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)

PIK3C3		location ⇒	6:87897304-87897519		CU457391,CH242-109O8,6:87850191-87940130 (Clone quality: bE109O8 on chr=6; Num_of_Contigs=2; )
PIK3CD		ENSSSCG00000003395	6:47123924-47158575		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PIK3CD		location ⇒	6:47123924-47124014		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PIK3CD		location ⇒	6:47144967-47145143		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PIK3CD		location ⇒	6:47148002-47148233		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PIK3CD		location ⇒	6:47148440-47148518		CU929791,CH242-402I11,6:47086277-47182066 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
PIK3CG		ENSSSCG00000015437	9:99816448-99891579
PIK3CG		location ⇒	9:99816630-99816855		CU928977,CH242-109A3,9:99815622-99821327 (Clone quality: bE109A3 on chr=9; Num_of_Contigs=19; )
PIK3CG		location ⇒	9:99891420-99891580		CU928977,CH242-109A3,9:99889521-99892087 (Clone quality: bE109A3 on chr=9; Num_of_Contigs=19; )
PIK3CG		location ⇒	9:99901797-99901124		CU928977,CH242-109A3,9:99898223-99909333 (Clone quality: bE109A3 on chr=9; Num_of_Contigs=19; )
PIK3CG		location ⇒	9:99921222-99922712
PIK3IP1		ENSSSCG00000010026	14:48927007-48936268	CT573044,XX-BE156J14,14:48785782-48970332 (No clone quality info on bE156J14)
PIK3R1		ENSSSCG00000016958	16:44114529-44120792		CU672251,CH242-378F17,16:44109364-44123105 (Clone quality: bE378F17 on chr=16; Num_of_Contigs=6; )
PIK3R1		location ⇒	16:44000255-43998954		FP017209,CH242-199G10,16:43979770-44011000 (Clone quality: bE199G10 on chr=16; Num_of_Contigs=3; )
PIK3R1		location ⇒	16:44011437-44011246		FP017209,CH242-199G10,16:44011101-44031814 (Clone quality: bE199G10 on chr=16; Num_of_Contigs=3; )
PIK3R1		location ⇒	16:44114489-44113441		CU672251,CH242-378F17,16:44109364-44123105 (Clone quality: bE378F17 on chr=16; Num_of_Contigs=6; )
PIK3R1		location ⇒	16:44116974-44116648		CU672251,CH242-378F17,16:44109364-44123105 (Clone quality: bE378F17 on chr=16; Num_of_Contigs=6; )
PIK3R2		ENSSSCG00000013900	2:62387523-62399642		CU915655,CH242-228H4,2:62376356-62402307 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
PIK3R2		location ⇒	2:62397240-62397375		CU915655,CH242-228H4,2:62376356-62402307 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
PIK3R2		location ⇒	2:62398187-62398258		CU915655,CH242-228H4,2:62376356-62402307 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
PIK3R2		location ⇒	2:62398425-62398596		CU915655,CH242-228H4,2:62376356-62402307 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
PIK3R2		location ⇒	2:62398944-62399157		CU915655,CH242-228H4,2:62376356-62402307 (Clone quality: bE228H4 on chr=2; Num_of_Contigs=13; )
PIK3R3		ENSSSCG00000003909	6:118327752-118488382
PIK3R3		location ⇒	6:118490532-118491883		CU442756,CH242-95G1,6:118479333-118621567 (Clone quality: bE95G1 on chr=6; Num_of_Contigs=2; )
PIK3R4		ENSSSCG00000011184	13:1379194-1385231		CU469211,CH242-358D17,13:1378387-1387263 (Clone quality: bE358D17 on chr=13; Num_of_Contigs=18; )
PIK3R5		ENSSSCG00000017991	12:50996662-51184210
PIK3R5		location ⇒	12:232736-232655		FP236791,CH242-196C17,12:232547-235496 (Clone quality: bE196C17 on chr=12; Num_of_Contigs=8; )
PIK3R5		location ⇒	12:278001-277936		FP236791,CH242-196C17,12:261191-287454 (Clone quality: bE196C17 on chr=12; Num_of_Contigs=8; )
PIK3R5		location ⇒	12:3018004-3018117		FP236793,CH242-280A10,12:3014388-3023903 (Clone quality: bE280A10 on chr=12; Num_of_Contigs=11; )
PIK3R5		location ⇒	12:43988-43923	FP085448,CH242-272C22,12:1-58755 (Clone quality: bE272C22 on chr=12; Num_of_Contigs=8; )
PIK3R6		ENSSSCG00000017990	12:50927246-50986874
PIKFYVE		ENSSSCG00000016147	15:104283524-104428800
PILRB		location ⇒	3:6595514-6595407		CU464007,CH242-351O3,3:6593493-6614733 (Clone quality: bE351O3 on chr=3; Num_of_Contigs=5; )
PIM1		ENSSSCG00000013526	2:49391167-49411637		FP089464,CH242-231P22,2:49368415-49462890 (Clone quality: bE231P22 on chr=2; Num_of_Contigs=4; )
PIM1		ENSSSCG00000001573	7:37421502-37425586
PIM1		location ⇒	7:37425488-37426026		CT954214,CH242-328K12,7:37421504-37477076 (Clone quality: bE328K12 on chr=7; Num_of_Contigs=3; )
PIN1		ENSSSCG00000010457	14:106413724-106495706
PIN1		ENSSSCG00000013669	2:53629449-53643038		CU694567,CH242-210G21,2:53585840-53657076 (Clone quality: bE210G21 on chr=2; Num_of_Contigs=8; )
PINK1		ENSSSCG00000003506	6:54215030-54329215
PIP4K2C		ENSSSCG00000000436	5:21698703-21709799		CU896550,CH242-139E23,5:21693100-21710229 (Clone quality: bE139E23 on chr=5; Num_of_Contigs=9; )
PIP5K1C		ENSSSCG00000013490	2:48179661-48362695
PIP5K2A		ENSSSCG00000011079	10:49742656-49925739
PIP5KL1		ENSSSCG00000005629	1:282896657-282900139		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
PIPOX		ENSSSCG00000017781	12:42986321-42999160		CU856290,CH242-166L10,12:42944694-43045711 (Clone quality: bE166L10 on chr=12; Num_of_Contigs=5; )
PIR		ENSSSCG00000012136	X:11204005-11301184
PISD		ENSSSCG00000010032	14:49189135-49226777
PITPNB		ENSSSCG00000009967	14:45775702-45838506		CT990610,CH242-129E1,14:45739276-45849595 (Clone quality: bE129E1 on chr=14; Num_of_Contigs=4; )
PITPNC1		ENSSSCG00000017274	12:11749168-12020183
PITPNM1		ENSSSCG00000012903	2:3411264-3423542		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
PITPNM2		ENSSSCG00000009781	14:29870515-29958520

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, 2201-21

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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).