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)

PXN		location ⇒	14:40368571-40368742		CU407045,CH242-216A8,14:40363299-40369237 (No clone quality info on )
PXR		ENSSSCG00000011890	13:104974812-104979179		CU464151,CH242-19K1,13:104974384-104979421 (Clone quality: bE19K1 on chr=13; Num_of_Contigs=7; )
PXR		location ⇒	13:104975962-104976241		CU464151,CH242-19K1,13:104974384-104979421 (Clone quality: bE19K1 on chr=13; Num_of_Contigs=7; )
PXR		location ⇒	13:105148467-105147313		CU464151,CH242-19K1,13:105146685-105149399 (Clone quality: bE19K1 on chr=13; Num_of_Contigs=7; )
PXR		location ⇒	13:105153065-105152844		CU464166,CH242-455B16,13:105149400-105184290 (Clone quality: bE455B16 on chr=13; Num_of_Contigs=7; )
PXR		location ⇒	13:105174431-105174223		CU464166,CH242-455B16,13:105149400-105184290 (Clone quality: bE455B16 on chr=13; Num_of_Contigs=7; )
PYCARD		ENSSSCG00000007758	3:15810753-15812359		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
PYCR2		ENSSSCG00000010855	10:14043653-14047760		CU914379,CH242-206B3,10:14028575-14068754 (Clone quality: bE206B3 on chr=10; Num_of_Contigs=3; )
PYCRL		ENSSSCG00000006952	4:135892287-135892760		CU927913,CH242-99E21,4:135892216-135896942 (Clone quality: bE99E21 on chr=4; Num_of_Contigs=20; )
PYGL		ENSSSCG00000005024	1:188921305-188980280
PYGM		ENSSSCG00000013022	2:5810420-5821868
PYGO1		ENSSSCG00000004607	1:121043815-121046372		CU570857,CH242-45M3,1:121035192-121118131 (Clone quality: bE45M3 on chr=1; Num_of_Contigs=5; )
PYGO2		ENSSSCG00000006540	4:98937927-98940465		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
PYROXD1		ENSSSCG00000000583	5:50063752-50076553
PYROXD2		ENSSSCG00000010533	14:114405275-114429579
PYY		ENSSSCG00000017369	12:17142714-17143966		CU914436,CH242-507H4,12:17130148-17144522 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )
PYY		ENSSSCG00000017363	12:17013175-17014427		CU469063,CH242-86P22,12:17005106-17017395 (Clone quality: bE86P22 on chr=12; Num_of_Contigs=21; )
PYY		location ⇒	12:17013674-17013863		CU469063,CH242-86P22,12:17005106-17017395 (Clone quality: bE86P22 on chr=12; Num_of_Contigs=21; )
PYY		location ⇒	12:17014180-17014417		CU469063,CH242-86P22,12:17005106-17017395 (Clone quality: bE86P22 on chr=12; Num_of_Contigs=21; )
PYY		location ⇒	12:17142961-17142724		CU914436,CH242-507H4,12:17130148-17144522 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )
PYY		location ⇒	12:17143467-17143278		CU914436,CH242-507H4,12:17130148-17144522 (Clone quality: bE507H4 on chr=12; Num_of_Contigs=9; )

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).