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)

TSPO		ENSSSCG00000000033	5:2428901-2432187		CU633237,CH242-1K8,5:2428281-2442327 (Clone quality: bE1K8 on chr=5; Num_of_Contigs=19; )
TSPO		location ⇒	5:2428924-2429128		CU633237,CH242-1K8,5:2428281-2442327 (Clone quality: bE1K8 on chr=5; Num_of_Contigs=19; )
TSPO		location ⇒	5:2431289-2431429		CU633237,CH242-1K8,5:2428281-2442327 (Clone quality: bE1K8 on chr=5; Num_of_Contigs=19; )
TSPO		location ⇒	5:2431822-2431928		CU633237,CH242-1K8,5:2428281-2442327 (Clone quality: bE1K8 on chr=5; Num_of_Contigs=19; )
TSPYL2		ENSSSCG00000012323	X:45395763-45398356
TSR1		ENSSSCG00000017828	12:45855391-45866443		CU640470,CH242-300A22,12:45800890-45898822 (Clone quality: bE300A22 on chr=12; Num_of_Contigs=5; )
TSR2		ENSSSCG00000012334	X:46801911-46806883		CU210851,CH242-402H2,X:46778102-46821221 (Clone quality: bE402H2 on chr=X; Num_of_Contigs=8; )
TSSK1B		ENSSSCG00000010112	14:52048808-52049902		CU468322,CH242-201I2,14:52029053-52055717 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
TSSK2		ENSSSCG00000010113	14:52053941-52055017		CU468322,CH242-201I2,14:52029053-52055717 (Clone quality: bE201I2 on chr=14; Num_of_Contigs=7; )
TSSK6		ENSSSCG00000013937	2:63500018-63500827		FP015820,CH242-73N10,2:63437356-63592582 (Clone quality: bE73N10 on chr=2; Num_of_Contigs=2; )
TST		ENSSSCG00000000133	5:7059811-7069806		CU633243,CH242-20D10,5:7039128-7109453 (Clone quality: bE20D10 on chr=5; Num_of_Contigs=6; )
TSTA3		location ⇒	4:135863885-135863825		CU927913,CH242-99E21,4:135857496-135863885 (Clone quality: bE99E21 on chr=4; Num_of_Contigs=20; )
TSTD1		ENSSSCG00000006370	4:93002968-93004355		CU137698,CH242-71N12,4:92983937-93019431 (Clone quality: bE71N12 on chr=4; Num_of_Contigs=19; )
TTBK1		ENSSSCG00000001664	7:44126541-44163580	CR974479,PigE-150P18,7:44038129-44188858 (Clone quality: bT150P18 on chr=7; Num_of_Contigs=4; )
TTBK2		ENSSSCG00000004718	1:134643557-134764211
TTC1		ENSSSCG00000017039	16:61072834-61097809
TTC12		ENSSSCG00000015047	9:39974571-40018618		CU570935,CH242-240E24,9:39843626-40020360 (Clone quality: bE240E24 on chr=9; Num_of_Contigs=2; )
TTC13		ENSSSCG00000010180	14:61737986-61820490	CT737333,CH242-133K23,14:61634928-61823678 (Clone quality: bE133K23 on chr=14; Num_of_Contigs=2; )
TTC14		ENSSSCG00000011767	13:90259259-90268451		CU582920,CH242-292I17,13:90197484-90315587 (Clone quality: bE292I17 on chr=13; Num_of_Contigs=3; )
TTC16		ENSSSCG00000005616	1:282474468-282492321
TTC17		ENSSSCG00000013284	2:17178350-17318725
TTC18		ENSSSCG00000010298	14:79336343-79457123
TTC19		ENSSSCG00000018038	12:56367958-56390932
TTC21A		ENSSSCG00000011263	13:19722636-19755650		CU856480,CH242-203F12,13:19659552-19771103 (Clone quality: bE203F12 on chr=13; Num_of_Contigs=3; )
TTC22		ENSSSCG00000003842	6:112200331-112208994		CU929610,CH242-266G21,6:112199806-112275212 (Clone quality: bE266G21 on chr=6; Num_of_Contigs=3; )
TTC23		ENSSSCG00000004813	1:145566639-145597829		CU651639,CH242-13E4,1:145561470-145622210 (Clone quality: bE13E4 on chr=1; Num_of_Contigs=6; )
TTC23L		ENSSSCG00000016825	16:17979577-18037154		CU914241,CH242-186I1,16:17966592-18131621 (Clone quality: bE186I1 on chr=16; Num_of_Contigs=2; )
TTC24		ENSSSCG00000006479	4:97316353-97323706
TTC25		ENSSSCG00000017415	12:18374756-18552242
TTC26		ENSSSCG00000016511	18:8656508-8700010		FP236740,CH242-273C18,18:8642177-8754841 (Clone quality: bE273C18 on chr=18; Num_of_Contigs=4; )
TTC27		ENSSSCG00000008512	3:100509099-100615949
TTC28		ENSSSCG00000009968	14:45909917-46201117
TTC29		ENSSSCG00000009033	8:70420476-70461450
TTC3		ENSSSCG00000012062	13:141003285-141123174
TTC3		location ⇒	13:141011616-141011702		CU582925,CH242-344D7,13:140981499-141025650 (Clone quality: bE344D7 on chr=13; Num_of_Contigs=9; )
TTC3		location ⇒	13:141014295-141014356		CU582925,CH242-344D7,13:140981499-141025650 (Clone quality: bE344D7 on chr=13; Num_of_Contigs=9; )
TTC3		location ⇒	13:141074648-141074717		CU582925,CH242-344D7,13:141025751-141087539 (Clone quality: bE344D7 on chr=13; Num_of_Contigs=9; )
TTC3		location ⇒	13:141121618-141121695		CU633248,CH242-236G11,13:141105329-141169098 (Clone quality: bE236G11 on chr=13; Num_of_Contigs=8; )
TTC31		ENSSSCG00000008275	3:63007436-63106095
TTC32		ENSSSCG00000008605	3:109862923-109869263		CU463914,CH242-276H10,3:109833383-109873326 (Clone quality: bE276H10 on chr=3; Num_of_Contigs=8; )
TTC34		ENSSSCG00000003355	6:43137326-43142040		FP103036,CH242-9E8,6:43135785-43142286 (Clone quality: bE9E8 on chr=6; Num_of_Contigs=13; )
TTC35		ENSSSCG00000006032	4:28965215-29006881
TTC37		ENSSSCG00000014165	2:91091137-91118123
TTC38		ENSSSCG00000000003	5:88483-110232
TTC38		location ⇒	5:102394-102344		FP016092,CH242-185O3,5:95796-114895 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
TTC38		location ⇒	5:103581-103407		FP016092,CH242-185O3,5:95796-114895 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
TTC38		location ⇒	5:109166-109090		FP016092,CH242-185O3,5:95796-114895 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
TTC38		location ⇒	5:92592-92429		FP016092,CH242-185O3,5:73327-95695 (Clone quality: bE185O3 on chr=5; Num_of_Contigs=8; )
TTC39A		ENSSSCG00000003875	6:114804147-114822873		CU928826,CH242-403F11,6:114802247-114823694 (Clone quality: bE403F11 on chr=6; Num_of_Contigs=11; )
TTC39B		ENSSSCG00000005186	1:216840600-216893578

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).