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)

PRDM5		ENSSSCG00000009101	8:88779615-88866662
PRDM8		ENSSSCG00000009255	8:118701381-118703793		FP103094,CH242-235G2,8:118699918-118703794 (Clone quality: bE235G2 on chr=8; Num_of_Contigs=16; )
PRDX1		ENSSSCG00000003914	6:118771088-118783212		CU442720,CH242-94F19,6:118759178-118889484 (Clone quality: bE94F19 on chr=6; Num_of_Contigs=3; )
PRDX2		ENSSSCG00000013736	2:56062674-56066310		CU914382,CH242-275M24,2:56025074-56111468 (Clone quality: bE275M24 on chr=2; Num_of_Contigs=7; )
PRDX2		location ⇒	8:35101101-35101599		CU928696,CH242-300A20,8:35070263-35114326 (Clone quality: bE300A20 on chr=8; Num_of_Contigs=1; )
PRDX2		location ⇒	8:35101625-35101741		CU928696,CH242-300A20,8:35070263-35114326 (Clone quality: bE300A20 on chr=8; Num_of_Contigs=1; )
PRDX3		ENSSSCG00000010682	14:135062827-135073820
PRDX3		ENSSSCG00000005135	1:209618709-209668877		CU582802,CH242-276P14,1:209585174-209748628 (Clone quality: bE276P14 on chr=1; Num_of_Contigs=1; )
PRDX4		ENSSSCG00000012171	X:18634358-18653742		CU462995,CH242-81M14,X:18562318-18677937 (Clone quality: bE81M14 on chr=X; Num_of_Contigs=4; )
PRDX5		ENSSSCG00000013030	2:6170436-6173823		CU861533,CH242-1H13,2:6169679-6176765 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PRDX5		location ⇒	2:6170519-6170707		CU861533,CH242-1H13,2:6169679-6176765 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PRDX5		location ⇒	2:6171863-6171999		CU861533,CH242-1H13,2:6169679-6176765 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PRDX5		location ⇒	2:6173038-6173173		CU861533,CH242-1H13,2:6169679-6176765 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PRDX5		location ⇒	2:6173581-6173814		CU861533,CH242-1H13,2:6169679-6176765 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
PRDX6		ENSSSCG00000015490	9:108779722-108783068		FP089545,CH242-181N7,9:108775072-108784220 (Clone quality: bE181N7 on chr=9; Num_of_Contigs=5; )
PREB		ENSSSCG00000008553	3:104428646-104432250		CU896571,CH242-143O19,3:104398046-104492436 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
PRELID1		ENSSSCG00000014042	2:69747970-69752516	CU915382,CH242-167E23,2:69697156-69852996 (Clone quality: bE167E23 on chr=2; Num_of_Contigs=8; )
PRELID2		ENSSSCG00000014406	2:133464789-133485533		FP236415,CH242-37G8,2:133439694-133496384 (Clone quality: bE37G8 on chr=2; Num_of_Contigs=5; )
PRELP		ENSSSCG00000015271	9:61929161-61934298		CU466494,CH242-478D23,9:61895916-61982932 (Clone quality: bE478D23 on chr=9; Num_of_Contigs=6; )
PREP		ENSSSCG00000004368	1:75036691-75170752
PREPL		ENSSSCG00000008448	3:89474545-89536557
PREX2		ENSSSCG00000006199	4:69212022-69424562
PRF1		ENSSSCG00000010271	14:76667277-76671604		CT827802,CH242-224L10,14:76656698-76735939 (Clone quality: bE224L10 on chr=14; Num_of_Contigs=2; )
PRF1		location ⇒	14:76668409-76668108		CT827802,CH242-224L10,14:76656698-76735939 (Clone quality: bE224L10 on chr=14; Num_of_Contigs=2; )
PRF1		location ⇒	14:76669886-76669576		CT827802,CH242-224L10,14:76656698-76735939 (Clone quality: bE224L10 on chr=14; Num_of_Contigs=2; )
PRG2		ENSSSCG00000008655	3:121265240-121274481		FP102317,CH242-206A23,3:121263634-121296355 (Clone quality: bE206A23 on chr=3; Num_of_Contigs=8; )
PRG2		location ⇒	2:46118069-46117953		FP015903,CH242-504E7,2:46113883-46123195 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRG2		location ⇒	2:46248298-46248101		FP015903,CH242-504E7,2:46244527-46249943 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRG2		location ⇒	2:46248533-46248390		FP015903,CH242-504E7,2:46244527-46249943 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRG2		location ⇒	2:46248795-46248608		FP015903,CH242-504E7,2:46244527-46249943 (Clone quality: bE504E7 on chr=2; Num_of_Contigs=12; )
PRHOXNB		ENSSSCG00000009316	11:4864555-4873056
PRICKLE1		ENSSSCG00000000794	5:69776633-69952508
PRICKLE2		ENSSSCG00000011495	13:38479159-38643037
PRICKLE3		ENSSSCG00000012293	X:42684489-42696320		FP067404,CH242-247J8,X:42680766-42706990 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
PRIM1		ENSSSCG00000000408	5:21142224-21156544		CU468457,CH242-203P23,5:21129279-21156977 (Clone quality: bE203P23 on chr=5; Num_of_Contigs=4; )
PRIM2		ENSSSCG00000001493	7:32611231-32963336
PRIMA1		ENSSSCG00000002464	7:123366370-123445557
PRKAA1		ENSSSCG00000016858	16:23126720-23134109		CU928705,CH242-505A11,16:23038458-23135687 (Clone quality: bE505A11 on chr=16; Num_of_Contigs=2; )
PRKAA2		ENSSSCG00000003837	6:110603615-110674680
PRKAB1		ENSSSCG00000009840	14:33237945-33252263		CT737295,CH242-206D4,14:33142163-33293136 (Clone quality: bE206D4 on chr=14; Num_of_Contigs=1; )
PRKAB2		ENSSSCG00000006703	4:104491275-104503277		FP085517,CH242-271H18,4:104442547-104562336 (Clone quality: bE271H18 on chr=4; Num_of_Contigs=2; )
PRKAB2		ENSSSCG00000006703	4:104491275-104503277		FP085517,CH242-271H18,4:104442547-104562336 (Clone quality: bE271H18 on chr=4; Num_of_Contigs=2; )
PRKACA		ENSSSCG00000013771	2:57071837-57092296		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
PRKACA		location ⇒	2:57079610-57079546		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
PRKACA		location ⇒	2:57080888-57080787		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
PRKACA		location ⇒	2:57082943-57082809		FP086609,CH242-184K22,2:57071290-57093017 (Clone quality: bE184K22 on chr=2; Num_of_Contigs=6; )
PRKAG1		ENSSSCG00000000185	5:13657225-13859223
PRKAG1		location ⇒	1:280755325-280754625		CU041411,CH242-95A24,1:280727173-280776523 (Clone quality: bE95A24 on chr=1; Num_of_Contigs=8; )
PRKAG1		location ⇒	1:280755615-280755324		CU041411,CH242-95A24,1:280727173-280776523 (Clone quality: bE95A24 on chr=1; Num_of_Contigs=8; )
PRKAG2		ENSSSCG00000016432	18:4683541-4951931

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).