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)

PIAS1		location ⇒	1:173268994-173269441		CU929738,CH242-251L9,1:173264863-173270971 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
PIAS1		location ⇒	1:173345883-173346064		CU929738,CH242-251L9,1:173339169-173353987 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
PIAS1		location ⇒	1:173355370-173355757		CU929738,CH242-251L9,1:173354088-173356469 (Clone quality: bE251L9 on chr=1; Num_of_Contigs=5; )
PIAS1		location ⇒	1:173392059-173392447		CU468716,CH242-496M3,1:173384574-173394750 (Clone quality: bE496M3 on chr=1; Num_of_Contigs=17; )
PIAS3		ENSSSCG00000006689	4:103550263-103559169		CU606940,CH242-153I6,4:103542731-103564425 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
PIAS3		location ⇒	4:103557298-103557379		CU606940,CH242-153I6,4:103542731-103564425 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
PIAS3		location ⇒	4:103557527-103557663		CU606940,CH242-153I6,4:103542731-103564425 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
PIAS3		location ⇒	4:103558439-103559624		CU606940,CH242-153I6,4:103542731-103564425 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
PIBF1		ENSSSCG00000009461	11:44338871-44452351
PICA		location ⇒	12:37286306-37286614		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
PICA		location ⇒	12:37286966-37287080		CU929934,CH242-43L9,12:37209174-37292498 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
PICA		location ⇒	12:37316932-37317034		CU929934,CH242-43L9,12:37292599-37376417 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
PICA		location ⇒	12:37321712-37321815		CU929934,CH242-43L9,12:37292599-37376417 (Clone quality: bE43L9 on chr=12; Num_of_Contigs=3; )
PICALM		ENSSSCG00000014913	9:20088973-20195723
PICALM		location ⇒	9:20089705-20088346		CU657909,CH242-372F7,9:20064711-20093515 (Clone quality: bE372F7 on chr=9; Num_of_Contigs=9; )
PICALM		location ⇒	9:20111687-20111570		CU657909,CH242-372F7,9:20093616-20130532 (Clone quality: bE372F7 on chr=9; Num_of_Contigs=9; )
PICALM		location ⇒	9:20130172-20130034		CU657909,CH242-372F7,9:20093616-20130532 (Clone quality: bE372F7 on chr=9; Num_of_Contigs=9; )
PICALM		location ⇒	9:20144754-20144632		CU657909,CH242-372F7,9:20136465-20155709 (Clone quality: bE372F7 on chr=9; Num_of_Contigs=9; )
PICK1		ENSSSCG00000000114	5:6364735-6381115		CU633351,CH242-161B9,5:6340838-6445691 (Clone quality: bE161B9 on chr=5; Num_of_Contigs=5; )
PID1		ENSSSCG00000016257	15:122934762-122934911		CU550652,CH242-134E9,15:122917809-122951925 (Clone quality: bE134E9 on chr=15; Num_of_Contigs=5; )
PIF1		ENSSSCG00000004548	1:110394910-110398975		CU582916,CH242-24C1,1:110394552-110418941 (Clone quality: bE24C1 on chr=1; Num_of_Contigs=8; )
PIGA		ENSSSCG00000012134	X:11143586-11153496		CU302208,CH242-168N3,X:11122113-11177076 (Clone quality: bE168N3 on chr=X; Num_of_Contigs=5; )
PIGA		location ⇒	X:11153361-11152670		CU302208,CH242-168N3,X:11122113-11177076 (Clone quality: bE168N3 on chr=X; Num_of_Contigs=5; )
PIGB		ENSSSCG00000004611	1:121224328-121251287
PIGC		ENSSSCG00000015486	9:108110567-108111460		CU856594,CH242-328D16,9:108089158-108119668 (Clone quality: bE328D16 on chr=9; Num_of_Contigs=7; )
PIGF		ENSSSCG00000008440	3:87389844-87437663
PIGH		ENSSSCG00000002293	7:99712515-99721493		CT868701,CH242-284D22,7:99703246-99745569 (Clone quality: bE284D22 on chr=7; Num_of_Contigs=4; )
PIGL		ENSSSCG00000018035	12:56257783-56352233
PIGO		ENSSSCG00000005303	1:247011595-247018690		CU856695,CH242-238C15,1:246903923-247036412 (Clone quality: bE238C15 on chr=1; Num_of_Contigs=2; )
PIGP		ENSSSCG00000012061	13:140982108-140990727		CU582925,CH242-344D7,13:140981499-141025650 (Clone quality: bE344D7 on chr=13; Num_of_Contigs=9; )
PIGQ		ENSSSCG00000007992	3:35557722-35566808
PIGR		ENSSSCG00000015651	9:131905590-131914191		CU655936,CH242-369P7,9:131905191-131929992 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
PIGR		ENSSSCG00000015657	9:132097631-132118328		CU694720,CH242-352B19,9:132076515-132163275 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
PIGR		location ⇒	9:131905589-131906232		CU655936,CH242-369P7,9:131905191-131929992 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
PIGR		location ⇒	9:131907960-131908295		CU655936,CH242-369P7,9:131905191-131929992 (Clone quality: bE369P7 on chr=9; Num_of_Contigs=10; )
PIGR		location ⇒	9:132106235-132105592		CU694720,CH242-352B19,9:132076515-132163275 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
PIGR		location ⇒	9:132107506-132107157		CU694720,CH242-352B19,9:132076515-132163275 (Clone quality: bE352B19 on chr=9; Num_of_Contigs=11; )
PIGS		ENSSSCG00000017760	12:42459100-42471280
PIGU		ENSSSCG00000007282	17:40051472-40146920
PIGV		ENSSSCG00000003560	6:57798637-57807450		FP015947,CH242-485K18,6:57798539-57822484 (Clone quality: bE485K18 on chr=6; Num_of_Contigs=2; )
PIGW		ENSSSCG00000017687	12:36142158-36142427		CU694727,CH242-39G9,12:36140030-36142429 (Clone quality: bE39G9 on chr=12; Num_of_Contigs=15; )
PIGY		ENSSSCG00000009211	8:112166286-112168437		FP015981,CH242-34G15,8:112134360-112168622 (Clone quality: bE34G15 on chr=8; Num_of_Contigs=3; )
PIH1D1		ENSSSCG00000003169	6:38015068-38019379
PIH1D2		ENSSSCG00000015031	9:38630273-38637911		CU655934,CH242-367F19,9:38605255-38672831 (Clone quality: bE367F19 on chr=9; Num_of_Contigs=8; )
PIK3AP1		ENSSSCG00000010509	14:113138812-113256635		CT737321,CH242-202C18,14:113085488-113278246 (Clone quality: bE202C18 on chr=14; Num_of_Contigs=1; )
PIK3C2B		ENSSSCG00000015283	9:62664457-62716803
PIK3C2G		ENSSSCG00000000591	5:52057551-52485798
PIK3C3		location ⇒	6:87723004-87723192		CU466974,CH242-472K8,6:87714316-87766707 (Clone quality: bE472K8 on chr=6; Num_of_Contigs=4; )
PIK3C3		location ⇒	6:87784425-87784239		CU466974,CH242-472K8,6:87766808-87796898 (Clone quality: bE472K8 on chr=6; Num_of_Contigs=4; )
PIK3C3		location ⇒	6:87810797-87810983		CU457391,CH242-109O8,6:87796899-87850090 (Clone quality: bE109O8 on chr=6; Num_of_Contigs=2; )

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).