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)

TUBAL3		ENSSSCG00000011144	10:61769767-61773311		FP016037,CH242-134E10,10:61759415-61783112 (Clone quality: bE134E10 on chr=10; Num_of_Contigs=5; )
TUBB		ENSSSCG00000001361	7:26940752-26945261	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
TUBB		location ⇒	7:26942766-26941617	CU326403,CH242-198M20,7:26882096-27123407 (Clone quality: bE198M20 on chr=7; Num_of_Contigs=9; )
TUBB		location ⇒	7:27207271-27208420	CU480634,CH242-391N4,7:27128408-27216112 (Clone quality: bE391N4 on chr=7; Num_of_Contigs=11; )
TUBB		location ⇒	7:2809926-2810917		CU407341,CH242-81A10,7:2805734-2826021 (Clone quality: bE81A10 on chr=7; Num_of_Contigs=13; )
TUBB		location ⇒	7:2848408-2849399		CU407341,CH242-81A10,7:2847920-2859204 (Clone quality: bE81A10 on chr=7; Num_of_Contigs=13; )
TUBB1		ENSSSCG00000007523	17:61778289-61785255	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
TUBB2B		ENSSSCG00000001006	7:2808124-2810969		CU407341,CH242-81A10,7:2805734-2826021 (Clone quality: bE81A10 on chr=7; Num_of_Contigs=13; )
TUBB2C		ENSSSCG00000005849	1:294347025-294349339		CU928955,CH242-34I15,1:294322778-294354935 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
TUBB3		ENSSSCG00000002639	6:163123-172126		FP102308,CH242-96G18,6:154048-173531 (Clone quality: bE96G18 on chr=6; Num_of_Contigs=17; )
TUBB4		ENSSSCG00000013545	2:49927632-49931371
TUBB4		ENSSSCG00000002639	6:163123-172126		FP102308,CH242-96G18,6:154048-173531 (Clone quality: bE96G18 on chr=6; Num_of_Contigs=17; )
TUBB4		location ⇒	2:49927741-49927796		CU929921,CH242-352E11,2:49910048-49929429 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
TUBB4		location ⇒	2:49928543-49928657		CU929921,CH242-352E11,2:49910048-49929429 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
TUBB4		location ⇒	2:49930313-49931322		CU929921,CH242-352E11,2:49929530-49957978 (Clone quality: bE352E11 on chr=2; Num_of_Contigs=12; )
TUBB4		location ⇒	2:50063947-50064956		CU694937,CH242-71B7,2:50063281-50092112 (Clone quality: bE71B7 on chr=2; Num_of_Contigs=4; )
TUBD1		ENSSSCG00000017669	12:34177352-34247531		CU463348,CH242-175J3,12:34165606-34300471 (Clone quality: bE175J3 on chr=12; Num_of_Contigs=1; )
TUBE1		ENSSSCG00000004423	1:81660121-81689023
TUBG2		ENSSSCG00000017394	12:17771209-17777399		FP016109,CH242-242A5,12:17741333-17788405 (Clone quality: bE242A5 on chr=12; Num_of_Contigs=4; )
TUBGCP2		ENSSSCG00000010773	14:147978830-147999180
TUBGCP3		ENSSSCG00000009553	11:78563442-78604226	CU207380,CH242-239P7,11:78415790-78615641 (Clone quality: bE239P7 on chr=11; Num_of_Contigs=7; )
TUBGCP4		ENSSSCG00000004708	1:134120932-134175216
TUBGCP5		ENSSSCG00000015736	15:29090707-29092535		CU606932,CH242-515L21,15:29088375-29092558 (Clone quality: bE515L21 on chr=15; Num_of_Contigs=27; )
TUBGCP6		ENSSSCG00000000972	5:99820009-99841779
TUFM		ENSSSCG00000007803	3:16633667-16637048		CU928476,CH242-24P1,3:16614299-16641736 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
TUFM		location ⇒	3:16634040-16633863		CU928476,CH242-24P1,3:16614299-16641736 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
TUFM		location ⇒	3:16634875-16634720		CU928476,CH242-24P1,3:16614299-16641736 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
TUFM		location ⇒	3:16636801-16636636		CU928476,CH242-24P1,3:16614299-16641736 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
TUFM		location ⇒	3:16636981-16636930		CU928476,CH242-24P1,3:16614299-16641736 (Clone quality: bE24P1 on chr=3; Num_of_Contigs=5; )
TUFT1_PIG		ENSSSCG00000006620	4:101604530-101657838
TUFT1_PIG		ENSSSCG00000006615	4:101381938-101392188		CU469480,CH242-269C4,4:101376883-101413203 (Clone quality: bE269C4 on chr=4; Num_of_Contigs=13; )
TULP1		ENSSSCG00000001545	7:35950192-35961862
TULP2		ENSSSCG00000003149	6:37727313-37734940
TULP3		ENSSSCG00000000737	5:63077873-63114462		CU856242,CH242-195D5,5:63054017-63118628 (Clone quality: bE195D5 on chr=5; Num_of_Contigs=10; )
TULP4		ENSSSCG00000004059	1:9768478-9770087		CU914176,CH242-157G12,1:9761086-9775855 (Clone quality: bE157G12 on chr=1; Num_of_Contigs=9; )
TUSC1		ENSSSCG00000005128	1:206192199-206192828		CU855511,CH242-258I17,1:206159768-206249232 (Clone quality: bE258I17 on chr=1; Num_of_Contigs=2; )
TUSC2		ENSSSCG00000011406	13:27473729-27476374		CU861907,CH242-10C8,13:27455563-27490719 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
TUSC4		ENSSSCG00000011409	13:27491534-27494819		CU861907,CH242-10C8,13:27490820-27610755 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
TUSC5		ENSSSCG00000017801	12:44559906-44570485
TUT1		ENSSSCG00000013063	2:7499168-7512481		FP102338,CH242-94E13,2:7490082-7534927 (Clone quality: bE94E13 on chr=2; Num_of_Contigs=10; )
TWF1		ENSSSCG00000000798	5:70896710-70907659		FP102342,PigI-719A6,5:70839195-70984027 (Clone quality: bI719A6 on chr=5; Num_of_Contigs=1; )
TWF2		location ⇒	13:28827629-28827780		CU914695,CH242-195P19,13:28826862-28830391 (Clone quality: bE195P19 on chr=13; Num_of_Contigs=14; )
TWF2		location ⇒	13:29041189-29041371		CU915558,CH242-407L22,13:29031196-29046914 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
TWF2		location ⇒	13:29042270-29042397		CU915558,CH242-407L22,13:29031196-29046914 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
TWF2		location ⇒	13:29043146-29043297		CU915558,CH242-407L22,13:29031196-29046914 (Clone quality: bE407L22 on chr=13; Num_of_Contigs=4; )
TWIST1		ENSSSCG00000015370	9:82730209-82730954
TWIST2		ENSSSCG00000016343	15:130724935-130725417		CU972369,CH242-158N5,15:130722843-130768237 (Clone quality: bE158N5 on chr=15; Num_of_Contigs=1; )
TWISTNB		ENSSSCG00000015372	9:83375291-83484643
TWSG1		ENSSSCG00000003681	6:67309206-67355512
TXK		ENSSSCG00000008819	8:32499454-32566755

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).