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)

TMEM106C		ENSSSCG00000000814	5:73625293-73629095		CU582786,CH242-499H9,5:73625084-73630004 (Clone quality: bE499H9 on chr=5; Num_of_Contigs=8; )
TMEM108		ENSSSCG00000011635	13:61191406-61392774
TMEM109		ENSSSCG00000013110	2:9394597-9402428
TMEM110		ENSSSCG00000011452	13:29526939-29596466
TMEM111		ENSSSCG00000011562	13:55405473-55425524		CU464019,CH242-82C2,13:55403896-55455839 (Clone quality: bE82C2 on chr=13; Num_of_Contigs=5; )
TMEM114		ENSSSCG00000007915	3:30171966-30172100		CU915426,CH242-478G12,3:30161546-30172606 (Clone quality: bE478G12 on chr=3; Num_of_Contigs=3; )
TMEM115		ENSSSCG00000011411	13:27498374-27503021		CU861907,CH242-10C8,13:27490820-27610755 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
TMEM116		ENSSSCG00000009893	14:39928992-39951363		CU468463,CH242-214J14,14:39899719-39967338 (Clone quality: bE214J14 on chr=14; Num_of_Contigs=5; )
TMEM117		ENSSSCG00000000801	5:71427055-71509720
TMEM120B		ENSSSCG00000009808	14:30963566-31010980
TMEM121		ENSSSCG00000008507	3:99273645-99355084
TMEM125		location ⇒	6:120205503-120205989		CU694684,CH242-210N13,6:120172350-120225775 (Clone quality: bE210N13 on chr=6; Num_of_Contigs=11; )
TMEM125		location ⇒	6:120313723-120313392		FP102012,CH242-136J24,6:120277096-120383099 (Clone quality: bE136J24 on chr=6; Num_of_Contigs=3; )
TMEM125		location ⇒	6:120314071-120313757		FP102012,CH242-136J24,6:120277096-120383099 (Clone quality: bE136J24 on chr=6; Num_of_Contigs=3; )
TMEM125		location ⇒	6:120314604-120314118		FP102012,CH242-136J24,6:120277096-120383099 (Clone quality: bE136J24 on chr=6; Num_of_Contigs=3; )
TMEM126A		ENSSSCG00000014906	9:19825949-19836075
TMEM126B		ENSSSCG00000014905	9:19794667-19802267		CU855624,CH242-106C22,9:19777112-19813203 (Clone quality: bE106C22 on chr=9; Num_of_Contigs=4; )
TMEM127		ENSSSCG00000008131	3:42068849-42080017		CU896688,CH242-167G10,3:42056126-42096960 (Clone quality: bE167G10 on chr=3; Num_of_Contigs=16; )
TMEM128		ENSSSCG00000008732	8:4616530-4626875
TMEM129		ENSSSCG00000008678	8:206623-211094		FP102127,CH242-261D5,8:206084-213100 (Clone quality: bE261D5 on chr=8; Num_of_Contigs=8; )
TMEM130		ENSSSCG00000007605	3:5098330-5113015
TMEM130		location ⇒	3:4973721-4973657		CU856473,CH242-90I19,3:4972926-4977524 (Clone quality: bE90I19 on chr=3; Num_of_Contigs=6; )
TMEM130		location ⇒	3:4979859-4979795		CU856473,CH242-90I19,3:4977625-4996063 (Clone quality: bE90I19 on chr=3; Num_of_Contigs=6; )
TMEM130		location ⇒	3:5097396-5097332		CU915307,CH242-144A12,3:5082703-5108327 (Clone quality: bE144A12 on chr=3; Num_of_Contigs=10; )
TMEM130		location ⇒	3:5103443-5103379		CU915307,CH242-144A12,3:5082703-5108327 (Clone quality: bE144A12 on chr=3; Num_of_Contigs=10; )
TMEM131		ENSSSCG00000008192	3:51652178-51779803
TMEM132A		ENSSSCG00000013113	2:9489357-9502016
TMEM132B		ENSSSCG00000009754	14:27674898-27817067
TMEM132C		ENSSSCG00000009753	14:26239884-26435132
TMEM132D		ENSSSCG00000009752	14:25391692-26074407
TMEM132E		ENSSSCG00000017718	12:38014574-38026232		FP236720,CH242-36F24,12:38004303-38032559 (Clone quality: bE36F24 on chr=12; Num_of_Contigs=8; )
TMEM134		ENSSSCG00000012905	2:3438571-3443453		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
TMEM135		ENSSSCG00000014922	9:21057632-21128883
TMEM136		ENSSSCG00000015128	9:46095276-46095521		CU595407,CH242-180M7,9:46093130-46110875 (Clone quality: bE180M7 on chr=9; Num_of_Contigs=16; )
TMEM138		ENSSSCG00000013085	2:8442363-8448801
TMEM139		ENSSSCG00000016465	18:5969508-5972725		CU928380,CH242-107B19,18:5868328-5998133 (Clone quality: bE107B19 on chr=18; Num_of_Contigs=4; )
TMEM140		ENSSSCG00000016530	18:12372285-12372845		FP236477,CH242-106A2,18:12349582-12433361 (Clone quality: bE106A2 on chr=18; Num_of_Contigs=4; )
TMEM142A		ENSSSCG00000009810	14:31066124-31082030
TMEM142A		location ⇒	14:31066736-31066126		CU467994,CH242-404B6,14:31022818-31072924 (Clone quality: bE404B6 on chr=14; Num_of_Contigs=4; )
TMEM142A		location ⇒	14:31081658-31081499		CU693466,CH242-414G9,14:31072925-31112963 (Clone quality: bE414G9 on chr=14; Num_of_Contigs=9; )
TMEM144		ENSSSCG00000008874	8:40924190-40977964
TMEM145		ENSSSCG00000003022	6:34222589-34230417
TMEM146		ENSSSCG00000013527	2:49412275-49470056
TMEM14A		ENSSSCG00000002622	7:135597178-135604571		CU633247,CH242-235D18,7:135597028-135604616 (Clone quality: bE235D18 on chr=7; Num_of_Contigs=14; )
TMEM150A		ENSSSCG00000008233	3:54052314-54056386		CU928286,CH242-219K12,3:54043219-54085564 (Clone quality: bE219K12 on chr=3; Num_of_Contigs=4; )
TMEM151A		ENSSSCG00000012952	2:4468909-4472713
TMEM151B		ENSSSCG00000001704	7:45791333-45794796	CT009542,CH242-272H8,7:45714746-45890644 (Clone quality: bE272H8 on chr=7; Num_of_Contigs=13; )
TMEM154		ENSSSCG00000009012	8:65469385-65508906
TMEM155		ENSSSCG00000009095	8:87832990-87833334		CU861488,CH242-360D22,8:87831800-87834057 (Clone quality: bE360D22 on chr=8; Num_of_Contigs=23; )
TMEM156		ENSSSCG00000008786	8:25850602-25903803		CU457408,CH242-334B21,8:25835575-25907162 (Clone quality: bE334B21 on chr=8; 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).