Clone quality: bE119D24 on chr=7; Num_of_Contigs=31; )
SLA		ENSSSCG00000001398	7:27604072-27608114	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
SLA		ENSSSCG00000005949	4:7264040-7285290		CU469018,CH242-373B14,4:7253315-7292353 (Clone quality: bE373B14 on chr=4; Num_of_Contigs=10; )
SLA		ENSSSCG00000001459	7:29301032-29308499	CU633196,CH242-203E5,7:29272940-29352095 (Clone quality: bE203E5 on chr=7; Num_of_Contigs=1; )
SLA		ENSSSCG00000001457	7:29239625-29247871	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA		ENSSSCG00000001455	7:29171940-29184604	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA		ENSSSCG00000001453	7:29095605-29101239	CU468849,CH242-213K14,7:29079506-29272939 (Clone quality: bE213K14 on chr=7; Num_of_Contigs=6; )
SLA-1		ENSSSCG00000001231	7:24498283-24532919
SLA-1		ENSSSCG00000001229	7:24459993-24463671		FP085552,CH242-74M17,7:24423533-24504970 (Clone quality: bE74M17 on chr=7; Num_of_Contigs=9; )
SLA-1*		location ⇒	7:4426-4309		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-1*		location ⇒	7:4665-4758		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
SLA-1*		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )

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).