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)

C14orf21		ENSSSCG00000001990	7:81326690-81333052		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
C14orf37		ENSSSCG00000005071	1:196157688-196203628		CU582858,CH242-38E9,1:196156628-196206222 (Clone quality: bE38E9 on chr=1; Num_of_Contigs=2; )
C14orf39		ENSSSCG00000005085	1:198153332-198215581
C14orf4		ENSSSCG00000002392	7:108114318-108116669		CU012040,CH242-394H10,7:108038511-108238028 (Clone quality: bE394H10 on chr=7; Num_of_Contigs=3; )
C14orf43		ENSSSCG00000002350	7:105088039-105091430		CT943655,CH242-523I15,7:105084418-105139300 (Clone quality: bE523I15 on chr=7; Num_of_Contigs=3; )
C14orf45		ENSSSCG00000002356	7:105330779-105381906		CT797481,CH242-31K14,7:105227853-105414617 (Clone quality: bE31K14 on chr=7; Num_of_Contigs=1; )
C14orf49		ENSSSCG00000002495	7:125501939-125558410
C14orf50		ENSSSCG00000002275	7:97095317-97132727	CT842159,CH242-270B4,7:97057191-97273886 (Clone quality: bE270B4 on chr=7; Num_of_Contigs=6; )
C14orf54		ENSSSCG00000002286	7:99317462-99341868		CT737407,CH242-215J18,7:99238532-99347797 (Clone quality: bE215J18 on chr=7; Num_of_Contigs=2; )
C14orf73		ENSSSCG00000002521	7:130698108-130707021		CU467770,CH242-452K19,7:130694368-130736902 (Clone quality: bE452K19 on chr=7; Num_of_Contigs=13; )
C14orf79		ENSSSCG00000002556	7:133166385-133222232
C15orf23		ENSSSCG00000004775	1:137383759-137396279		CU234165,CH242-252B18,1:137339871-137454558 (Clone quality: bE252B18 on chr=1; Num_of_Contigs=2; )
C15orf26		ENSSSCG00000001786	7:56064191-56076877		CT841542,CH242-241P18,7:55970950-56105857 (Clone quality: bE241P18 on chr=7; Num_of_Contigs=3; )
C15orf27		ENSSSCG00000001863	7:61729358-61804243
C15orf29		ENSSSCG00000002245	7:88062025-88122264		CU407046,CH242-221M18,7:88060959-88156232 (Clone quality: bE221M18 on chr=7; Num_of_Contigs=3; )
C15orf33		ENSSSCG00000004648	1:127441812-127457952
C15orf37		ENSSSCG00000008822	8:32800767-32800949		CU915396,CH242-250L20,8:32791869-32806078 (Clone quality: bE250L20 on chr=8; Num_of_Contigs=5; )
C15orf38		ENSSSCG00000001850	7:60820868-60903101
C15orf39		ENSSSCG00000001885	7:63638347-63640883		CT990537,CH242-196K6,7:63614161-63652927 (Clone quality: bE196K6 on chr=7; Num_of_Contigs=8; )
C15orf40		ENSSSCG00000001802	7:57974263-57979660		CU407315,CH242-258B16,7:57856098-58033288 (Clone quality: bE258B16 on chr=7; Num_of_Contigs=2; )
C15orf42		ENSSSCG00000001842	7:60573031-60629259		CT990467,CH242-141I20,7:60495252-60643606 (Clone quality: bE141I20 on chr=7; Num_of_Contigs=3; )
C15orf43		ENSSSCG00000004680	1:132526077-132554898
C15orf44		ENSSSCG00000004936	1:170672165-170706347
C15orf48		ENSSSCG00000004670	1:131951949-131955414		CU457441,CH242-247F23,1:131950006-132050038 (Clone quality: bE247F23 on chr=1; Num_of_Contigs=7; )
C15orf58		ENSSSCG00000001859	7:61394207-61395361		CU571213,CH242-243O5,7:61382831-61401542 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
C15orf59		ENSSSCG00000001916	7:65115126-65126323		CU137731,CH242-449C4,7:65113175-65198803 (Clone quality: bE449C4 on chr=7; Num_of_Contigs=5; )
C15orf60		ENSSSCG00000001919	7:65287253-65390327
C15orf61		ENSSSCG00000004954	1:172599737-172604587		CU311196,CH242-507P4,1:172538538-172670822 (Clone quality: bE507P4 on chr=1; Num_of_Contigs=3; )
C15orf62		ENSSSCG00000004763	1:137053346-137053873		CU633257,CH242-257P7,1:137003112-137140964 (Clone quality: bE257P7 on chr=1; Num_of_Contigs=3; )
C16orf11		ENSSSCG00000007989	3:35548373-35553402
C16orf14		ENSSSCG00000007995	3:35636587-35641426		CU928306,CH242-153F7,3:35635547-35642049 (Clone quality: bE153F7 on chr=3; Num_of_Contigs=18; )
C16orf28		ENSSSCG00000008027	3:36183590-36198358		CU467714,CH242-272G6,3:36177390-36200259 (Clone quality: bE272G6 on chr=3; Num_of_Contigs=16; )
C16orf30		ENSSSCG00000008021	3:36031752-36043933		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
C16orf30		location ⇒	3:35586351-35586412		CU928306,CH242-153F7,3:35586053-35594985 (Clone quality: bE153F7 on chr=3; Num_of_Contigs=18; )
C16orf30		location ⇒	3:36032162-36031944		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
C16orf30		location ⇒	3:36039654-36039497		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
C16orf42		ENSSSCG00000008030	3:36221999-36224557		CU467714,CH242-272G6,3:36207929-36224650 (Clone quality: bE272G6 on chr=3; Num_of_Contigs=16; )
C16orf5		ENSSSCG00000007941	3:33833325-33856201		CU928821,CH242-271C18,3:33828913-33892865 (Clone quality: bE271C18 on chr=3; Num_of_Contigs=7; )
C16orf57		ENSSSCG00000002807	6:19688577-19705031
C16orf58		ENSSSCG00000007753	3:15591019-15598365		CU915579,CH242-114I19,3:15590161-15599077 (Clone quality: bE114I19 on chr=3; Num_of_Contigs=28; )
C16orf59		ENSSSCG00000008055	3:36790332-36794394
C16orf65		ENSSSCG00000007844	3:21821208-21835127
C16orf68		ENSSSCG00000007914	3:30115000-30133102
C16orf68		location ⇒	3:30115073-30115004		CU914444,CH242-80G22,3:30114999-30122911 (Clone quality: bE80G22 on chr=3; Num_of_Contigs=12; )
C16orf68		location ⇒	3:30119291-30119214		CU914444,CH242-80G22,3:30114999-30122911 (Clone quality: bE80G22 on chr=3; Num_of_Contigs=12; )
C16orf68		location ⇒	3:30122291-30122144		CU914444,CH242-80G22,3:30114999-30122911 (Clone quality: bE80G22 on chr=3; Num_of_Contigs=12; )
C16orf71		ENSSSCG00000007935	3:33676099-33685774		CU929765,CH242-314I20,3:33640963-33685776 (Clone quality: bE314I20 on chr=3; Num_of_Contigs=8; )
C16orf72		ENSSSCG00000012715	X:112735284-112736114	FP015841,CH242-141J21,X:112697081-112759101 (Clone quality: bE141J21 on chr=X; Num_of_Contigs=2; )
C16orf74		ENSSSCG00000002662	6:1808261-1810310		FP102522,CH242-14M1,6:1801177-1834779 (Clone quality: bE14M1 on chr=6; Num_of_Contigs=5; )
C16orf75		ENSSSCG00000007900	3:28395589-28400121		FP102689,CH242-377M20,3:28376954-28403624 (Clone quality: bE377M20 on chr=3; Num_of_Contigs=4; )

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).