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)

ACSL4		location ⇒	X:88862463-88860887		FP102602,CH242-17O13,X:88856316-88942322 (Clone quality: bE17O13 on chr=X; Num_of_Contigs=3; )
ACSL4		location ⇒	X:88956086-88954834		FP102252,CH242-3M24,X:88947323-88979232 (Clone quality: bE3M24 on chr=X; Num_of_Contigs=3; )
ACSL4		location ⇒	X:88957716-88956140		FP102252,CH242-3M24,X:88947323-88979232 (Clone quality: bE3M24 on chr=X; Num_of_Contigs=3; )
ACSL5		ENSSSCG00000010636	14:128525831-128723985
ACSL6		ENSSSCG00000014272	2:122199995-122253668		CU694579,CH242-236B14,2:122166991-122285332 (Clone quality: bE236B14 on chr=2; Num_of_Contigs=4; )
ACSM3		ENSSSCG00000007857	3:22866216-22895205
ACSS1		ENSSSCG00000007133	17:32401466-32439474
ACSS2		ENSSSCG00000007286	17:40325771-40381390
ACSS3		ENSSSCG00000000939	5:94236008-94404011
ACTA1		ENSSSCG00000010190	14:62713314-62716162		CU468504,CH242-54G23,14:62667892-62725607 (Clone quality: bE54G23 on chr=14; Num_of_Contigs=3; )
ACTA2		ENSSSCG00000010447	14:105767451-105786296		CT737322,CH242-203A14,14:105756080-105909175 (Clone quality: bE203A14 on chr=14; Num_of_Contigs=1; )
ACTB		ENSSSCG00000007585	3:3868537-3871915		FP102569,CH242-151E19,3:3862886-3877824 (Clone quality: bE151E19 on chr=3; Num_of_Contigs=3; )
ACTC		location ⇒	1:143734426-143734464		CU633172,CH242-367L17,1:143731030-143743680 (Clone quality: bE367L17 on chr=1; Num_of_Contigs=16; )
ACTC		location ⇒	1:143736323-143736650		CU633172,CH242-367L17,1:143731030-143743680 (Clone quality: bE367L17 on chr=1; Num_of_Contigs=16; )
ACTC		location ⇒	1:143903482-143903520		CU074288,CH242-130A20,1:143896024-143918989 (Clone quality: bE130A20 on chr=1; Num_of_Contigs=5; )
ACTC		location ⇒	1:143908405-143908732		CU074288,CH242-130A20,1:143896024-143918989 (Clone quality: bE130A20 on chr=1; Num_of_Contigs=5; )
ACTC1		ENSSSCG00000004803	1:143734388-143908734
ACTG2		ENSSSCG00000008294	3:63607036-63615297
Actin		location ⇒	3:3870282-3870718		FP102569,CH242-151E19,3:3862886-3877824 (Clone quality: bE151E19 on chr=3; Num_of_Contigs=3; )
Actin		location ⇒	3:3870815-3870997		FP102569,CH242-151E19,3:3862886-3877824 (Clone quality: bE151E19 on chr=3; Num_of_Contigs=3; )
Actin		location ⇒	3:63607243-63607171		CU657932,CH242-344L19,3:63585641-63613367 (Clone quality: bE344L19 on chr=3; Num_of_Contigs=5; )
Actin		location ⇒	3:63611727-63611551		CU657932,CH242-344L19,3:63585641-63613367 (Clone quality: bE344L19 on chr=3; Num_of_Contigs=5; )
ACTL6A		ENSSSCG00000011762	13:89354287-89383159
ACTL6B		ENSSSCG00000007670	3:6865731-6880850
ACTL7A		ENSSSCG00000005439	1:262638470-262639789		CU571147,CH242-6L21,1:262605498-262654893 (Clone quality: bE6L21 on chr=1; Num_of_Contigs=4; )
ACTL7B		ENSSSCG00000005438	1:262632086-262633339		CU571147,CH242-6L21,1:262605498-262654893 (Clone quality: bE6L21 on chr=1; Num_of_Contigs=4; )
ACTL8		ENSSSCG00000003487	6:52710185-52714152
ACTL9		ENSSSCG00000013605	2:51819829-51821079		CU914395,CH242-109L6,2:51805327-51871830 (Clone quality: bE109L6 on chr=2; Num_of_Contigs=6; )
ACTN1		ENSSSCG00000002300	7:100916496-100960471		CU683824,CH242-124P13,7:100905633-101006560 (Clone quality: bE124P13 on chr=7; Num_of_Contigs=3; )
ACTN2		ENSSSCG00000010144	14:55841319-55911445
ACTN2		location ⇒	14:55847616-55847468		CU467009,CH242-473N13,14:55802618-55906356 (Clone quality: bE473N13 on chr=14; Num_of_Contigs=6; )
ACTN2		location ⇒	14:55848425-55848244		CU467009,CH242-473N13,14:55802618-55906356 (Clone quality: bE473N13 on chr=14; Num_of_Contigs=6; )
ACTN2		location ⇒	14:55849477-55849340		CU467009,CH242-473N13,14:55802618-55906356 (Clone quality: bE473N13 on chr=14; Num_of_Contigs=6; )
ACTN2		location ⇒	14:55852752-55852565		CU467009,CH242-473N13,14:55802618-55906356 (Clone quality: bE473N13 on chr=14; Num_of_Contigs=6; )
ACTN4		ENSSSCG00000002965	6:32736161-32760621
ACTR1A		ENSSSCG00000010585	14:118506798-118524008		CT990623,CH242-417I15,14:118488646-118541403 (Clone quality: bE417I15 on chr=14; Num_of_Contigs=3; )
ACTR1B		ENSSSCG00000008194	3:51927127-51933701
ACTR2		location ⇒	3:70567268-70566527		CU861554,CH242-286M19,3:70506212-70650791 (Clone quality: bE286M19 on chr=3; Num_of_Contigs=1; )
ACTR2		location ⇒	3:70579109-70578965		CU861554,CH242-286M19,3:70506212-70650791 (Clone quality: bE286M19 on chr=3; Num_of_Contigs=1; )
ACTR2		location ⇒	3:70587806-70587585		CU861554,CH242-286M19,3:70506212-70650791 (Clone quality: bE286M19 on chr=3; Num_of_Contigs=1; )
ACTR2		location ⇒	3:70594209-70594097		CU861554,CH242-286M19,3:70506212-70650791 (Clone quality: bE286M19 on chr=3; Num_of_Contigs=1; )
ACTR3		ENSSSCG00000015710	15:18463905-18526707
ACTR3		location ⇒	5:85316837-85317835		CU457421,CH242-86L11,5:85310023-85317855 (Clone quality: bE86L11 on chr=5; Num_of_Contigs=18; )
ACTR3		location ⇒	5:85316837-85317835		CU457421,CH242-86L11,5:85310023-85317855 (Clone quality: bE86L11 on chr=5; Num_of_Contigs=18; )
ACTR5		ENSSSCG00000007349	17:43988025-44007927
ACTR6		ENSSSCG00000000879	5:79668152-79675353
ACTR8		ENSSSCG00000011458	13:30200890-30224250		CU466421,CH242-96K10,13:30195284-30280608 (Clone quality: bE96K10 on chr=13; Num_of_Contigs=2; )
ACTRT1		ENSSSCG00000012648	X:103026366-103027499	CU550660,CH242-196N11,X:102984061-103140424 (Clone quality: bE196N11 on chr=X; Num_of_Contigs=1; )
ACTRT2		ENSSSCG00000003357	6:43371888-43373021		FP245399,CH242-395N22,6:43366536-43382106 (Clone quality: bE395N22 on chr=6; Num_of_Contigs=7; )
ACVR1		ENSSSCG00000015874	15:60075213-60214837

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, 1751-32

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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).