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)

B8YQC2_PIG		ENSSSCG00000007569	3:1840915-1842294		FP102725,CH242-525I24,3:1840702-1842890 (Clone quality: bE525I24 on chr=3; Note=un_improved;)
B8YQC2_PIG		ENSSSCG00000007566	3:1504604-1508334		FP102176,CH242-180P18,3:1485841-1540496 (Clone quality: bE180P18 on chr=3; Num_of_Contigs=8; )
B8YQC2_PIG		ENSSSCG00000007569	3:1840915-1842294		FP102725,CH242-525I24,3:1840702-1842890 (Clone quality: bE525I24 on chr=3; Note=un_improved;)
B8YQC2_PIG		ENSSSCG00000007566	3:1504604-1508334		FP102176,CH242-180P18,3:1485841-1540496 (Clone quality: bE180P18 on chr=3; Num_of_Contigs=8; )
B9D2		ENSSSCG00000003013	6:34055717-34061260
B9TRW8_PIG		ENSSSCG00000003783	6:97391356-97398399		CU694582,CH242-24J21,6:97368472-97411008 (Clone quality: bE24J21 on chr=6; Num_of_Contigs=3; )
B9VNW9_PIG		ENSSSCG00000007019	17:10744933-10764212		CU607010,CH242-309J7,17:10738322-10775478 (Clone quality: bE309J7 on chr=17; Num_of_Contigs=6; )
B9VNZ6_PIG		ENSSSCG00000006011	4:21165159-21203671
B9VNZ6_PIG		ENSSSCG00000006011	4:21165159-21203671
BAALC		ENSSSCG00000006053	4:34273811-34363456
BAAT		ENSSSCG00000005398	1:254770032-254774282		CU469282,CH242-469F7,1:254763320-254778964 (Clone quality: bE469F7 on chr=1; Num_of_Contigs=22; )
BACE1		ENSSSCG00000015079	9:43560055-43579984
BACE2		ENSSSCG00000012074	13:144159699-144222529
BACH1		ENSSSCG00000012029	13:137187096-137224463		CU640452,CH242-251G20,13:137179154-137224693 (Clone quality: bE251G20 on chr=13; Num_of_Contigs=5; )
BACH2		ENSSSCG00000004332	1:61013836-61027925
BAD		ENSSSCG00000013033	2:6217555-6228600
BAD		location ⇒	2:6227410-6227605		CU861533,CH242-1H13,2:6220423-6230787 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
BAD		location ⇒	2:6228098-6228599		CU861533,CH242-1H13,2:6220423-6230787 (Clone quality: bE1H13 on chr=2; Num_of_Contigs=14; )
BAG1		ENSSSCG00000010996	10:31752865-31765753
BAG1		location ⇒	10:31753059-31753374		CU856468,CH242-364H6,10:31743216-31763639 (Clone quality: bE364H6 on chr=10; Num_of_Contigs=8; )
BAG1		location ⇒	10:31754901-31755030		CU856468,CH242-364H6,10:31743216-31763639 (Clone quality: bE364H6 on chr=10; Num_of_Contigs=8; )
BAG1		location ⇒	10:31759533-31759649		CU856468,CH242-364H6,10:31743216-31763639 (Clone quality: bE364H6 on chr=10; Num_of_Contigs=8; )
BAG1		location ⇒	10:31765118-31766123		CU694297,CH242-168B13,10:31763640-31823504 (Clone quality: bE168B13 on chr=10; Num_of_Contigs=6; )
Bag2		location ⇒	7:33013848-33013961		CT963091,CH242-57D23,7:33009443-33025009 (Clone quality: bE57D23 on chr=7; Num_of_Contigs=3; )
Bag2		location ⇒	7:33015684-33016285		CT963091,CH242-57D23,7:33009443-33025009 (Clone quality: bE57D23 on chr=7; Num_of_Contigs=3; )
Bag2		location ⇒	7:33085713-33085112		CT998546,CH242-417N10,7:33065011-33146630 (Clone quality: bE417N10 on chr=7; Num_of_Contigs=2; )
Bag2		location ⇒	7:33087549-33087436		CT998546,CH242-417N10,7:33065011-33146630 (Clone quality: bE417N10 on chr=7; Num_of_Contigs=2; )
BAG3		ENSSSCG00000010686	14:135493542-135516967		CT826370,CH242-151G12,14:135430149-135546133 (Clone quality: bE151G12 on chr=14; Num_of_Contigs=3; )
BAG3		location ⇒	14:135493543-135493794		CT826370,CH242-151G12,14:135430149-135546133 (Clone quality: bE151G12 on chr=14; Num_of_Contigs=3; )
BAG3		location ⇒	14:135510132-135510460		CT826370,CH242-151G12,14:135430149-135546133 (Clone quality: bE151G12 on chr=14; Num_of_Contigs=3; )
BAG3		location ⇒	14:135512570-135512976		CT826370,CH242-151G12,14:135430149-135546133 (Clone quality: bE151G12 on chr=14; Num_of_Contigs=3; )
BAG3		location ⇒	14:135516156-135517520		CT826370,CH242-151G12,14:135430149-135546133 (Clone quality: bE151G12 on chr=14; Num_of_Contigs=3; )
BAG4		ENSSSCG00000015817	15:45762923-45773350		CU570721,CH242-1H2,15:45760716-45803992 (Clone quality: bE1H2 on chr=15; Num_of_Contigs=6; )
BAG4		location ⇒	15:45773140-45773735		CU570721,CH242-1H2,15:45760716-45803992 (Clone quality: bE1H2 on chr=15; Num_of_Contigs=6; )
BAGE2		ENSSSCG00000016429	18:4251169-4371122
BAHD1		ENSSSCG00000004772	1:137318532-137325210		CU234165,CH242-252B18,1:137235363-137339770 (Clone quality: bE252B18 on chr=1; Num_of_Contigs=2; )
BAI1		ENSSSCG00000017142	12:785777-798275
BAI1		ENSSSCG00000011497	13:39290222-39403689
BAI1		ENSSSCG00000000111	5:6283965-6303901
BAI1		ENSSSCG00000007602	3:4666274-4688695
BAI1		ENSSSCG00000008029	3:36212736-36222212		CU467714,CH242-272G6,3:36207929-36224650 (Clone quality: bE272G6 on chr=3; Num_of_Contigs=16; )
BAI2		ENSSSCG00000003604	6:60551753-60582291
BAI3		ENSSSCG00000004270	1:51586217-51726374
BAIAP2		ENSSSCG00000017142	12:785777-798275
BAIAP2L1		ENSSSCG00000007602	3:4666274-4688695
BAIAP2L2		ENSSSCG00000000111	5:6283965-6303901
BAIAP3		ENSSSCG00000008029	3:36212736-36222212		CU467714,CH242-272G6,3:36207929-36224650 (Clone quality: bE272G6 on chr=3; Num_of_Contigs=16; )
BAK1		ENSSSCG00000001516	7:34217587-34222793	CU498854,CH242-216B14,7:34138678-34237511 (Clone quality: bE216B14 on chr=7; Num_of_Contigs=6; )
BAK1		location ⇒	7:34219423-34219277	CU498854,CH242-216B14,7:34138678-34237511 (Clone quality: bE216B14 on chr=7; Num_of_Contigs=6; )
BAK1		location ⇒	7:34219799-34219744	CU498854,CH242-216B14,7:34138678-34237511 (Clone quality: bE216B14 on chr=7; Num_of_Contigs=6; )

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, 651-28

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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).