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)

MCP		ENSSSCG00000017723	12:38372460-38374364
MCP		ENSSSCG00000008239	3:54148993-54163461		CU951451,CH242-157C24,3:54090565-54166505 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
MCP		ENSSSCG00000012367	X:51601619-51607239		CU468312,CH242-149K13,X:51591006-51616408 (Clone quality: bE149K13 on chr=X; Num_of_Contigs=13; )
MCP		ENSSSCG00000015014	9:37327558-37355760
MCP		ENSSSCG00000017721	12:38305186-38307206		CU928660,CH242-280M5,12:38302849-38308872 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
MCP		location ⇒	9:127186055-127185898		FP089691,CH242-273B10,9:127173594-127190150 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
MCP		location ⇒	9:127188733-127188668		FP089691,CH242-273B10,9:127173594-127190150 (Clone quality: bE273B10 on chr=9; Num_of_Contigs=7; )
MCP-1		ENSSSCG00000017723	12:38372460-38374364
MCP-1		location ⇒	12:38372958-38372465		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; )
MCP-1		location ⇒	12:38373462-38373343		CU928660,CH242-280M5,12:38371176-38373405 (Clone quality: bE280M5 on chr=12; Num_of_Contigs=19; ) CU571289,CH242-352D21,12:38373406-38427513 (Clone quality: bE352D21 on chr=12; Num_of_Contigs=4; )
MCP-1		location ⇒	12:38374361-38374237		CU571289,CH242-352D21,12:38373406-38427513 (Clone quality: bE352D21 on chr=12; Num_of_Contigs=4; )
MCPH1		ENSSSCG00000015754	15:34624698-34659925
MCRS1		ENSSSCG00000000202	5:14313203-14318508
MCR_PIG		ENSSSCG00000009027	8:69534309-69570851
MCTP1		ENSSSCG00000014164	2:90813844-90954546
MCTP2		ENSSSCG00000002257	7:92826203-93013829
MDC1		ENSSSCG00000001362	7:26949503-26963051	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
MDFI		ENSSSCG00000001620	7:42301210-42317353	CT737369,CH242-217D23,7:42195308-42367650 (Clone quality: bE217D23 on chr=7; Num_of_Contigs=4; )
MDFIC		ENSSSCG00000016638	18:29708665-29785121
MDGA1		ENSSSCG00000001582	7:37847673-37874697	CT757481,CH242-210D24,7:37817071-37992965 (Clone quality: bE210D24 on chr=7; Num_of_Contigs=2; )
MDGA1		location ⇒	7:37860530-37860232	CT757481,CH242-210D24,7:37817071-37992965 (Clone quality: bE210D24 on chr=7; Num_of_Contigs=2; )
MDGA1		location ⇒	7:37864172-37863843	CT757481,CH242-210D24,7:37817071-37992965 (Clone quality: bE210D24 on chr=7; Num_of_Contigs=2; )
MDGA1		location ⇒	7:37866312-37866042	CT757481,CH242-210D24,7:37817071-37992965 (Clone quality: bE210D24 on chr=7; Num_of_Contigs=2; )
MDGA1		location ⇒	7:37907445-37907391	CT757481,CH242-210D24,7:37817071-37992965 (Clone quality: bE210D24 on chr=7; Num_of_Contigs=2; )
MDGA2		ENSSSCG00000005002	1:185435791-185559863
MDH1		ENSSSCG00000008369	3:72255304-72273546
MDH1B		ENSSSCG00000016133	15:102767831-102782805
MDK		location ⇒	13:30751394-30750816		CU467090,CH242-77H19,13:30717805-30753823 (Clone quality: bE77H19 on chr=13; Num_of_Contigs=5; )
MDM1		ENSSSCG00000000483	5:31860674-31893206
MDM1		location ⇒	5:31735970-31736346		CU694828,CH242-167J2,5:31722757-31740767 (Clone quality: bE167J2 on chr=5; Num_of_Contigs=11; )
MDM1		location ⇒	5:31886947-31886642		CU582882,CH242-236H8,5:31870546-31935759 (Clone quality: bE236H8 on chr=5; Num_of_Contigs=7; )
MDM1		location ⇒	5:31888695-31888319		CU582882,CH242-236H8,5:31870546-31935759 (Clone quality: bE236H8 on chr=5; Num_of_Contigs=7; )
MDM1		location ⇒	5:31892083-31891966		CU582882,CH242-236H8,5:31870546-31935759 (Clone quality: bE236H8 on chr=5; Num_of_Contigs=7; )
MDM2		ENSSSCG00000000488	5:32309302-32339201		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
MDM2		ENSSSCG00000015284	9:62762598-62799967		CU571195,CH242-165H6,9:62751768-62844728 (Clone quality: bE165H6 on chr=9; Num_of_Contigs=4; )
MDM2		ENSSSCG00000015195	9:50325514-50336035		CU633633,CH242-140J10,9:50258982-50355264 (Clone quality: bE140J10 on chr=9; Num_of_Contigs=3; )
MDM2		ENSSSCG00000005995	4:18164500-18237494		CU468161,CH242-67P22,4:18091221-18240979 (Clone quality: bE67P22 on chr=4; Num_of_Contigs=4; )
MDM2		location ⇒	5:32104221-32104132		CU469229,CH242-468E12,5:32103307-32108761 (Clone quality: bE468E12 on chr=5; Num_of_Contigs=30; )
MDM2		location ⇒	5:32310389-32310478		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
MDM2		location ⇒	5:32313668-32313739		CU695219,CH242-44D2,5:32246845-32376912 (Clone quality: bE44D2 on chr=5; Num_of_Contigs=5; )
MDM4		ENSSSCG00000015284	9:62762598-62799967		CU571195,CH242-165H6,9:62751768-62844728 (Clone quality: bE165H6 on chr=9; Num_of_Contigs=4; )
MDP1		ENSSSCG00000001997	7:81424834-81426338		CU019590,CH242-406B17,7:81421108-81438799 (Clone quality: bE406B17 on chr=7; Num_of_Contigs=4; )
ME1		ENSSSCG00000004454	1:87012811-87200539
ME2		ENSSSCG00000004522	1:103637088-103714191
ME3		ENSSSCG00000014919	9:20546397-20647476
ME491		ENSSSCG00000000361	5:20079426-20127422
MEA1		ENSSSCG00000001655	7:43925284-43927207	CR956379,CH242-196P11,7:43779717-43958428 (No clone quality info on bE196P11)
MECP2		ENSSSCG00000012796	X:122848367-122896149	CU914490,CH242-115P19,X:122810839-122896667 (Clone quality: bE115P19 on chr=X; Num_of_Contigs=7; )
MECR		ENSSSCG00000003589	6:58983509-59013247
MED1		ENSSSCG00000011586	13:57202526-57213347		CU656036,CH242-92G17,13:57179246-57221467 (Clone quality: bE92G17 on chr=13; Num_of_Contigs=31; )

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, 1401-46

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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).