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)

ACVR1		location ⇒	15:60075618-60074401		CU570747,CH242-367O9,15:60064359-60089021 (Clone quality: bE367O9 on chr=15; Num_of_Contigs=6; )
ACVR1		location ⇒	15:60100503-60100225		CU468991,CH242-236D6,15:60100086-60235807 (Clone quality: bE236D6 on chr=15; Num_of_Contigs=2; )
ACVR1		location ⇒	15:60115811-60115601		CU468991,CH242-236D6,15:60100086-60235807 (Clone quality: bE236D6 on chr=15; Num_of_Contigs=2; )
ACVR1		location ⇒	15:60118425-60118159		CU468991,CH242-236D6,15:60100086-60235807 (Clone quality: bE236D6 on chr=15; Num_of_Contigs=2; )
ACVR1B		ENSSSCG00000000233	5:16023608-16057075		CU606912,CH242-90A20,5:16023396-16077450 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
ACVR1B		location ⇒	5:16060052-16059684		CU606912,CH242-90A20,5:16023396-16077450 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
ACVR1C		ENSSSCG00000015873	15:59787229-59823186
ACVR2A		ENSSSCG00000015669	15:902174-936087
ACVR2A		location ⇒	15:902023-901883		FP015824,CH242-13P22,15:881001-923237 (Clone quality: bE13P22 on chr=15; Num_of_Contigs=1; )
ACVR2A		location ⇒	15:902327-901532		FP015824,CH242-13P22,15:881001-923237 (Clone quality: bE13P22 on chr=15; Num_of_Contigs=1; )
ACVR2B		ENSSSCG00000011257	13:19167289-19195793		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
ACVR2B		location ⇒	13:19189476-19189685		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
ACVR2B		location ⇒	13:19190164-19190318		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
ACVR2B		location ⇒	13:19191358-19191509		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
ACVR2B		location ⇒	13:19195586-19195791		CU633398,CH242-322L18,13:19166931-19224321 (Clone quality: bE322L18 on chr=13; Num_of_Contigs=3; )
ACVRL1		ENSSSCG00000000232	5:15977317-15991021
ACVRL1		location ⇒	5:15977334-15977428		CU457457,CH242-172O10,5:15953309-15977949 (Clone quality: bE172O10 on chr=5; Num_of_Contigs=16; )
ACVRL1		location ⇒	5:15982427-15982498		CU606912,CH242-90A20,5:15977950-16003999 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
ACVRL1		location ⇒	5:15983039-15983291		CU606912,CH242-90A20,5:15977950-16003999 (Clone quality: bE90A20 on chr=5; Num_of_Contigs=3; )
ACYP1		ENSSSCG00000002379	7:106503595-106518968	CT737372,CH242-134B18,7:106458379-106624048 (Clone quality: bE134B18 on chr=7; Num_of_Contigs=4; )
ADAD1		ENSSSCG00000009089	8:87149818-87279868
ADAL		ENSSSCG00000004710	1:134190323-134217683	CU210852,CH242-452O20,1:134123075-134309699 (Clone quality: bE452O20 on chr=1; Num_of_Contigs=4; )
ADAM10		ENSSSCG00000004595	1:117373024-117514373
ADAM10		location ⇒	1:117306973-117306789		CU633628,CH242-125G24,1:117305928-117311383 (Clone quality: bE125G24 on chr=1; Num_of_Contigs=17; )
ADAM10		location ⇒	1:117325298-117325450		CU633628,CH242-125G24,1:117313858-117328976 (Clone quality: bE125G24 on chr=1; Num_of_Contigs=17; )
ADAM10		location ⇒	1:117348146-117348305		CU633628,CH242-125G24,1:117329077-117349186 (Clone quality: bE125G24 on chr=1; Num_of_Contigs=17; )
ADAM10		location ⇒	1:117398218-117398053		CU633628,CH242-125G24,1:117353415-117403775 (Clone quality: bE125G24 on chr=1; Num_of_Contigs=17; )
ADAM11		ENSSSCG00000017349	12:16431993-16440513
ADAM12		ENSSSCG00000010746	14:142301890-142409636
ADAM12		location ⇒	14:142390953-142391024		CU407210,CH242-351F9,14:142387620-142415057 (Clone quality: bE351F9 on chr=14; Num_of_Contigs=4; )
ADAM12		location ⇒	14:142394185-142394356		CU407210,CH242-351F9,14:142387620-142415057 (Clone quality: bE351F9 on chr=14; Num_of_Contigs=4; )
ADAM15		ENSSSCG00000006533	4:98814493-98825886		CU207227,CH242-365J2,4:98805490-98833519 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
ADAM15		location ⇒	4:98818978-98818671		CU207227,CH242-365J2,4:98805490-98833519 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
ADAM15		location ⇒	4:98819198-98819106		CU207227,CH242-365J2,4:98805490-98833519 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
ADAM15		location ⇒	4:98819645-98819470		CU207227,CH242-365J2,4:98805490-98833519 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
ADAM15		location ⇒	4:98819876-98819727		CU207227,CH242-365J2,4:98805490-98833519 (Clone quality: bE365J2 on chr=4; Num_of_Contigs=9; )
ADAM17		ENSSSCG00000008639	3:117218060-117288182
ADAM17		location ⇒	3:117233424-117232915		CU972371,CH242-102L8,3:117221959-117249863 (Clone quality: bE102L8 on chr=3; Num_of_Contigs=13; )
ADAM17		location ⇒	3:117245674-117245472		CU972371,CH242-102L8,3:117221959-117249863 (Clone quality: bE102L8 on chr=3; Num_of_Contigs=13; )
ADAM17		location ⇒	3:117250846-117250692		CU972371,CH242-102L8,3:117249964-117256362 (Clone quality: bE102L8 on chr=3; Num_of_Contigs=13; )
ADAM17		location ⇒	3:117282178-117282348		CU972371,CH242-102L8,3:117262090-117288514 (Clone quality: bE102L8 on chr=3; Num_of_Contigs=13; )
ADAM18		ENSSSCG00000007008	17:9693966-9748465
ADAM19		ENSSSCG00000017052	16:63398943-63494131
ADAM19		location ⇒	16:63401772-63401857		CU570950,CH242-337F3,16:63356519-63418846 (Clone quality: bE337F3 on chr=16; Num_of_Contigs=6; )
ADAM19		location ⇒	16:63432489-63432568		CU638679,CH242-277N21,16:63418847-63575815 (Clone quality: bE277N21 on chr=16; Num_of_Contigs=1; )
ADAM19		location ⇒	16:63446678-63446872		CU638679,CH242-277N21,16:63418847-63575815 (Clone quality: bE277N21 on chr=16; Num_of_Contigs=1; )
ADAM19		location ⇒	16:63452644-63452801		CU638679,CH242-277N21,16:63418847-63575815 (Clone quality: bE277N21 on chr=16; Num_of_Contigs=1; )
ADAM2		ENSSSCG00000015804	15:44379050-44629057
ADAM2		ENSSSCG00000015805	15:44434709-44589417
ADAM2		location ⇒	15:44488317-44488514		CU570964,CH242-96G4,15:44475014-44491013 (Clone quality: bE96G4 on chr=15; Num_of_Contigs=11; )

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).