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)

SH2D2A		ENSSSCG00000006466	4:96975677-96984979		CU151867,CH242-283E3,4:96970968-96992486 (Clone quality: bE283E3 on chr=4; Num_of_Contigs=3; )
SH2D3A		ENSSSCG00000013555	2:50284042-50291369		CU856214,CH242-17I12,2:50262831-50301105 (Clone quality: bE17I12 on chr=2; Num_of_Contigs=13; )
SH2D3C		ENSSSCG00000005620	1:282590719-282617749		FP102445,CH242-434F23,1:282582851-282621872 (Clone quality: bE434F23 on chr=1; Num_of_Contigs=8; )
SH2D4A		ENSSSCG00000007006	17:9072985-9113790
SH2D4B		ENSSSCG00000010342	14:85862244-85946762		CT737327,CH242-94O23,14:85788343-85946849 (Clone quality: bE94O23 on chr=14; Num_of_Contigs=2; )
SH2D5		ENSSSCG00000003509	6:54263378-54269985		FP243370,CH242-400E6,6:54255937-54276513 (Clone quality: bE400E6 on chr=6; Num_of_Contigs=4; )
SH2D6		ENSSSCG00000008240	3:54190886-54196554		CU951451,CH242-157C24,3:54186194-54215172 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
SH2D6		location ⇒	3:54194735-54195034		CU951451,CH242-157C24,3:54186194-54215172 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
SH2D6		location ⇒	3:54195199-54195359		CU951451,CH242-157C24,3:54186194-54215172 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
SH2D6		location ⇒	3:54195981-54196085		CU951451,CH242-157C24,3:54186194-54215172 (Clone quality: bE157C24 on chr=3; Num_of_Contigs=5; )
SH2D7		ENSSSCG00000001764	7:53837411-53847004		CU467054,CH242-222N19,7:53795062-53849472 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
SH3BGRL		ENSSSCG00000012452	X:64306911-64307096		FP067414,CH242-270H1,X:64304821-64310762 (Clone quality: bE270H1 on chr=X; Num_of_Contigs=10; )
SH3BGRL		location ⇒	X:64307097-64306918		FP067414,CH242-270H1,X:64304821-64310762 (Clone quality: bE270H1 on chr=X; Num_of_Contigs=10; )
SH3BGRL		location ⇒	X:64351847-64351699		FP067414,CH242-270H1,X:64349382-64352009 (Clone quality: bE270H1 on chr=X; Num_of_Contigs=10; )
SH3BGRL		location ⇒	X:64359497-64359415		FP067414,CH242-270H1,X:64352110-64364737 (Clone quality: bE270H1 on chr=X; Num_of_Contigs=10; )
SH3BGRL		location ⇒	X:64398226-64398305		FP067414,CH242-270H1,X:64396239-64400880 (Clone quality: bE270H1 on chr=X; Num_of_Contigs=10; )
SH3BGRL2		ENSSSCG00000004468	1:91464800-91465556		CU075379,CH242-145F12,1:91438879-91473511 (Clone quality: bE145F12 on chr=1; Num_of_Contigs=7; )
SH3BP5		ENSSSCG00000011191	13:2087876-2121004		CU915680,CH242-245B17,13:2056801-2127030 (Clone quality: bE245B17 on chr=13; Num_of_Contigs=5; )
SH3BP5L		ENSSSCG00000013979	2:65645480-65657194		CU972405,CH242-131P19,2:65612170-65673696 (Clone quality: bE131P19 on chr=2; Num_of_Contigs=4; )
SH3D19		ENSSSCG00000009018	8:66913895-66979740
SH3D20		ENSSSCG00000017328	12:15936753-15942869		FP016139,CH242-68H24,12:15863328-15943192 (Clone quality: bE68H24 on chr=12; Num_of_Contigs=2; )
SH3GL1		ENSSSCG00000013508	2:48584668-48614909		CU972396,CH242-401E10,2:48541506-48658119 (Clone quality: bE401E10 on chr=2; Num_of_Contigs=4; )
SH3GL2		ENSSSCG00000005177	1:213976806-214178492
SH3GL3		ENSSSCG00000001795	7:57419980-57555322
SH3GLB1		ENSSSCG00000006930	4:134256175-134280292	CU695038,CH242-252F2,4:134247814-134289275 (Clone quality: bE252F2 on chr=13; Num_of_Contigs=4; )
SH3GLB2		ENSSSCG00000005668	1:283988486-284006610	CU076102,CH242-68C14,1:283855073-284074390 (Clone quality: bE68C14 on chr=1; Num_of_Contigs=6; )
SH3KBP1		ENSSSCG00000012160	X:15098687-15256316
SH3KBP1		location ⇒	X:15104120-15103852		FP015812,CH242-6I13,X:15102112-15253839 (Clone quality: bE6I13 on chr=X; Num_of_Contigs=3; )
SH3KBP1		location ⇒	X:15109859-15109728		FP015812,CH242-6I13,X:15102112-15253839 (Clone quality: bE6I13 on chr=X; Num_of_Contigs=3; )
SH3KBP1		location ⇒	X:15113326-15113216		FP015812,CH242-6I13,X:15102112-15253839 (Clone quality: bE6I13 on chr=X; Num_of_Contigs=3; )
SH3KBP1		location ⇒	X:15156419-15156287		FP015812,CH242-6I13,X:15102112-15253839 (Clone quality: bE6I13 on chr=X; Num_of_Contigs=3; )
SH3PXD2A		ENSSSCG00000010604	14:119625068-119891611
SH3PXD2B		ENSSSCG00000016993	16:49182275-49266006
SH3RF1		ENSSSCG00000009716	14:20537396-20578855
SH3RF2		ENSSSCG00000014410	2:133615751-133631427		CU928414,CH242-495G3,2:133557524-133651075 (Clone quality: bE495G3 on chr=2; Num_of_Contigs=5; )
SH3RF3		ENSSSCG00000008133	3:42388270-42491808		CU914503,CH242-223B15,3:42350228-42520767 (Clone quality: bE223B15 on chr=3; Num_of_Contigs=5; )
SH3TC1		ENSSSCG00000008722	8:3477163-3486608		FP003588,CH242-515K21,8:3475999-3487297 (Clone quality: bE515K21 on chr=8; Num_of_Contigs=11; )
SH3YL1		ENSSSCG00000008660	3:121540973-121557947		FP102370,CH242-323F11,3:121518511-121558380 (Clone quality: bE323F11 on chr=3; Num_of_Contigs=8; )
SHANK1		ENSSSCG00000003215	6:38985752-39116792
SHANK2		ENSSSCG00000012864	2:1273564-1283402
SHARPIN		ENSSSCG00000005914	4:587436-592087		FP085492,CH242-176F2,4:573710-645862 (Clone quality: bE176F2 on chr=4; Num_of_Contigs=15; )
SHAS2		ENSSSCG00000005992	4:17286752-17317131		CU302381,CH242-235I2,4:17213494-17395022 (Clone quality: bE235I2 on chr=4; Num_of_Contigs=1; )
SHAS2		location ⇒	4:17300090-17300720		CU302381,CH242-235I2,4:17213494-17395022 (Clone quality: bE235I2 on chr=4; Num_of_Contigs=1; )
SHAS2		location ⇒	4:17315455-17316903		CU302381,CH242-235I2,4:17213494-17395022 (Clone quality: bE235I2 on chr=4; Num_of_Contigs=1; )
SHAS2		location ⇒	4:17376145-17377080		CU302381,CH242-235I2,4:17213494-17395022 (Clone quality: bE235I2 on chr=4; Num_of_Contigs=1; )
SHAS2		location ⇒	4:17377504-17377575		CU302381,CH242-235I2,4:17213494-17395022 (Clone quality: bE235I2 on chr=4; Num_of_Contigs=1; )
SHB		ENSSSCG00000005358	1:250081544-250196451
SHC1		ENSSSCG00000006539	4:98928835-98935863		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
SHC1		location ⇒	4:98925542-98925671		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
SHC1		location ⇒	4:98929161-98929329		CU207227,CH242-365J2,4:98889060-98947503 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )

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, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).