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)

COX7A2L		ENSSSCG00000008466	3:91462156-91494024
COX7B		ENSSSCG00000001870	7:62737396-62737635	CT841554,CH242-267N7,7:62491859-62740329 (Clone quality: bE267N7 on chr=7; Num_of_Contigs=3; )
COX7C		ENSSSCG00000014145	2:83936922-83939617		CU855504,CH242-232C14,2:83908383-83956815 (Clone quality: bE232C14 on chr=2; Num_of_Contigs=8; )
COX8A		ENSSSCG00000013046	2:6475191-6476907		CU914709,CH242-316G24,2:6453896-6478840 (Clone quality: bE316G24 on chr=2; Num_of_Contigs=6; )
COX8C		ENSSSCG00000002462	7:122946116-122947299		CT797466,CH242-199A4,7:122927075-122995092 (Clone quality: bE199A4 on chr=7; Num_of_Contigs=3; )
CP		ENSSSCG00000000589	5:51989283-51990179		CU457757,CH242-219O8,5:51933888-52027325 (Clone quality: bE219O8 on chr=5; Num_of_Contigs=1; )
CP		ENSSSCG00000011636	13:61213059-61294052		CU466342,CH242-17F10,13:61189858-61308403 (Clone quality: bE17F10 on chr=13; Num_of_Contigs=4; )
CP		ENSSSCG00000011700	13:72709742-72763129		CU469412,CH242-12C2,13:72709569-72803132 (Clone quality: bE12C2 on chr=13; Num_of_Contigs=5; )
CP		ENSSSCG00000007084	17:26567776-26599837
CP242_PIG		ENSSSCG00000010490	14:111721928-111757286		CU392852,CH242-517O10,14:111696262-111826906 (Clone quality: bE517O10 on chr=14; Num_of_Contigs=2; )
CP2DP_PIG		ENSSSCG00000000046	5:3025486-3030169	BX296515,PigE-121D21,5:2907737-3087427 (Clone quality: bT121D21 on chr=5; Num_of_Contigs=8; )
CP2DP_PIG		ENSSSCG00000000046	5:3025486-3030169	BX296515,PigE-121D21,5:2907737-3087427 (Clone quality: bT121D21 on chr=5; Num_of_Contigs=8; )
CP4AL_PIG		ENSSSCG00000003893	6:117740149-117756528		FP102856,CH242-411M18,6:117731449-117792877 (Clone quality: bE411M18 on chr=6; Num_of_Contigs=16; )
CPA1		ENSSSCG00000016557	18:16656773-16663190		CU466438,CH242-113D18,18:16655823-16668412 (Clone quality: bE113D18 on chr=18; Num_of_Contigs=9; )
CPA2		ENSSSCG00000016559	18:16729344-16748802
CPA3		ENSSSCG00000016555	18:16579822-16592749		CU466438,CH242-113D18,18:16577515-16592940 (Clone quality: bE113D18 on chr=18; Num_of_Contigs=9; )
CPA4		ENSSSCG00000016555	18:16579822-16592749		CU466438,CH242-113D18,18:16577515-16592940 (Clone quality: bE113D18 on chr=18; Num_of_Contigs=9; )
CPA5		ENSSSCG00000016558	18:16671639-16694138
CPA6		ENSSSCG00000006200	4:69822261-69901082
CPAMD8		ENSSSCG00000013869	2:61413944-61520376
CPB1		ENSSSCG00000011694	13:72404930-72448842
CPB2		ENSSSCG00000009413	11:20614101-20675720
CPB2		location ⇒	11:20614137-20614319		CU367850,CH242-196G1,11:20603980-20666036 (Clone quality: bE196G1 on chr=11; Num_of_Contigs=7; )
CPB2		location ⇒	11:20640047-20640159		CU367850,CH242-196G1,11:20603980-20666036 (Clone quality: bE196G1 on chr=11; Num_of_Contigs=7; )
CPB2		location ⇒	11:20666712-20666915		CU367850,CH242-196G1,11:20666137-20758943 (Clone quality: bE196G1 on chr=11; Num_of_Contigs=7; )
CPB2		location ⇒	11:20675369-20675557		CU367850,CH242-196G1,11:20666137-20758943 (Clone quality: bE196G1 on chr=11; Num_of_Contigs=7; )
CPD		ENSSSCG00000017799	12:44398427-44465670		FP102529,CH242-9D9,12:44372175-44547741 (Clone quality: bE9D9 on chr=12; Num_of_Contigs=1; )
CPE		ENSSSCG00000008856	8:37729569-37798234
CPEB1		ENSSSCG00000001808	7:58347244-58423465
CPEB2		ENSSSCG00000008736	8:7472641-7564494
CPEB2		location ⇒	8:7564778-7563920		CU928505,CH242-480J9,8:7553673-7574035 (Clone quality: bE480J9 on chr=8; Num_of_Contigs=4; )
CPEB3		ENSSSCG00000019824	14:108928606-108928683		CT868714,CH242-512F23,14:108897801-108934134 (Clone quality: bE512F23 on chr=14; Num_of_Contigs=2; )
CPEB3		ENSSSCG00000010468	14:108798459-108955909
CPEB3_ribozym		ENSSSCG00000019824	14:108928606-108928683		CT868714,CH242-512F23,14:108897801-108934134 (Clone quality: bE512F23 on chr=14; Num_of_Contigs=2; )
CPEB4		ENSSSCG00000016981	16:47720623-47784065
CPEB4		location ⇒	16:47719230-47719283		CU930011,CH242-55K9,16:47719143-47753490 (Clone quality: bE55K9 on chr=16; Num_of_Contigs=3; )
CPEB4		location ⇒	16:47720111-47721748		CU930011,CH242-55K9,16:47719143-47753490 (Clone quality: bE55K9 on chr=16; Num_of_Contigs=3; )
CPEB4		location ⇒	16:47785258-47786357		CU930011,CH242-55K9,16:47780326-47806225 (Clone quality: bE55K9 on chr=16; Num_of_Contigs=3; )
CPEB4		location ⇒	16:47786420-47787758		CU930011,CH242-55K9,16:47780326-47806225 (Clone quality: bE55K9 on chr=16; Num_of_Contigs=3; )
CPLX3		ENSSSCG00000001895	7:64140311-64217409
CPLX4		ENSSSCG00000004909	1:168525765-168552563		CU076088,CH242-77M4,1:168411868-168596075 (Clone quality: bE77M4 on chr=1; Num_of_Contigs=1; )
CPM		location ⇒	5:32369959-32369839		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
CPM		location ⇒	5:32372003-32371970		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
CPM		location ⇒	5:32372134-32372082		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
CPM		location ⇒	5:32373702-32373660		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
CPN1		ENSSSCG00000010545	14:115943090-115973964
CPNE1		ENSSSCG00000007306	17:41090782-41131536
CPNE3		ENSSSCG00000006135	4:52040293-52095621		CU462951,CH242-345F16,4:51977268-52163454 (Clone quality: bE345F16 on chr=4; Num_of_Contigs=1; )
CPNE4		ENSSSCG00000011178	13:550475-748906
CPNE5		ENSSSCG00000001567	7:37044106-37140766	CU326356,CH242-61G11,7:36975834-37183903 (Clone quality: bE61G11 on chr=7; Num_of_Contigs=4; )

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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).