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)

PITRM1		ENSSSCG00000011157	10:63284254-63301383
PITX2		ENSSSCG00000009131	8:95915280-95917240
PITX2		location ⇒	8:95915127-95914595		CU463881,CH242-262D4,8:95914423-95916588 (Clone quality: bE262D4 on chr=8; Num_of_Contigs=10; )
PITX2		location ⇒	8:95915844-95915186		CU463881,CH242-262D4,8:95914423-95916588 (Clone quality: bE262D4 on chr=8; Num_of_Contigs=10; )
PITX3		ENSSSCG00000010578	14:118212599-118214207		CU407032,CH242-176B16,14:118180747-118362423 (Clone quality: bE176B16 on chr=14; Num_of_Contigs=3; )
PIWIL1		ENSSSCG00000009749	14:24814875-24841510
PIWIL4		ENSSSCG00000014959	9:27041966-27089566
PJA1		location ⇒	X:56006310-56007419		CU462993,CH242-406N9,X:56005231-56035451 (Clone quality: bE406N9 on chr=X; Num_of_Contigs=7; )
PJA1		location ⇒	X:56007476-56008553		CU462993,CH242-406N9,X:56005231-56035451 (Clone quality: bE406N9 on chr=X; Num_of_Contigs=7; )
PJA1		location ⇒	X:56251693-56250616		CU694617,CH242-377A22,X:56233342-56272145 (Clone quality: bE377A22 on chr=X; Num_of_Contigs=2; )
PJA1		location ⇒	X:56252859-56251750		CU694617,CH242-377A22,X:56233342-56272145 (Clone quality: bE377A22 on chr=X; Num_of_Contigs=2; )
PJA2		ENSSSCG00000014194	2:102853440-102856104		CU466452,CH242-234F21,2:102848628-102887724 (Clone quality: bE234F21 on chr=2; Num_of_Contigs=6; )
PK4P		ENSSSCG00000015878	15:61058427-61119399
PKD1		ENSSSCG00000008041	3:36451941-36500695
PKD1		location ⇒	3:36466225-36466078		FP102350,CH242-207G4,3:36428189-36469809 (Clone quality: bE207G4 on chr=3; Num_of_Contigs=8; )
PKD1		location ⇒	3:36466493-36466319		FP102350,CH242-207G4,3:36428189-36469809 (Clone quality: bE207G4 on chr=3; Num_of_Contigs=8; )
PKD1		location ⇒	3:36467897-36467732		FP102350,CH242-207G4,3:36428189-36469809 (Clone quality: bE207G4 on chr=3; Num_of_Contigs=8; )
PKD1L3		ENSSSCG00000002744	6:10651542-10683261
PKD2		ENSSSCG00000009217	8:112520831-112574248
PKD2L1		ENSSSCG00000010552	14:116267783-116303215		CT827831,CH242-224L12,14:116263324-116390345 (Clone quality: bE224L12 on chr=14; Num_of_Contigs=2; )
PKDREJ		ENSSSCG00000000004	5:115309-121710		FP016092,CH242-185O3,5:114996-122369 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
PKHD1		ENSSSCG00000006025	4:27723083-27918235
PKHD1		ENSSSCG00000001746	7:52966007-53029118
PKHD1		location ⇒	7:52981107-52980805		CU467028,CH242-362P8,7:52979932-52984373 (Clone quality: bE362P8 on chr=7; Num_of_Contigs=9; )
PKHD1L1		ENSSSCG00000006025	4:27723083-27918235
PKIA		ENSSSCG00000006163	4:59928788-60032301
PKIA		location ⇒	4:59930247-59926802		CU469062,CH242-83E10,4:59805393-59988276 (Clone quality: bE83E10 on chr=4; Num_of_Contigs=1; )
PKIA		location ⇒	4:59933873-59933694		CU469062,CH242-83E10,4:59805393-59988276 (Clone quality: bE83E10 on chr=4; Num_of_Contigs=1; )
PKIB		ENSSSCG00000004236	1:41415699-41446444
PKM2		ENSSSCG00000001930	7:66373822-66399229		CU468866,CH242-150C14,7:66357007-66467327 (Clone quality: bE150C14 on chr=7; Num_of_Contigs=3; )
PKN1		ENSSSCG00000013783	2:57306942-57311220		FP103015,CH242-135B13,2:57305111-57311746 (Clone quality: bE135B13 on chr=2; Num_of_Contigs=14; )
PKN2		ENSSSCG00000006927	4:132238495-132316018		CU179630,CH242-295H8,4:132189179-132328462 (Clone quality: bE295H8 on chr=4; Num_of_Contigs=2; )
PKN3		ENSSSCG00000005657	1:283750917-283762816		FP236218,CH242-328B23,1:283737933-283763718 (Clone quality: bE328B23 on chr=1; Num_of_Contigs=4; )
PKNOX2		ENSSSCG00000015211	9:51037411-51079261
PKP2		ENSSSCG00000000528	5:40611156-40675368
PKP4		location ⇒	15:61067975-61068168		CU469217,CH242-509I9,15:61066802-61075232 (Clone quality: bE509I9 on chr=15; Num_of_Contigs=19; )
PKP4		location ⇒	15:61070049-61070268		CU469217,CH242-509I9,15:61066802-61075232 (Clone quality: bE509I9 on chr=15; Num_of_Contigs=19; )
PKP4		location ⇒	15:61078988-61079125		CU469217,CH242-509I9,15:61075333-61084699 (Clone quality: bE509I9 on chr=15; Num_of_Contigs=19; )
PKP4		location ⇒	15:61080213-61080403		CU469217,CH242-509I9,15:61075333-61084699 (Clone quality: bE509I9 on chr=15; Num_of_Contigs=19; )
PLA2G12A		ENSSSCG00000009139	8:96645687-96674838		CU694741,CH242-514C2,8:96640360-96675254 (Clone quality: bE514C2 on chr=8; Num_of_Contigs=10; )
PLA2G12B		ENSSSCG00000010291	14:78985086-79009484		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
PLA2G12B		location ⇒	14:78994425-78994260		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
PLA2G12B		location ⇒	14:78997401-78997312		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
PLA2G12B		location ⇒	14:79009352-79009124		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
PLA2G15		ENSSSCG00000002765	6:12760583-12832697
PLA2G16		ENSSSCG00000013055	2:6945295-6973514
PLA2G2A		ENSSSCG00000003494	6:53636266-53675696
PLA2G2A		location ⇒	6:53636266-53636463		FP016073,CH242-147M21,6:53585388-53637720 (Clone quality: bE147M21 on chr=6; Num_of_Contigs=9; )
PLA2G2A		location ⇒	6:53663892-53663988		FP016073,CH242-147M21,6:53645215-53687668 (Clone quality: bE147M21 on chr=6; Num_of_Contigs=9; )
PLA2G2A		location ⇒	6:53672781-53672926		FP016073,CH242-147M21,6:53645215-53687668 (Clone quality: bE147M21 on chr=6; Num_of_Contigs=9; )

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).