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)

THRSP		ENSSSCG00000014888	9:12487203-12487655		FP090886,CH242-508E3,9:12476781-12503029 (Clone quality: bE508E3 on chr=9; Num_of_Contigs=14; )
THSD1		ENSSSCG00000009377	11:15704666-15730465		CU856639,CH242-171M18,11:15650799-15766267 (Clone quality: bE171M18 on chr=11; Num_of_Contigs=3; )
THSD4		ENSSSCG00000004980	1:177224311-177257750		CU570658,CH242-34C23,1:177218018-177258440 (Clone quality: bE34C23 on chr=1; Num_of_Contigs=5; )
THSD7A		ENSSSCG00000015350	9:75987884-76022553
THTPA		ENSSSCG00000002016	7:81882271-81886361		CU468006,CH242-243D20,7:81876674-81897268 (Clone quality: bE243D20 on chr=7; Num_of_Contigs=16; )
THUMPD2		ENSSSCG00000008470	3:93694698-93734479
THUMPD3		ENSSSCG00000011542	13:54924763-54945977
THY1		ENSSSCG00000015122	9:45309364-45310847		CU951455,CH242-416J8,9:45293029-45311092 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
THY1		location ⇒	9:45216531-45216473		CU951455,CH242-416J8,9:45215017-45226078 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
THY1		location ⇒	9:45310000-45308769		CU951455,CH242-416J8,9:45293029-45311092 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
THY1		location ⇒	9:45310813-45310475		CU951455,CH242-416J8,9:45293029-45311092 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
THYN1		ENSSSCG00000015262	9:59363750-59366567		CU695185,CH242-262D16,9:59357111-59367186 (Clone quality: bE262D16 on chr=9; Num_of_Contigs=8; )
TIA1		ENSSSCG00000008329	3:66216145-66228854
TIA1		location ⇒	3:66259135-66258891		CU929337,CH242-249L10,3:66258065-66269192 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
TIA1		location ⇒	3:66259758-66259461		CU929337,CH242-249L10,3:66258065-66269192 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
TIA1		location ⇒	3:66261598-66259954		CU929337,CH242-249L10,3:66258065-66269192 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
TIA1		location ⇒	3:66262837-66262690		CU929337,CH242-249L10,3:66258065-66269192 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
TIAF1		location ⇒	12:43013520-43012993		CU856290,CH242-166L10,12:42944694-43045711 (Clone quality: bE166L10 on chr=12; Num_of_Contigs=5; )
Tial1		ENSSSCG00000010685	14:135428787-135450213
TIAL1		ENSSSCG00000010685	14:135428787-135450213
Tial1		location ⇒	9:126208622-126207623		CU929885,CH242-210K13,9:126207320-126220087 (Clone quality: bE210K13 on chr=9; Num_of_Contigs=7; )
Tial1		location ⇒	9:126208931-126208761		CU929885,CH242-210K13,9:126207320-126220087 (Clone quality: bE210K13 on chr=9; Num_of_Contigs=7; )
TIAM1		ENSSSCG00000004065	1:12300862-12417973
TIAM1		location ⇒	16:26631975-26632149		CU929947,CH242-507D16,16:26631190-26634229 (Clone quality: bE507D16 on chr=16; Num_of_Contigs=14; )
TIAM2		ENSSSCG00000004065	1:12300862-12417973
TICAM2		ENSSSCG00000014216	2:108436037-108436750		CU928874,CH242-1H4,2:108426372-108445484 (Clone quality: bE1H4 on chr=2; Num_of_Contigs=9; )
TIE1		ENSSSCG00000003950	6:120267462-120280686
TIFA		ENSSSCG00000009129	8:94802669-94803223		CU928659,CH242-251I11,8:94798741-94825226 (Clone quality: bE251I11 on chr=8; Num_of_Contigs=13; )
TIGD3		ENSSSCG00000012994	2:5267231-5268676		CU856029,CH242-276E8,2:5261731-5284684 (Clone quality: bE276E8 on chr=2; Num_of_Contigs=9; )
TIGD7		ENSSSCG00000007960	3:34867636-34868997		CU469160,CH242-310A1,3:34860832-34869079 (Clone quality: bE310A1 on chr=3; Num_of_Contigs=18; )
TIMD4		ENSSSCG00000017062	16:63924562-63936462
TIMD4		location ⇒	16:63928126-63927996		CU928514,CH242-128C9,16:63927649-63984410 (Clone quality: bE128C9 on chr=16; Num_of_Contigs=9; )
TIMD4		location ⇒	16:63930959-63930621		CU928514,CH242-128C9,16:63927649-63984410 (Clone quality: bE128C9 on chr=16; Num_of_Contigs=9; )
TIMD4		location ⇒	16:63936462-63936377		CU928514,CH242-128C9,16:63927649-63984410 (Clone quality: bE128C9 on chr=16; Num_of_Contigs=9; )
TIMELESS		ENSSSCG00000000399	5:20751948-20776285		CU655980,CH242-195E17,5:20728687-20784383 (Clone quality: bE195E17 on chr=5; Num_of_Contigs=4; )
TIMM17A		ENSSSCG00000010920	10:24346976-24358397		CU896694,CH242-111D22,10:24267978-24372745 (Clone quality: bE111D22 on chr=10; Num_of_Contigs=6; )
TIMM22		ENSSSCG00000017803	12:44757163-44760586		FP102566,CH242-147O24,12:44749318-44761416 (Clone quality: bE147O24 on chr=12; Num_of_Contigs=11; )
TIMM23		ENSSSCG00000010397	14:94453011-94476463		CU607060,CH242-161K20,14:94357070-94491956 (Clone quality: bE161K20 on chr=14; Num_of_Contigs=18; )
TIMM44		ENSSSCG00000013591	2:51298005-51314013		CU929699,CH242-182L23,2:51289316-51437705 (Clone quality: bE182L23 on chr=2; Num_of_Contigs=2; )
TIMM8A		ENSSSCG00000012494	X:76328723-76331252	FP015816,CH242-60D3,X:76261139-76360009 (Clone quality: bE60D3 on chr=X; Num_of_Contigs=4; )
TIMM9		ENSSSCG00000005074	1:196353419-196355974		CU582907,CH242-119K11,1:196211223-196387617 (Clone quality: bE119K11 on chr=1; Num_of_Contigs=1; )
TIMP1		ENSSSCG00000012277	X:42070430-42074211
TIMP1		location ⇒	X:42071371-42071486		FP015952,CH242-69I19,X:42060518-42073465 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
TIMP1		location ⇒	X:42073019-42073148		FP015952,CH242-69I19,X:42060518-42073465 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
TIMP1		location ⇒	X:42073386-42073465
TIMP1		location ⇒	X:42074041-42074302		FP015952,CH242-69I19,X:42073566-42111685 (Clone quality: bE69I19 on chr=X; Num_of_Contigs=6; )
TIMP2		ENSSSCG00000017164	12:1873679-1917802	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
TIMP2		location ⇒	12:1874141-1873996	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
TIMP2		location ⇒	12:1909074-1908963	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )
TIMP2		location ⇒	12:1915751-1915624	CU942393,CH242-200M2,12:1864056-2044534 (Clone quality: bE200M2 on chr=14; Num_of_Contigs=6; )

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, 1851-8

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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).