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)

CHIT1		location ⇒	9:106930299-106930117		CU928698,CH242-36A5,9:106913686-107009377 (Clone quality: bE36A5 on chr=9; Num_of_Contigs=1; )
CHKA		ENSSSCG00000012889	2:3133576-3190746		CU856479,CH242-200O4,2:3088400-3194485 (Clone quality: bE200O4 on chr=2; Num_of_Contigs=4; )
CHL1		ENSSSCG00000011524	13:48016132-48088858
CHL1		location ⇒	13:48060203-48060334		FP236294,CH242-126M22,13:48050752-48060598 (Clone quality: bE126M22 on chr=13; Num_of_Contigs=5; )
CHM		ENSSSCG00000009442	11:25007261-25025006		FP236201,CH242-140F21,11:25001563-25038008 (Clone quality: bE140F21 on chr=11; Num_of_Contigs=6; )
CHM		ENSSSCG00000012463	X:67856503-67980987		FP102371,CH242-33O21,X:67849691-68016283 (Clone quality: bE33O21 on chr=X; Num_of_Contigs=2; )
CHM		ENSSSCG00000014315	2:125546729-125557469		FP089688,CH242-222D16,2:125503932-125628875 (Clone quality: bE222D16 on chr=2; Num_of_Contigs=7; )
CHM		location ⇒	X:67855033-67854975		FP102371,CH242-33O21,X:67849691-68016283 (Clone quality: bE33O21 on chr=X; Num_of_Contigs=2; )
CHM		location ⇒	X:67901257-67901182		FP102371,CH242-33O21,X:67849691-68016283 (Clone quality: bE33O21 on chr=X; Num_of_Contigs=2; )
CHM		location ⇒	X:67955673-67955462		FP102371,CH242-33O21,X:67849691-68016283 (Clone quality: bE33O21 on chr=X; Num_of_Contigs=2; )
CHM		location ⇒	X:67962386-67961997		FP102371,CH242-33O21,X:67849691-68016283 (Clone quality: bE33O21 on chr=X; Num_of_Contigs=2; )
CHML		ENSSSCG00000010844	10:12060277-12062091		FP236746,CH242-115K6,10:12056871-12062108 (Clone quality: bE115K6 on chr=10; Num_of_Contigs=10; )
CHMP2B		ENSSSCG00000011997	13:123204749-123239571		CU633644,CH242-171D11,13:123151316-123247028 (Clone quality: bE171D11 on chr=13; Num_of_Contigs=4; )
CHMP4A		ENSSSCG00000001998	7:81426795-81431185		CU019590,CH242-406B17,7:81421108-81438799 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
CHMP4B		ENSSSCG00000007272	17:39241189-39247912		CU407167,CH242-230G19,17:39238265-39289854 (Clone quality: bE230G19 on chr=17; Num_of_Contigs=9; )
CHMP4C		ENSSSCG00000006150	4:56520846-56528569		CU633211,CH242-12D19,4:56513740-56598488 (Clone quality: bE12D19 on chr=4; Num_of_Contigs=3; )
CHMP5		ENSSSCG00000010995	10:31744120-31752630		CU856468,CH242-364H6,10:31743216-31763639 (Clone quality: bE364H6 on chr=10; Num_of_Contigs=8; )
CHMP6		ENSSSCG00000017140	12:715061-718654		CU993801,CH242-26A11,12:713221-732220 (Clone quality: bE26A11 on chr=12; Num_of_Contigs=7; )
CHN1		ENSSSCG00000015971	15:75649319-75741572
CHN2		ENSSSCG00000016687	18:41598524-41717406
CHODL		ENSSSCG00000012018	13:131781216-131802686
CHORDC1		ENSSSCG00000014934	9:23202742-23339927
CHP		ENSSSCG00000004758	1:136935073-136936535		CU571034,CH242-27B2,1:136928842-136947852 (Clone quality: bE27B2 on chr=1; Num_of_Contigs=24; )
CHP		location ⇒	1:136494252-136492279		CU633507,CH242-270N10,1:136486803-136538620 (Clone quality: bE270N10 on chr=1; Num_of_Contigs=9; )
CHP		location ⇒	1:136494529-136494403		CU633507,CH242-270N10,1:136486803-136538620 (Clone quality: bE270N10 on chr=1; Num_of_Contigs=9; )
CHP		location ⇒	1:136508377-136508249		CU633507,CH242-270N10,1:136486803-136538620 (Clone quality: bE270N10 on chr=1; Num_of_Contigs=9; )
CHP		location ⇒	1:136530819-136530510		CU633507,CH242-270N10,1:136486803-136538620 (Clone quality: bE270N10 on chr=1; Num_of_Contigs=9; )
CHPT1		ENSSSCG00000000864	5:77877258-77920943
CHRAC1		ENSSSCG00000005933	4:1630826-1633644		CU570940,CH242-286B11,4:1630166-1633646 (Clone quality: bE286B11 on chr=4; Num_of_Contigs=25; )
CHRDL1		ENSSSCG00000012576	X:87874406-87996150
CHRDL2		ENSSSCG00000014843	9:8695224-8730142
CHRM2		location ⇒	2:14239088-14238814		CU467768,CH242-445K9,2:14222547-14372056 (Clone quality: bE445K9 on chr=2; Num_of_Contigs=4; )
CHRM4		ENSSSCG00000013261	2:14237793-14239232		CU467768,CH242-445K9,2:14222547-14372056 (Clone quality: bE445K9 on chr=2; Num_of_Contigs=4; )
CHRM5		ENSSSCG00000002246	7:88174816-88176414		CU633891,CH242-195C13,7:88161233-88310281 (Clone quality: bE195C13 on chr=7; Num_of_Contigs=3; )
CHRNA1		ENSSSCG00000015969	15:75611929-75617106		CU469346,CH242-447A8,15:75611326-75617202 (Clone quality: bE447A8 on chr=15; Num_of_Contigs=17; )
CHRNA10		ENSSSCG00000014796	9:5833070-5837806		CU928773,CH242-1I9,9:5824602-5854720 (Clone quality: bE1I9 on chr=9; Num_of_Contigs=1; )
CHRNA2		ENSSSCG00000009665	14:11315686-11324112
CHRNA3		ENSSSCG00000001752	7:53408570-53426370
CHRNA5		ENSSSCG00000001751	7:53390427-53404417		CT967296,CH242-156L20,7:53389713-53423755 (Clone quality: bE156L20 on chr=7; Num_of_Contigs=5; )
CHRNB2		ENSSSCG00000006545	4:99269654-99277820	CU469085,CH242-42I4,4:99200352-99380372 (Clone quality: bE42I4 on chr=4; Num_of_Contigs=1; )
CHRNB4		ENSSSCG00000001753	7:53429900-53444836		CT967296,CH242-156L20,7:53423856-53517050 (Clone quality: bE156L20 on chr=7; Num_of_Contigs=5; )
CHRND		ENSSSCG00000016287	15:125407322-125414782		CU855838,CH242-255F5,15:125392142-125414865 (Clone quality: bE255F5 on chr=15; Num_of_Contigs=16; )
CHRNE		ENSSSCG00000017909	12:49207360-49211738		FP015831,CH242-271O18,12:49169208-49243291 (Clone quality: bE271O18 on chr=12; Num_of_Contigs=4; )
CHRNG		ENSSSCG00000016288	15:125419005-125425409
CHST1		ENSSSCG00000013273	2:15057046-15058281		CU914249,CH242-221H16,2:15019477-15074226 (Clone quality: bE221H16 on chr=2; Num_of_Contigs=5; )
CHST1		location ⇒	2:15056700-15056193		CU914249,CH242-221H16,2:15019477-15074226 (Clone quality: bE221H16 on chr=2; Num_of_Contigs=5; )
CHST1		location ⇒	2:15056935-15056749		CU914249,CH242-221H16,2:15019477-15074226 (Clone quality: bE221H16 on chr=2; Num_of_Contigs=5; )
CHST1		location ⇒	2:15215941-15216138		CU695178,CH242-13O11,2:15215772-15238451 (Clone quality: bE13O11 on chr=2; Num_of_Contigs=26; )
CHST1		location ⇒	2:15216187-15216695		CU695178,CH242-13O11,2:15215772-15238451 (Clone quality: bE13O11 on chr=2; Num_of_Contigs=26; )
CHST10		ENSSSCG00000008175	3:49597731-49631933		CU407314,CH242-21N16,3:49539268-49635275 (Clone quality: bE21N16 on chr=3; 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, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).