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)

MSR		ENSSSCG00000017100	16:71437908-71462478		CU695161,CH242-40A14,16:71420211-71475456 (Clone quality: bE40A14 on chr=16; Num_of_Contigs=8; )
MSR		location ⇒	6:57378956-57379053		CU457419,CH242-59A10,6:57375113-57413854 (Clone quality: bE59A10 on chr=6; Num_of_Contigs=10; )
MSR		location ⇒	6:57383562-57385648		CU457419,CH242-59A10,6:57375113-57413854 (Clone quality: bE59A10 on chr=6; Num_of_Contigs=10; )
MSR1		ENSSSCG00000006979	17:3672614-3753871
MSR1		location ⇒	17:3673014-3672799		CU927923,CH242-177H19,17:3595305-3710043 (Clone quality: bE177H19 on chr=17; Num_of_Contigs=2; )
MSR1		location ⇒	17:3686164-3685973		CU927923,CH242-177H19,17:3595305-3710043 (Clone quality: bE177H19 on chr=17; Num_of_Contigs=2; )
MSR1		location ⇒	17:3734633-3734240		CU927923,CH242-177H19,17:3710144-3750336 (Clone quality: bE177H19 on chr=17; Num_of_Contigs=2; )
MSR1		location ⇒	17:3753868-3753815		CU856052,CH242-457I4,17:3750337-3763232 (Clone quality: bE457I4 on chr=17; Num_of_Contigs=3; )
MSRA		ENSSSCG00000009684	14:13641085-13868167
MSRB2		ENSSSCG00000011077	10:49406600-49468921
MSRB3		ENSSSCG00000000470	5:29406217-29561170
MST1		ENSSSCG00000007386	17:49278757-49431613
MST1		location ⇒	13:26974375-26974608		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
MST1		location ⇒	13:26974710-26974852		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
MST1		location ⇒	13:26974945-26975056		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
MST1		location ⇒	13:26975135-26975282		CU914539,CH242-222N14,13:26945819-27078203 (Clone quality: bE222N14 on chr=13; Num_of_Contigs=2; )
MSTN		ENSSSCG00000016047	15:89151697-89157090
MSX1		ENSSSCG00000008727	8:4267194-4270451		CU915529,CH242-94K3,8:4258867-4270512 (Clone quality: bE94K3 on chr=8; Num_of_Contigs=14; )
MSX2		ENSSSCG00000016978	16:46965341-46970202		CU695143,CH242-275B20,16:46900693-46973595 (Clone quality: bE275B20 on chr=16; Num_of_Contigs=9; )
MT-CO2		ENSSSCG00000018078	MT:8203-8890
MT-CYB		ENSSSCG00000018094	MT:15342-16481
MT-III		ENSSSCG00000004611	1:121224328-121251287
MT1-MMP		ENSSSCG00000002039	7:82408683-82419655		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
MT1-MMP		location ⇒	7:82410538-82408847		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
MT1-MMP		location ⇒	7:82412513-82412351		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
MT1-MMP		location ⇒	7:82413212-82413049		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
MT1-MMP		location ⇒	7:82414335-82414026		CT737318,CH242-17H24,7:82408265-82613937 (Clone quality: bE17H24 on chr=7; Num_of_Contigs=1; )
MT2A		location ⇒	2:31964038-31964132	CU914651,CH242-259D15,2:31888461-32060002 (Clone quality: bE259D15 on chr=2; Num_of_Contigs=7; )
MT3		ENSSSCG00000006132	4:50225464-50382640
MTA2		ENSSSCG00000013062	2:7488708-7497133
MTA3		ENSSSCG00000008464	3:91173007-91293249
MTAP		ENSSSCG00000005135	1:209618709-209668877		CU582802,CH242-276P14,1:209585174-209748628 (Clone quality: bE276P14 on chr=1; Num_of_Contigs=1; )
MTBP		ENSSSCG00000005995	4:18164500-18237494		CU468161,CH242-67P22,4:18091221-18240979 (Clone quality: bE67P22 on chr=4; Num_of_Contigs=4; )
MTCH1		ENSSSCG00000001571	7:37250480-37268529	CT841548,CH242-123L1,7:37183904-37318303 (Clone quality: bE123L1 on chr=7; Num_of_Contigs=1; )
MTCH2		ENSSSCG00000013232	2:13114682-13135473
MTCH2		location ⇒	18:46005578-46006596		FP236676,CH242-236O10,18:45995820-46011919 (Clone quality: bE236O10 on chr=18; Num_of_Contigs=8; )
MTCP1		ENSSSCG00000002497	7:125742462-125747424	CT867964,CH242-267C2,7:125614014-125812235 (Clone quality: bE267C2 on chr=7; Num_of_Contigs=1; )
MTCP1		ENSSSCG00000012815	X:123541536-123542052	CU861979,CH242-305A15,X:123389549-123544360 (Clone quality: bE305A15 on chr=X; Num_of_Contigs=11; )
MTCP1		ENSSSCG00000012816	X:123542283-123546487
MTCP1		location ⇒	X:123546213-123546485	CU914693,CH242-146E2,X:123544361-123560506 (Clone quality: bE146E2 on chr=X; Num_of_Contigs=16; )
MTCP1NB		ENSSSCG00000012816	X:123542283-123546487
MTDH		location ⇒	4:39382735-39382605		CU571149,CH242-82O8,4:39360823-39418721 (Clone quality: bE82O8 on chr=4; Num_of_Contigs=6; )
MTDH		location ⇒	4:39387012-39385248		CU571149,CH242-82O8,4:39360823-39418721 (Clone quality: bE82O8 on chr=4; Num_of_Contigs=6; )
MTDH		location ⇒	4:39413411-39413173		CU571149,CH242-82O8,4:39360823-39418721 (Clone quality: bE82O8 on chr=4; Num_of_Contigs=6; )
MTDH		location ⇒	4:39659500-39660197		CU468022,CH242-236P6,4:39610301-39685201 (Clone quality: bE236P6 on chr=4; Num_of_Contigs=6; )
MTERF		ENSSSCG00000015309	9:67331173-67337271		CU693404,CH242-252J8,9:67192562-67372611 (Clone quality: bE252J8 on chr=9; Num_of_Contigs=2; )
MTERFD1		ENSSSCG00000006090	4:40784491-40828708
MTERFD2		ENSSSCG00000016380	15:132131010-132136088		FP102549,CH242-125C7,15:132124535-132139351 (Clone quality: bE125C7 on chr=15; Num_of_Contigs=15; )
MTERFD3		ENSSSCG00000000165	5:11588233-11589390		CU463085,CH242-354A15,5:11585115-11599431 (Clone quality: bE354A15 on chr=5; Num_of_Contigs=4; )
MTF1		ENSSSCG00000003641	6:63457980-63458548	CR956649,PigE-92E11,6:63451761-63579213 (No clone quality info on bT92E11)

Go to records:
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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).