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)

PMM1		ENSSSCG00000000061	5:3510467-3521513
PMP2		ENSSSCG00000006152	4:56634430-56639963		CU179652,CH242-259L11,4:56618115-56800213 (Clone quality: bE259L11 on chr=4; Num_of_Contigs=1; )
PMPCB		ENSSSCG00000015422	9:96358618-96372084		CU570825,CH242-232P7,9:96290209-96447239 (Clone quality: bE232P7 on chr=9; Num_of_Contigs=1; )
PMS1		ENSSSCG00000016045	15:88917303-89006719
PMS2		ENSSSCG00000007590	3:4068724-4094386
PMVK		ENSSSCG00000006535	4:98857618-98869439
PNCK		ENSSSCG00000012773	X:122519890-122522698		FP245398,CH242-390A7,X:122519885-122526389 (Clone quality: bE390A7 on chr=X; Num_of_Contigs=13; )
PNKD		ENSSSCG00000016188	15:113524542-113526622		CU550681,CH242-392C2,15:113522054-113526809 (Clone quality: bE392C2 on chr=15; Num_of_Contigs=23; )
PNKP		ENSSSCG00000003195	6:38486342-38492934
PNLDC1		ENSSSCG00000004046	1:8687881-8706454
PNLIPRP1		ENSSSCG00000010659	14:132614445-132629698		CU633249,CH242-237J21,14:132606680-132662168 (Clone quality: bE237J21 on chr=14; Num_of_Contigs=12; )
PNLIPRP3		ENSSSCG00000010657	14:132438131-132459278		CU469112,CH242-267E6,14:132437696-132531232 (Clone quality: bE267E6 on chr=14; Num_of_Contigs=5; )
PNMA1		ENSSSCG00000002346	7:104942037-104943098		CT943655,CH242-523I15,7:104924151-105020426 (Clone quality: bE523I15 on chr=7; Num_of_Contigs=3; )
PNMA2		ENSSSCG00000009659	14:10565128-10566222		CU468375,CH242-98K7,14:10562483-10595341 (Clone quality: bE98K7 on chr=14; Num_of_Contigs=4; )
PNMAL1		ENSSSCG00000003102	6:36290296-36291603		FP102354,CH242-94J5,6:36287686-36300933 (Clone quality: bE94J5 on chr=6; Num_of_Contigs=21; )
PNMT		ENSSSCG00000017501	12:20618539-20620121		CU640399,CH242-251F23,12:20578579-20644206 (Clone quality: bE251F23 on chr=12; Num_of_Contigs=5; )
PNN		location ⇒	1:177450407-177449014		CU639454,CH242-168O7,1:177425380-177461060 (Clone quality: bE168O7 on chr=1; Num_of_Contigs=4; )
PNN		location ⇒	1:177454759-177454689		CU639454,CH242-168O7,1:177425380-177461060 (Clone quality: bE168O7 on chr=1; Num_of_Contigs=4; )
PNN		location ⇒	1:177653226-177653296		FP067374,CH242-259E12,1:177602688-177664256 (Clone quality: bE259E12 on chr=1; Num_of_Contigs=2; )
PNN		location ⇒	1:177657578-177658975		FP067374,CH242-259E12,1:177602688-177664256 (Clone quality: bE259E12 on chr=1; Num_of_Contigs=2; )
PNO1		ENSSSCG00000008352	3:68100638-68113853		CU915705,CH242-440I14,3:68081039-68131854 (Clone quality: bE440I14 on chr=3; Num_of_Contigs=1; )
PNOC		ENSSSCG00000009675	14:12085566-12116891		CT737320,CH242-198J10,14:11977333-12124098 (Clone quality: bE198J10 on chr=14; Num_of_Contigs=2; )
PNOC		location ⇒	14:12097654-12097810		CT737320,CH242-198J10,14:11977333-12124098 (Clone quality: bE198J10 on chr=14; Num_of_Contigs=2; )
PNOC		location ⇒	14:12112879-12113339		CT737320,CH242-198J10,14:11977333-12124098 (Clone quality: bE198J10 on chr=14; Num_of_Contigs=2; )
PNOC		location ⇒	14:12116814-12116891		CT737320,CH242-198J10,14:11977333-12124098 (Clone quality: bE198J10 on chr=14; Num_of_Contigs=2; )
PNPLA1		ENSSSCG00000001559	7:36617836-36688890
PNPLA2		ENSSSCG00000012841	2:148626-153498		CU928976,CH242-144M19,2:43742-170991 (Clone quality: bE144M19 on chr=2; Num_of_Contigs=17; )
PNPLA4		ENSSSCG00000012100	X:3428814-3458822	CU694849,CH242-236E18,X:3326006-3459219 (Clone quality: bE236E18 on chr=X; Num_of_Contigs=4; )
PNPLA6		ENSSSCG00000013572	2:50955871-50984485
PNPLA8		ENSSSCG00000015446	9:101139895-101164070
PNPO		ENSSSCG00000017523	12:21640003-21643502
PNPT1		ENSSSCG00000008399	3:79568667-79591438
PNRC1		ENSSSCG00000004312	1:59901989-59902531		CU469321,CH242-187O16,1:59900218-59902721 (Clone quality: bE187O16 on chr=1; Num_of_Contigs=20; )
po-IL27		location ⇒	3:68750590-68750613		CU929685,CH242-132G23,3:68720554-68766510 (Clone quality: bE132G23 on chr=3; Num_of_Contigs=4; )
PODNL1		ENSSSCG00000013762	2:56934034-56939022		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
PODXL		ENSSSCG00000016548	18:15635640-15642260		CU914675,CH242-449K18,18:15606063-15666559 (Clone quality: bE449K18 on chr=18; Num_of_Contigs=3; )
POF1B		ENSSSCG00000012462	X:67506761-67616334
POFUT1		ENSSSCG00000007244	17:37836533-37860865		CU928633,CH242-263B18,17:37807325-37865251 (Clone quality: bE263B18 on chr=17; Num_of_Contigs=9; )
POFUT2		ENSSSCG00000012088	13:145118424-145125297		CU466368,CH242-15J19,13:145117921-145126074 (Clone quality: bE15J19 on chr=13; Num_of_Contigs=15; )
POGK		ENSSSCG00000006319	4:87559362-87563286		CU207249,CH242-383G23,4:87517520-87566826 (Clone quality: bE383G23 on chr=4; Num_of_Contigs=5; )
POGZ		ENSSSCG00000006622	4:101750743-101785498	CU179724,CH242-246E20,4:101737894-101911024 (Clone quality: bE246E20 on chr=4; Num_of_Contigs=5; )
POLA1		ENSSSCG00000012184	X:19639405-19669606
POLA2		ENSSSCG00000012997	2:5322633-5349964		CU856029,CH242-276E8,2:5308192-5352105 (Clone quality: bE276E8 on chr=2; Num_of_Contigs=9; )
POLB		ENSSSCG00000007031	17:11843524-11865707
POLD1		ENSSSCG00000003216	6:39000770-39015171		FP102476,CH242-133P5,6:39000388-39018494 (Clone quality: bE133P5 on chr=6; Num_of_Contigs=12; )
POLD2		ENSSSCG00000016753	18:49580749-49589221		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
POLD3		ENSSSCG00000014842	9:8594841-8646291
POLD4		ENSSSCG00000012916	2:3562263-3564074		CU914251,CH242-230J11,2:3561382-3573634 (Clone quality: bE230J11 on chr=2; Num_of_Contigs=8; )
POLDIP3		ENSSSCG00000000039	5:2874787-2886770
POLE2		ENSSSCG00000005008	1:187911288-187945836

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).