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)

TAF1B		ENSSSCG00000008637	3:116976426-117021112		CU914691,CH242-131N23,3:116974642-117032882 (Clone quality: bE131N23 on chr=3; Num_of_Contigs=10; )
TAF1C		ENSSSCG00000002680	6:3031187-3038925		FP085590,CH242-130L20,6:2950464-3147598 (Clone quality: bE130L20 on chr=6; Num_of_Contigs=2; )
TAF1D		ENSSSCG00000014945	9:26386365-26387376		CU694898,CH242-364L8,9:26386311-26391934 (Clone quality: bE364L8 on chr=9; Num_of_Contigs=25; )
TAF2		ENSSSCG00000006000	4:18881965-18950001
TAF3		ENSSSCG00000011127	10:59941441-59979245		CU694853,CH242-240K20,10:59937267-59990271 (Clone quality: bE240K20 on chr=10; Num_of_Contigs=7; )
TAF4B		ENSSSCG00000003718	6:76386691-76501819
TAF5		ENSSSCG00000010597	14:119419172-119435453		CT956026,CH242-70J4,14:119384903-119545395 (Clone quality: bE70J4 on chr=14; Num_of_Contigs=4; )
TAF5L		ENSSSCG00000010187	14:62554361-62585055		CU468504,CH242-54G23,14:62550769-62610051 (Clone quality: bE54G23 on chr=14; Num_of_Contigs=3; )
TAF7L		ENSSSCG00000012493	X:76280753-76297657	FP015816,CH242-60D3,X:76261139-76360009 (Clone quality: bE60D3 on chr=X; Num_of_Contigs=4; )
TAF8		ENSSSCG00000001635	7:42868619-43071454
TAF9		ENSSSCG00000003403	6:47509650-47525984		CU929886,CH242-214O13,6:47459319-47565046 (Clone quality: bE214O13 on chr=6; Num_of_Contigs=3; )
TAF9		ENSSSCG00000016962	16:44795182-44813403		FP085444,CH242-185P14,16:44789989-44813481 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
TAF9		ENSSSCG00000016967	16:44944046-44944843		FP085466,CH242-439N13,16:44942490-44944891 (Clone quality: bE439N13 on chr=16; Num_of_Contigs=9; )
TAF9		location ⇒	16:44807525-44807578		FP085444,CH242-185P14,16:44789989-44813481 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
TAF9		location ⇒	16:44813202-44813267		FP085444,CH242-185P14,16:44789989-44813481 (Clone quality: bE185P14 on chr=16; Num_of_Contigs=5; )
TAF9		location ⇒	16:44930448-44930383		FP085466,CH242-439N13,16:44926219-44933502 (Clone quality: bE439N13 on chr=16; Num_of_Contigs=9; )
TAF9		location ⇒	16:44936171-44936118		FP085466,CH242-439N13,16:44933603-44942389 (Clone quality: bE439N13 on chr=16; Num_of_Contigs=9; )
TAF9B		ENSSSCG00000012442	X:61770720-61782856	CU407109,CH242-173B9,X:61749277-61827164 (Clone quality: bE173B9 on chr=X; Num_of_Contigs=3; )
TAGAP		ENSSSCG00000004053	1:9322641-9331253		CU062408,CH242-82J18,1:9287628-9335226 (Clone quality: bE82J18 on chr=1; Num_of_Contigs=4; )
TAGLN		ENSSSCG00000015073	9:43290832-43296577		CU633260,CH242-267D22,9:43263576-43314400 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )
TAGLN2		ENSSSCG00000006395	4:93948562-93956534		CU856127,CH242-86L20,4:93927306-93957544 (Clone quality: bE86L20 on chr=4; Num_of_Contigs=6; )
TAL1		ENSSSCG00000003887	6:117586510-117593114
TAL1		ENSSSCG00000003888	6:117616501-117640328		CU694906,CH242-407D16,6:117591962-117641359 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
TAL1		location ⇒	6:117583812-117583365		CU694906,CH242-407D16,6:117563083-117591861 (Clone quality: bE407D16 on chr=6; Num_of_Contigs=5; )
Tal2		location ⇒	1:259003449-259003649		CU372900,CH242-201E4,1:258974460-259090674 (Clone quality: bE201E4 on chr=1; Num_of_Contigs=3; )
TALDO1		ENSSSCG00000012847	2:193760-201722
TANC1		ENSSSCG00000015880	15:61502268-61597464
TANC2		ENSSSCG00000017298	12:13039305-13130221		FP085544,CH242-506F5,12:13034350-13132382 (Clone quality: bE506F5 on chr=12; Num_of_Contigs=2; )
TANK		ENSSSCG00000015889	15:63234458-63286480
TANK		ENSSSCG00000017515	12:21457362-21472440		CU655852,CH242-166I5,12:21455434-21477393 (Clone quality: bE166I5 on chr=12; Num_of_Contigs=13; )
TANK		location ⇒	15:63173585-63173797		CU694776,CH242-204F10,15:63069759-63213229 (Clone quality: bE204F10 on chr=15; Num_of_Contigs=3; )
TANK		location ⇒	15:63235276-63234437		CU463159,CH242-223K1,15:63221152-63261321 (Clone quality: bE223K1 on chr=15; Num_of_Contigs=6; )
TANK		location ⇒	15:63239277-63238711		CU463159,CH242-223K1,15:63221152-63261321 (Clone quality: bE223K1 on chr=15; Num_of_Contigs=6; )
TANK		location ⇒	15:63286480-63286333		CU463159,CH242-223K1,15:63277508-63293101 (Clone quality: bE223K1 on chr=15; Num_of_Contigs=6; )
TAOK1		ENSSSCG00000017790	12:43500749-43596046
TAOK3		ENSSSCG00000009850	14:34521823-34744996
TAP1		ENSSSCG00000001462	7:29333762-29342388	CU633196,CH242-203E5,7:29272940-29352095 (Clone quality: bE203E5 on chr=7; Num_of_Contigs=1; )
TAP1		ENSSSCG00000007289	17:40444809-40467374
TAP1		ENSSSCG00000001467	7:29438870-29447509	BX323833,PigI-554F3,7:29352096-29473578 (No clone quality info on bS554F3)
TAP1		location ⇒	7:29333989-29333762	CU633196,CH242-203E5,7:29272940-29352095 (Clone quality: bE203E5 on chr=7; Num_of_Contigs=1; )
TAP1		location ⇒	7:29342382-29341776	CU633196,CH242-203E5,7:29272940-29352095 (Clone quality: bE203E5 on chr=7; Num_of_Contigs=1; )
TAP1		location ⇒	7:29439097-29438870	BX323833,PigI-554F3,7:29352096-29473578 (No clone quality info on bS554F3)
TAP1		location ⇒	7:29447503-29446897	BX323833,PigI-554F3,7:29352096-29473578 (No clone quality info on bS554F3)
TAP2		ENSSSCG00000007289	17:40444809-40467374
TAP2		ENSSSCG00000010008	14:48216507-48227116		CT956025,CH242-69C12,14:48142322-48239134 (Clone quality: bE69C12 on chr=14; Num_of_Contigs=15; )
TAP2		location ⇒	7:21595-21676		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAP2		location ⇒	7:24861-24974		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAP2		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAP2		location ⇒	7:4758-4665		CU657920,CH242-367F14,7:1-36410 (Clone quality: bE367F14 on chr=7; Num_of_Contigs=10; )
TAPBP		ENSSSCG00000000704	5:60207659-60215384		CU633552,CH242-193I18,5:60186767-60298754 (Clone quality: bE193I18 on chr=5; Num_of_Contigs=2; )

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).