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)

CHST10		location ⇒	3:49626911-49627128		CU407314,CH242-21N16,3:49539268-49635275 (Clone quality: bE21N16 on chr=3; Num_of_Contigs=6; )
CHST10		location ⇒	3:49629436-49629542		CU407314,CH242-21N16,3:49539268-49635275 (Clone quality: bE21N16 on chr=3; Num_of_Contigs=6; )
CHST10		location ⇒	3:49631391-49631901		CU407314,CH242-21N16,3:49539268-49635275 (Clone quality: bE21N16 on chr=3; Num_of_Contigs=6; )
CHST11		ENSSSCG00000000837	5:74582458-74583327		CU462999,CH242-260K7,5:74568947-74617896 (Clone quality: bE260K7 on chr=5; Num_of_Contigs=1; )
CHST12		ENSSSCG00000007567	3:1541752-1543002		FP102176,CH242-180P18,3:1540597-1557017 (Clone quality: bE180P18 on chr=3; Num_of_Contigs=8; )
CHST13		ENSSSCG00000011625	13:60190890-60207100		CU856309,CH242-278B22,13:60136689-60224349 (Clone quality: bE278B22 on chr=13; Num_of_Contigs=6; )
CHST14		ENSSSCG00000004771	1:137312401-137313531		CU234165,CH242-252B18,1:137235363-137339770 (Clone quality: bE252B18 on chr=1; Num_of_Contigs=2; )
CHST4		ENSSSCG00000002737	6:10369832-10370995		FP016102,CH242-364C5,6:10306746-10373929 (Clone quality: bE364C5 on chr=6; Num_of_Contigs=10; )
CHST4		location ⇒	6:10253059-10253111		FP016102,CH242-364C5,6:10240959-10256957 (Clone quality: bE364C5 on chr=6; Num_of_Contigs=10; )
CHST4		location ⇒	6:10371012-10370230		FP016102,CH242-364C5,6:10306746-10373929 (Clone quality: bE364C5 on chr=6; Num_of_Contigs=10; )
CHST7		ENSSSCG00000012265	X:41296615-41298072		CU915478,CH242-29L4,X:41296324-41405064 (Clone quality: bE29L4 on chr=X; Num_of_Contigs=4; )
CHST9		ENSSSCG00000003721	6:77042695-77043783		CU462839,CH242-482C3,6:77000866-77205184 (Clone quality: bE482C3 on chr=6; Num_of_Contigs=2; )
CHSY1		ENSSSCG00000004825	1:147471088-147543510
CHSY3		location ⇒	2:120576419-120577345		CU694613,CH242-36E7,2:120576417-120584243 (Clone quality: bE36E7 on chr=2; Num_of_Contigs=10; )
CHSY3		location ⇒	2:120577446-120578168		CU694613,CH242-36E7,2:120576417-120584243 (Clone quality: bE36E7 on chr=2; Num_of_Contigs=10; )
CHSY3		location ⇒	2:120670650-120672237		CU915686,CH242-507D1,2:120662693-120703828 (Clone quality: bE507D1 on chr=2; Num_of_Contigs=4; )
CHSY3		location ⇒	2:120672338-120673060		CU915686,CH242-507D1,2:120662693-120703828 (Clone quality: bE507D1 on chr=2; Num_of_Contigs=4; )
CHTF18		ENSSSCG00000008010	3:35815877-35822535		FP016225,CH242-86N4,3:35815598-35830527 (Clone quality: bE86N4 on chr=3; Num_of_Contigs=9; )
CHTL1		ENSSSCG00000005425	1:258582618-258743259
CHUK		ENSSSCG00000010548	14:116075566-116220008
CHUK		location ⇒	14:116077678-116077578		CT868715,CH242-513L2,14:116015867-116113953 (Clone quality: bE513L2 on chr=14; Num_of_Contigs=23; )
CHUK		location ⇒	14:116080108-116079977		CT868715,CH242-513L2,14:116015867-116113953 (Clone quality: bE513L2 on chr=14; Num_of_Contigs=23; )
CHUK		location ⇒	14:116081060-116080911		CT868715,CH242-513L2,14:116015867-116113953 (Clone quality: bE513L2 on chr=14; Num_of_Contigs=23; )
CHUK		location ⇒	14:116081419-116081321		CT868715,CH242-513L2,14:116015867-116113953 (Clone quality: bE513L2 on chr=14; Num_of_Contigs=23; )
CIAO1		ENSSSCG00000008130	3:42064960-42068616		CU896688,CH242-167G10,3:42056126-42096960 (Clone quality: bE167G10 on chr=3; Num_of_Contigs=16; )
CIAS1		ENSSSCG00000013940	2:63853146-63860552		CU694944,CH242-8E21,2:63851105-63883829 (Clone quality: bE8E21 on chr=2; Num_of_Contigs=5; )
CIAS1		location ⇒	2:63854795-63854380		CU694944,CH242-8E21,2:63851105-63883829 (Clone quality: bE8E21 on chr=2; Num_of_Contigs=5; )
CIAS1		location ⇒	2:63861275-63861214		CU694944,CH242-8E21,2:63851105-63883829 (Clone quality: bE8E21 on chr=2; Num_of_Contigs=5; )
CIB1		ENSSSCG00000001858	7:61380594-61386242
CIB1		location ⇒	7:61383631-61383512		CU571213,CH242-243O5,7:61382831-61401542 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
CIB1		location ⇒	7:61383927-61383775		CU571213,CH242-243O5,7:61382831-61401542 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
CIB1		location ⇒	7:61384635-61384526		CU571213,CH242-243O5,7:61382831-61401542 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
CIB1		location ⇒	7:61386011-61385902		CU571213,CH242-243O5,7:61382831-61401542 (Clone quality: bE243O5 on chr=7; Num_of_Contigs=21; )
CIB2		ENSSSCG00000001762	7:53811144-53835612		CU467054,CH242-222N19,7:53795062-53849472 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
CIB3		ENSSSCG00000013854	2:60715969-60722453
CIB4		ENSSSCG00000008564	3:104862815-104913318
CIDEB		ENSSSCG00000001989	7:81323833-81326724		CU019590,CH242-406B17,7:81281809-81421007 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
CIDEC		ENSSSCG00000011557	13:55328371-55336332		CU633418,CH242-443E24,13:55326186-55338650 (Clone quality: bE443E24 on chr=13; Num_of_Contigs=9; )
CIITA		ENSSSCG00000007901	3:28602265-28633443
CIITA		location ⇒	3:28627682-28627837		CU467545,CH242-258E10,3:28625221-28633443 (Clone quality: bE258E10 on chr=3; Num_of_Contigs=21; )
CIITA		location ⇒	3:28628559-28628708		CU467545,CH242-258E10,3:28625221-28633443 (Clone quality: bE258E10 on chr=3; Num_of_Contigs=21; )
CIITA		location ⇒	3:28630101-28630252		CU467545,CH242-258E10,3:28625221-28633443 (Clone quality: bE258E10 on chr=3; Num_of_Contigs=21; )
CIITA		location ⇒	3:28701870-28701152		CU467545,CH242-258E10,3:28667239-28708658 (Clone quality: bE258E10 on chr=3; Num_of_Contigs=21; )
CILP		ENSSSCG00000013934	2:63473040-63480780		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
CILP		ENSSSCG00000004928	1:170270905-170285726		CU856492,CH242-206L6,1:170217076-170340216 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
CILP		ENSSSCG00000004933	1:170502342-170517164		CU633232,CH242-191H9,1:170493553-170531449 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
CILP		location ⇒	1:170271813-170271017		CU856492,CH242-206L6,1:170217076-170340216 (Clone quality: bE206L6 on chr=1; Num_of_Contigs=2; )
CILP		location ⇒	1:170516253-170517049		CU633232,CH242-191H9,1:170493553-170531449 (Clone quality: bE191H9 on chr=1; Num_of_Contigs=6; )
CILP2		ENSSSCG00000013934	2:63473040-63480780		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
CILP2		location ⇒	2:63473811-63473272		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )

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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).