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)

p150		ENSSSCG00000005441	1:262665218-262734412		CU442740,CH242-321N10,1:262654894-262770561 (Clone quality: bE321N10 on chr=1; Num_of_Contigs=3; )
p150		ENSSSCG00000005706	1:286004464-286034610	FP102068,CH242-374C22,1:285992963-286044374 (Clone quality: bE374C22 on chr=1; Num_of_Contigs=5; )
p150		ENSSSCG00000010824	10:9783270-9874349
p150		ENSSSCG00000011184	13:1379194-1385231		CU469211,CH242-358D17,13:1378387-1387263 (Clone quality: bE358D17 on chr=13; Num_of_Contigs=18; )
p150		ENSSSCG00000013509	2:48617722-48648678		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
P24		ENSSSCG00000002382	7:106584035-106616508	CT737372,CH242-134B18,7:106458379-106624048 (Clone quality: bE134B18 on chr=7; Num_of_Contigs=4; )
P24		ENSSSCG00000001084	7:20013984-20032380	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
P2RX1		ENSSSCG00000017872	12:47242490-47252790
P2RX1		location ⇒	12:47100679-47100590		FP236385,CH242-124I22,12:47098926-47104861 (Clone quality: bE124I22 on chr=12; Num_of_Contigs=11; )
P2RX1		location ⇒	12:47101074-47101006		FP236385,CH242-124I22,12:47098926-47104861 (Clone quality: bE124I22 on chr=12; Num_of_Contigs=11; )
P2RX1		location ⇒	12:47101825-47101732		FP236385,CH242-124I22,12:47098926-47104861 (Clone quality: bE124I22 on chr=12; Num_of_Contigs=11; )
P2RX1		location ⇒	12:47102397-47102266		FP236385,CH242-124I22,12:47098926-47104861 (Clone quality: bE124I22 on chr=12; Num_of_Contigs=11; )
P2RX2		ENSSSCG00000009735	14:22663386-22666095
P2RX4		ENSSSCG00000009816	14:31409802-31429925
P2RX6		ENSSSCG00000010101	14:51719911-51728095		CU633934,CH242-117H20,14:51553625-51738341 (Clone quality: bE117H20 on chr=14; Num_of_Contigs=1; )
P2RX7		ENSSSCG00000009817	14:31460685-31518391	CT737324,CH242-80K13,14:31438114-31616035 (Clone quality: bE80K13 on chr=14; Num_of_Contigs=1; )
P2RX7		location ⇒	14:31497194-31497024	CT737324,CH242-80K13,14:31438114-31616035 (Clone quality: bE80K13 on chr=14; Num_of_Contigs=1; )
P2RX7		location ⇒	14:31500661-31500427	CT737324,CH242-80K13,14:31438114-31616035 (Clone quality: bE80K13 on chr=14; Num_of_Contigs=1; )
P2RY1		ENSSSCG00000011721	13:75250199-75252251		CU633315,CH242-69G3,13:75201950-75341517 (Clone quality: bE69G3 on chr=13; Num_of_Contigs=3; )
P2RY1		location ⇒	13:75249925-75250700		CU633315,CH242-69G3,13:75201950-75341517 (Clone quality: bE69G3 on chr=13; Num_of_Contigs=3; )
P2RY1		location ⇒	13:75250764-75252501		CU633315,CH242-69G3,13:75201950-75341517 (Clone quality: bE69G3 on chr=13; Num_of_Contigs=3; )
P2RY1		location ⇒	13:75252546-75252634		CU633315,CH242-69G3,13:75201950-75341517 (Clone quality: bE69G3 on chr=13; Num_of_Contigs=3; )
P2RY10		ENSSSCG00000012446	X:62767221-62782926
P2RY11		ENSSSCG00000013661	2:53394600-53395724		CU462940,CH242-319N14,2:53390856-53454909 (Clone quality: bE319N14 on chr=2; Num_of_Contigs=3; )
P2RY12		ENSSSCG00000011713	13:74049446-74050483		CU467754,CH242-404L12,13:74041525-74105862 (Clone quality: bE404L12 on chr=13; Num_of_Contigs=3; )
P2RY12		location ⇒	13:74049799-74050577		CU467754,CH242-404L12,13:74041525-74105862 (Clone quality: bE404L12 on chr=13; Num_of_Contigs=3; )
P2RY13		ENSSSCG00000011716	13:74225377-74229479		CU467754,CH242-404L12,13:74141465-74229996 (Clone quality: bE404L12 on chr=13; Num_of_Contigs=3; )
P2RY14		ENSSSCG00000011712	13:73970263-73971279		CU655952,CH242-509P4,13:73969033-73973260 (Clone quality: bE509P4 on chr=13; Num_of_Contigs=21; )
P2RY4		ENSSSCG00000012380	X:54942707-54944914
P2RY6		ENSSSCG00000014823	9:7400246-7401232		FP102302,CH242-226L8,9:7387994-7417357 (Clone quality: bE226L8 on chr=9; Num_of_Contigs=9; )
P47PHOX		location ⇒	3:9876894-9876998		FP102709,CH242-44F19,3:9876784-9886476 (Clone quality: bE44F19 on chr=3; Num_of_Contigs=7; )
P47PHOX		location ⇒	3:9881201-9881281		FP102709,CH242-44F19,3:9876784-9886476 (Clone quality: bE44F19 on chr=3; Num_of_Contigs=7; )
P47PHOX		location ⇒	3:9883449-9883524		FP102709,CH242-44F19,3:9876784-9886476 (Clone quality: bE44F19 on chr=3; Num_of_Contigs=7; )
P47PHOX		location ⇒	3:9883641-9883812		FP102709,CH242-44F19,3:9876784-9886476 (Clone quality: bE44F19 on chr=3; Num_of_Contigs=7; )
P4HA		location ⇒	14:79058852-79057789		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
P4HA		location ⇒	14:79103231-79103054		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
P4HA		location ⇒	14:79105617-79105418		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
P4HA		location ⇒	14:79108878-79108637		FP085541,CH242-456C24,14:78979366-79114663 (Clone quality: bE456C24 on chr=14; Num_of_Contigs=9; )
P4HA1		ENSSSCG00000010292	14:79057786-79180456
P4HA3		ENSSSCG00000014840	9:8479089-8486013		CU928090,CH242-136E14,9:8475289-8487687 (Clone quality: bE136E14 on chr=9; Num_of_Contigs=5; )
P4HTM		ENSSSCG00000011368	13:26550173-26592603
p50		ENSSSCG00000002444	7:121441501-121529677		CU571096,CH242-116L10,7:121427557-121561625 (Clone quality: bE116L10 on chr=7; Num_of_Contigs=3; )
p50		ENSSSCG00000009551	11:77844097-77936464
p50		ENSSSCG00000010285	14:78256680-78301386
p50		ENSSSCG00000013239	2:13291220-13296948		CU856312,CH242-38I7,2:13257671-13307229 (Clone quality: bE38I7 on chr=2; Num_of_Contigs=10; )
p50		ENSSSCG00000013256	2:14123252-14139957
p50		ENSSSCG00000016753	18:49580749-49589221		CU928907,CH242-155A21,18:49534481-49598883 (Clone quality: bE155A21 on chr=18; Num_of_Contigs=2; )
p67		ENSSSCG00000000899	5:82956316-82964533		CU896600,CH242-366K23,5:82949454-82965890 (Clone quality: bE366K23 on chr=5; Num_of_Contigs=8; )
p67		ENSSSCG00000005617	1:282527722-282566109

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

Report problems to zhu

iastate.edu

$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).