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)

PROM1		location ⇒	8:8478440-8478864		CU929696,CH242-161H8,8:8468899-8478947 (Clone quality: bE161H8 on chr=8; Num_of_Contigs=2; )
PROM1		location ⇒	8:8482691-8482784		CU929696,CH242-161H8,8:8479048-8484613 (Clone quality: bE161H8 on chr=8; Num_of_Contigs=2; )
PROM2		ENSSSCG00000008118	3:41481639-41491244
PROS1		location ⇒	13:121532963-121533131		CU862055,CH242-32N15,13:121530052-121534616 (Clone quality: bE32N15 on chr=13; Num_of_Contigs=6; )
PROS1		location ⇒	13:121537769-121537918		CU862055,CH242-32N15,13:121534717-121547103 (Clone quality: bE32N15 on chr=13; Num_of_Contigs=6; )
PROS1		location ⇒	13:121540082-121540313		CU862055,CH242-32N15,13:121534717-121547103 (Clone quality: bE32N15 on chr=13; Num_of_Contigs=6; )
PROS1		location ⇒	13:121543700-121544179		CU862055,CH242-32N15,13:121534717-121547103 (Clone quality: bE32N15 on chr=13; Num_of_Contigs=6; )
PROSC		ENSSSCG00000015826	15:46123457-46133909		FP236525,CH242-315C20,15:46063691-46179411 (Clone quality: bE315C20 on chr=15; Num_of_Contigs=4; )
PROX1		ENSSSCG00000015584	9:122024292-122062744
PROX2		ENSSSCG00000002373	7:106318274-106328508		CT797477,CH242-140C11,7:106303131-106390499 (Clone quality: bE140C11 on chr=7; Num_of_Contigs=2; )
PRPF18		ENSSSCG00000011057	10:46056036-46112783
PRPF19		ENSSSCG00000013107	2:9267759-9276518		CU861565,CH242-480L10,2:9266479-9277312 (Clone quality: bE480L10 on chr=2; Num_of_Contigs=15; )
PRPF31		ENSSSCG00000003263	6:40543995-40560236
PRPF38A		ENSSSCG00000003858	6:113435217-113438688		CU929620,CH242-311I20,6:113433411-113451431 (Clone quality: bE311I20 on chr=6; Num_of_Contigs=11; )
PRPF38B		ENSSSCG00000006845	4:115854661-115861995		CU326386,CH242-265P14,4:115841878-115922954 (Clone quality: bE265P14 on chr=4; Num_of_Contigs=5; )
PRPF39		ENSSSCG00000004997	1:183755594-183787569		CU570961,CH242-89I4,1:183716500-183793685 (Clone quality: bE89I4 on chr=1; Num_of_Contigs=2; )
PRPF40A		ENSSSCG00000015867	15:56440871-56489468
PRPF40A		location ⇒	4:95246035-95246315		CU469040,CH242-470B17,4:95223150-95266021 (Clone quality: bE470B17 on chr=4; Num_of_Contigs=8; )
PRPF40A		location ⇒	4:95286872-95286592		CU633403,CH242-33K5,4:95266022-95329490 (Clone quality: bE33K5 on chr=4; Num_of_Contigs=5; )
PRPF40B		ENSSSCG00000000204	5:14356848-14371140
PRPF4B		ENSSSCG00000001002	7:2350771-2508253
PRPF8		ENSSSCG00000017817	12:45327326-45337611
PRPH2		ENSSSCG00000001644	7:43637359-43652035	CR956428,PigE-259M5,7:43612102-43779716 (No clone quality info on bT259M5)
PRPS1		ENSSSCG00000012560	X:86170932-86197041		FP074898,CH242-294L14,X:86138982-86203202 (Clone quality: bE294L14 on chr=X; Num_of_Contigs=4; )
PRPS2		ENSSSCG00000012116	X:8457935-8485486		FP236647,CH242-248C8,X:8407987-8522808 (Clone quality: bE248C8 on chr=X; Num_of_Contigs=1; )
PRPSAP1		ENSSSCG00000017184	12:3503944-3533869	CU466934,CH242-34E1,12:3420589-3631790 (Clone quality: bE34E1 on chr=9; Num_of_Contigs=4; )
PRPSAP2		ENSSSCG00000018049	12:56766317-56815164
PRR12		ENSSSCG00000003184	6:38288619-38314024
PRR13		ENSSSCG00000000273	5:17203786-17208521
PRR13		location ⇒	X:64206174-64206323		FP102824,CH242-238J6,X:64204292-64207380 (Clone quality: bE238J6 on chr=X; Num_of_Contigs=8; )
PRR14		ENSSSCG00000007790	3:16388050-16392935
PRR15		ENSSSCG00000016686	18:41568941-41569318		CU467534,CH242-219M9,18:41561490-41582954 (Clone quality: bE219M9 on chr=18; Num_of_Contigs=9; )
PRR16		ENSSSCG00000014229	2:112824775-112825533		CU928775,CH242-293N19,2:112820510-112826964 (Clone quality: bE293N19 on chr=2; Num_of_Contigs=6; )
PRR18		ENSSSCG00000004021	1:2649432-2919535
PRR3		ENSSSCG00000001355	7:26824132-26825028		FP067362,CH242-312H17,7:26814051-26826407 (Clone quality: bE312H17 on chr=7; Num_of_Contigs=15; )
PRR3		ENSSSCG00000001371	7:27073764-27079736	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
PRR3		ENSSSCG00000001345	7:26667785-26673758	CU498826,CH242-119D24,7:26553813-26728014 (Clone quality: bE119D24 on chr=7; Num_of_Contigs=31; )
PRR5L		ENSSSCG00000013292	2:23226697-23310051	CU861593,CH242-189L23,2:23199027-23396640 (Clone quality: bE189L23 on chr=2; Num_of_Contigs=5; )
PRRC1		ENSSSCG00000014252	2:118041354-118119335
PRRG1		ENSSSCG00000012225	X:32731785-32732267	CU928355,CH242-280I8,X:32692574-32732731 (Clone quality: bE280I8 on chr=X; Num_of_Contigs=8; )
PRRG4		ENSSSCG00000013313	2:26215319-26230799	CU928434,CH242-212M21,2:26147327-26334640 (Clone quality: bE212M21 on chr=2; Num_of_Contigs=7; )
PRRT4		ENSSSCG00000011561	13:55391284-55393572		CU464019,CH242-82C2,13:55391275-55403795 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
PRRX1		ENSSSCG00000006279	4:83493350-83562853
PRRX2		ENSSSCG00000005680	1:284579439-284791340
PRSS11		ENSSSCG00000010703	14:138468111-138528927
PRSS11		location ⇒	14:138496754-138496959		CU469121,CH242-146A14,14:138465620-138500960 (Clone quality: bE146A14 on chr=14; Num_of_Contigs=3; )
PRSS11		location ⇒	14:138518584-138518781		CU469326,CH242-256O2,14:138500961-138565414 (Clone quality: bE256O2 on chr=14; Num_of_Contigs=3; )
PRSS11		location ⇒	14:138522374-138522496		CU469326,CH242-256O2,14:138500961-138565414 (Clone quality: bE256O2 on chr=14; Num_of_Contigs=3; )
PRSS11		location ⇒	14:138528208-138528922		CU469326,CH242-256O2,14:138500961-138565414 (Clone quality: bE256O2 on chr=14; Num_of_Contigs=3; )
PRSS12		ENSSSCG00000009114	8:90700850-90774311		CU570724,CH242-203K14,8:90680257-90831171 (Clone quality: bE203K14 on chr=8; Num_of_Contigs=1; )

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).