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)

MBP		location ⇒	1:154975078-154973743		CU633304,CH242-510G7,1:154972433-154975134 (Clone quality: bE510G7 on chr=1; Num_of_Contigs=16; )
MBP		location ⇒	1:154984732-154984946		CU633304,CH242-510G7,1:154984541-154990234 (Clone quality: bE510G7 on chr=1; Num_of_Contigs=16; )
MBP		location ⇒	1:155011201-155011100		CU633304,CH242-510G7,1:155010932-155023115 (Clone quality: bE510G7 on chr=1; Num_of_Contigs=16; )
MBP		location ⇒	1:155017179-155017066		CU633304,CH242-510G7,1:155010932-155023115 (Clone quality: bE510G7 on chr=1; Num_of_Contigs=16; )
MBTD1		ENSSSCG00000017592	12:25122665-25144151		CU929012,CH242-205C11,12:25114535-25144401 (Clone quality: bE205C11 on chr=12; Num_of_Contigs=7; )
MBTPS1		ENSSSCG00000002682	6:3098553-3140681		FP085590,CH242-130L20,6:2950464-3147598 (Clone quality: bE130L20 on chr=6; Num_of_Contigs=2; )
MBTPS2		ENSSSCG00000012165	X:16745463-16778168		CU694699,CH242-266L17,X:16745172-16782996 (Clone quality: bE266L17 on chr=X; Num_of_Contigs=9; )
MC3R		ENSSSCG00000007491	17:59403370-59404545	CR956393,CH242-163M14,17:59226440-59420123 (No clone quality info on bE163M14)
MC4R		ENSSSCG00000004904	1:167726909-167728640
MCAM		ENSSSCG00000015116	9:45127586-45134356		CU915638,CH242-115L13,9:45114077-45138958 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
MCAM		location ⇒	9:45128386-45128315		CU915638,CH242-115L13,9:45114077-45138958 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
MCAM		location ⇒	9:45128812-45128700		CU915638,CH242-115L13,9:45114077-45138958 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
MCART6		ENSSSCG00000012540	X:82606767-82607687		FP085370,CH242-209D19,X:82542348-82608351 (Clone quality: bE209D19 on chr=X; Num_of_Contigs=17; )
MCAT		ENSSSCG00000000031	5:2378276-2386278		CU633237,CH242-1K8,5:2374690-2392078 (Clone quality: bE1K8 on chr=5; Num_of_Contigs=19; )
MCC		ENSSSCG00000014203	2:105231325-105337853
MCCD1		ENSSSCG00000001399	7:27615469-27616931	CU467793,CH242-60C3,7:27581747-27762222 (Clone quality: bE60C3 on chr=7; Num_of_Contigs=1; )
mCD48		ENSSSCG00000006379	4:93278346-93292708		CU915315,CH242-208F9,4:93261946-93408226 (Clone quality: bE208F9 on chr=4; Num_of_Contigs=2; )
mCD84		ENSSSCG00000006381	4:93381789-93570006
MCEE		ENSSSCG00000004846	1:151629912-151833127
MCEMP1		ENSSSCG00000013574	2:51019089-51021306		CU929919,CH242-334A8,2:51013584-51060863 (Clone quality: bE334A8 on chr=2; Num_of_Contigs=7; )
MCF2		ENSSSCG00000012712	X:112232954-112342243
MCF2L		ENSSSCG00000009559	11:78922393-78961985
MCFD2		ENSSSCG00000008435	3:87007827-87018545		CU468462,CH242-352K9,3:86991338-87021179 (Clone quality: bE352K9 on chr=3; Num_of_Contigs=5; )
MCFD2		location ⇒	3:87014681-87014834		CU468462,CH242-352K9,3:86991338-87021179 (Clone quality: bE352K9 on chr=3; Num_of_Contigs=5; )
MCFD2		location ⇒	3:87015871-87016031		CU468462,CH242-352K9,3:86991338-87021179 (Clone quality: bE352K9 on chr=3; Num_of_Contigs=5; )
MCFD2		location ⇒	3:87017989-87018876		CU468462,CH242-352K9,3:86991338-87021179 (Clone quality: bE352K9 on chr=3; Num_of_Contigs=5; )
MCFD2		location ⇒	3:87019343-87019740		CU468462,CH242-352K9,3:86991338-87021179 (Clone quality: bE352K9 on chr=3; Num_of_Contigs=5; )
MCHR1		ENSSSCG00000000074	5:3999586-4001914		CU633651,CH242-197C11,5:3905925-4011400 (Clone quality: bE197C11 on chr=5; Num_of_Contigs=3; )
MCHR2		ENSSSCG00000004356	1:70196486-70215299
MCL1		ENSSSCG00000006652	4:102518112-102522972		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
MCL1		location ⇒	4:102518898-102518120		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
MCL1		location ⇒	4:102520001-102519760		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
MCL1		location ⇒	4:102520975-102520062		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
MCL1		location ⇒	4:102521850-102521600		CU655899,CH242-160A10,4:102490407-102528327 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
MCM2		ENSSSCG00000011624	13:60084220-60122864
MCM3		location ⇒	7:53231823-53231759		CT737387,CH242-301B9,7:53164546-53326569 (Clone quality: bE301B9 on chr=7; Num_of_Contigs=2; )
MCM3		location ⇒	7:53233071-53232959		CT737387,CH242-301B9,7:53164546-53326569 (Clone quality: bE301B9 on chr=7; Num_of_Contigs=2; )
MCM3		location ⇒	7:53233776-53233535		CT737387,CH242-301B9,7:53164546-53326569 (Clone quality: bE301B9 on chr=7; Num_of_Contigs=2; )
MCM3AP		location ⇒	X:55834618-55834552		CU929942,CH242-488P24,X:55776125-55835310 (Clone quality: bE488P24 on chr=X; Num_of_Contigs=8; )
MCM3AP		location ⇒	X:59323890-59323839		FP102145,CH242-190N13,X:59314273-59359136 (Clone quality: bE190N13 on chr=X; Num_of_Contigs=22; )
MCM3AP		location ⇒	X:63919417-63919484		CU915379,CH242-123K13,X:63918631-63934986 (Clone quality: bE123K13 on chr=X; Num_of_Contigs=4; )
MCM3AP		location ⇒	X:93659829-93659883	CU467610,CH242-94D21,X:93508276-93675199 (Clone quality: bE94D21 on chr=X; Num_of_Contigs=10; )
MCM4		ENSSSCG00000006273	4:82641978-82651630
MCM8		ENSSSCG00000007047	17:13930830-13972520		CU311185,CH242-222G18,17:13889408-14007446 (Clone quality: bE222G18 on chr=17; Num_of_Contigs=4; )
MCM9		ENSSSCG00000004246	1:44967903-45062202
MCOLN1		ENSSSCG00000013570	2:50919778-50954272
MCOLN2		ENSSSCG00000003755	6:88815422-88875161
MCOLN3		ENSSSCG00000006949	4:135755791-135762123		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
MCP		ENSSSCG00000003392	6:47008315-47042622
MCP		ENSSSCG00000004109	1:17427345-17451645		CU459105,CH242-241M9,1:17419990-17464787 (Clone quality: bE241M9 on chr=1; Num_of_Contigs=5; )

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).