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)

TMEM159		ENSSSCG00000007852	3:22591987-22600786		CU928458,CH242-281E22,3:22588723-22602221 (Clone quality: bE281E22 on chr=3; Num_of_Contigs=10; )
TMEM160		ENSSSCG00000003109	6:36613531-36615864		FP103026,CH242-386A5,6:36609283-36635898 (Clone quality: bE386A5 on chr=6; Num_of_Contigs=5; )
TMEM161B		ENSSSCG00000014148	2:85152011-85226957
TMEM163		ENSSSCG00000015700	15:15543730-15915160
TMEM164		ENSSSCG00000012573	X:87274493-87471486
TMEM167A		ENSSSCG00000014134	2:80734369-80764969		CU856406,CH242-350K7,2:80624554-80768859 (Clone quality: bE350K7 on chr=2; Num_of_Contigs=2; )
TMEM167B		ENSSSCG00000006838	4:115469896-115470917		CU207233,CH242-432M23,4:115446550-115504367 (Clone quality: bE432M23 on chr=4; Num_of_Contigs=7; )
TMEM168		ENSSSCG00000016643	18:31647478-31672467
TMEM17		ENSSSCG00000008373	3:73093050-73093328		CU929252,CH242-205I9,3:73092353-73110349 (Clone quality: bE205I9 on chr=3; Num_of_Contigs=15; )
TMEM170A		ENSSSCG00000002710	6:8845482-8862882		CU469483,CH242-374F13,6:8839999-8873482 (Clone quality: bE374F13 on chr=6; Num_of_Contigs=6; )
TMEM170B		ENSSSCG00000001047	7:8467690-8497800
TMEM171		ENSSSCG00000014066	2:71350329-71360898	CU855746,CH242-226A12,2:71242919-71390699 (Clone quality: bE226A12 on chr=2; Num_of_Contigs=1; )
TMEM173		ENSSSCG00000014349	2:128410020-128416999		FP102079,CH242-22H3,2:128394290-128458712 (Clone quality: bE22H3 on chr=2; Num_of_Contigs=6; )
TMEM174		ENSSSCG00000014067	2:71399380-71400278		CU466403,CH242-443A20,2:71390700-71449583 (Clone quality: bE443A20 on chr=2; Num_of_Contigs=5; )
TMEM176A		ENSSSCG00000016443	18:5257305-5260377		CU928555,CH242-184M19,18:5256768-5286512 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
TMEM176B		ENSSSCG00000016444	18:5260670-5266701		CU928555,CH242-184M19,18:5256768-5286512 (Clone quality: bE184M19 on chr=18; Num_of_Contigs=14; )
TMEM177		ENSSSCG00000015742	15:29426065-29427000		CU466249,CH242-215E11,15:29424832-29455229 (Clone quality: bE215E11 on chr=15; Num_of_Contigs=11; )
TMEM178		ENSSSCG00000008471	3:93747853-93832852
TMEM180		ENSSSCG00000010584	14:118489409-118503360		CT990623,CH242-417I15,14:118488646-118541403 (Clone quality: bE417I15 on chr=14; Num_of_Contigs=3; )
TMEM182		ENSSSCG00000008150	3:46861089-46918070		CU928772,CH242-100B10,3:46821258-46942239 (Clone quality: bE100B10 on chr=3; Num_of_Contigs=3; )
TMEM183A		ENSSSCG00000015473	9:106701953-106714012		CU467092,CH242-90M12,9:106646310-106714283 (Clone quality: bE90M12 on chr=9; Num_of_Contigs=8; )
TMEM184A		ENSSSCG00000007560	3:789543-793092		FP103050,CH242-177C19,3:775729-794303 (Clone quality: bE177C19 on chr=3; Num_of_Contigs=4; )
TMEM184B		ENSSSCG00000000108	5:5993095-6039477	BX296548,PigE-193I9,5:5978065-6150316 (Clone quality: bT193I9 on chr=5; Num_of_Contigs=8; )
TMEM185A		ENSSSCG00000012739	X:120066452-120079917		FP102033,CH242-101J9,X:120065327-120099525 (Clone quality: bE101J9 on chr=X; Num_of_Contigs=8; )
TMEM187		ENSSSCG00000012794	X:122809928-122810857
TMEM189		ENSSSCG00000007467	17:53661012-53676305		CU682662,CH242-263E16,17:53654679-53714971 (Clone quality: bE263E16 on chr=17; Num_of_Contigs=5; )
TMEM19		ENSSSCG00000000510	5:34764420-34788383
TMEM192		ENSSSCG00000008859	8:38046870-38066491
TMEM194B		ENSSSCG00000016053	15:89699173-89725210
TMEM195		ENSSSCG00000015356	9:79125394-79469181
TMEM196		ENSSSCG00000015373	9:83520192-83525893		FP015893,CH242-198A20,9:83519044-83539705 (Clone quality: bE198A20 on chr=9; Num_of_Contigs=6; )
TMEM198		ENSSSCG00000000367	5:20226035-20229728	CU606916,CH242-141C7,5:20096881-20252808 (Clone quality: bE141C7 on chr=5; Num_of_Contigs=1; )
TMEM2		ENSSSCG00000005260	1:235398328-235441600
TMEM20		ENSSSCG00000010482	14:110615571-110623503
TMEM200A		ENSSSCG00000004201	1:34156102-34157577		CU062452,CH242-68O17,1:34135126-34190169 (Clone quality: bE68O17 on chr=1; Num_of_Contigs=5; )
TMEM201		ENSSSCG00000003393	6:47047055-47070148		CU929791,CH242-402I11,6:47022594-47086176 (Clone quality: bE402I11 on chr=6; Num_of_Contigs=3; )
TMEM202		ENSSSCG00000001926	7:66221146-66232596
TMEM203		ENSSSCG00000005860	1:294451590-294452000		CU928955,CH242-34I15,1:294431557-294452171 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
TMEM204		ENSSSCG00000008021	3:36031752-36043933		CU694571,CH242-220O7,3:36001073-36124729 (Clone quality: bE220O7 on chr=3; Num_of_Contigs=5; )
TMEM205		ENSSSCG00000013622	2:52308286-52311145		CU855518,CH242-272A5,2:52305877-52317098 (Clone quality: bE272A5 on chr=2; Num_of_Contigs=10; )
TMEM206		ENSSSCG00000015598	9:123431093-123463064		CU972375,CH242-105J20,9:123425470-123535928 (Clone quality: bE105J20 on chr=9; Num_of_Contigs=6; )
TMEM208		ENSSSCG00000002790	6:13374429-13377294		CU929920,CH242-351A16,6:13369150-13384764 (Clone quality: bE351A16 on chr=6; Num_of_Contigs=8; )
TMEM209		ENSSSCG00000016563	18:16882229-16901074		CU655939,CH242-371G20,18:16845786-16901352 (Clone quality: bE371G20 on chr=18; Num_of_Contigs=7; )
TMEM211		ENSSSCG00000009952	14:43246090-43250259		CU468632,CH242-228L5,14:43236373-43254892 (Clone quality: bE228L5 on chr=14; Num_of_Contigs=11; )
TMEM212		ENSSSCG00000011751	13:83792807-83812741		CU467804,CH242-91K14,13:83747916-83834035 (Clone quality: bE91K14 on chr=13; Num_of_Contigs=3; )
TMEM213		ENSSSCG00000016514	18:9018813-9024193		CU640415,CH242-310G20,18:8932802-9029284 (Clone quality: bE310G20 on chr=18; Num_of_Contigs=9; )
TMEM214		ENSSSCG00000008559	3:104508890-104517222		CU896571,CH242-143O19,3:104492537-104523996 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
TMEM215		ENSSSCG00000011002	10:32244410-32245117		CU570728,CH242-239M16,10:32220202-32285067 (Clone quality: bE239M16 on chr=10; Num_of_Contigs=4; )
TMEM216		ENSSSCG00000013084	2:8422044-8428268		CU896534,CH242-169N17,2:8417872-8437313 (Clone quality: bE169N17 on chr=2; Num_of_Contigs=6; )
TMEM217		ENSSSCG00000001576	7:37458401-37458979		CT954214,CH242-328K12,7:37421504-37477076 (Clone quality: bE328K12 on chr=7; Num_of_Contigs=3; )

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).