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)

NECAP2		ENSSSCG00000003477	6:51994888-52010171		FP102632,CH242-221K5,6:51987613-52017906 (Clone quality: bE221K5 on chr=6; Num_of_Contigs=7; )
NEDD4		ENSSSCG00000004604	1:120599631-120801395
NEDD4L		ENSSSCG00000004920	1:169377480-169418181
NEDD8		ENSSSCG00000001996	7:81410697-81423296
NEDD9		ENSSSCG00000001046	7:8176002-8202200		CT998542,CH242-393O5,7:8171516-8370198 (Clone quality: bE393O5 on chr=7; Num_of_Contigs=2; )
NEDD9		ENSSSCG00000004412	1:80468963-80478183		CU075452,CH242-39D23,1:80450203-80633251 (Clone quality: bE39D23 on chr=1; Num_of_Contigs=2; )
NEDD9		location ⇒	7:8176514-8176455		CT998542,CH242-393O5,7:8171516-8370198 (Clone quality: bE393O5 on chr=7; Num_of_Contigs=2; )
NEDD9		location ⇒	7:8179454-8179363		CT998542,CH242-393O5,7:8171516-8370198 (Clone quality: bE393O5 on chr=7; Num_of_Contigs=2; )
NEDD9		location ⇒	7:8181355-8181001		CT998542,CH242-393O5,7:8171516-8370198 (Clone quality: bE393O5 on chr=7; Num_of_Contigs=2; )
NEFH		ENSSSCG00000009979	14:47114134-47120633		CU468008,CH242-428E7,14:47112030-47129566 (Clone quality: bE428E7 on chr=14; Num_of_Contigs=5; )
NEFL		ENSSSCG00000009649	14:9151231-9155342		CT978650,CH242-252H13,14:9123196-9234608 (Clone quality: bE252H13 on chr=14; Num_of_Contigs=2; )
NEFM		ENSSSCG00000009648	14:9120373-9125266
NEGR1		location ⇒	6:98955412-98955177		FP236560,CH242-210I22,6:98912947-99030504 (Clone quality: bE210I22 on chr=6; Num_of_Contigs=1; )
NEGR1		location ⇒	6:99130024-99130151		CU929711,CH242-197D10,6:99095666-99130783 (Clone quality: bE197D10 on chr=6; Num_of_Contigs=10; )
NEGR1		location ⇒	6:99210544-99210411		CU929711,CH242-197D10,6:99175311-99219147 (Clone quality: bE197D10 on chr=6; Num_of_Contigs=10; )
NEGR1		location ⇒	6:99322273-99322140		CU929494,CH242-299A21,6:99306436-99366446 (Clone quality: bE299A21 on chr=6; Num_of_Contigs=3; )
NEIL1		ENSSSCG00000001882	7:63518229-63524559		CT990537,CH242-196K6,7:63503819-63528405 (Clone quality: bE196K6 on chr=7; Num_of_Contigs=8; )
NEIL3		ENSSSCG00000015771	15:36639113-36686382
NEK1		ENSSSCG00000009714	14:20059588-20246063
NEK10		ENSSSCG00000011217	13:11529368-11672490
NEK11		ENSSSCG00000011181	13:1086753-1220512
NEK2		ENSSSCG00000015604	9:124014632-124027627		CU657933,CH242-352F10,9:123979535-124029339 (Clone quality: bE352F10 on chr=9; Num_of_Contigs=5; )
NEK3		ENSSSCG00000009379	11:15791480-15817569		CU856639,CH242-171M18,11:15766368-15830462 (Clone quality: bE171M18 on chr=11; Num_of_Contigs=3; )
NEK4		ENSSSCG00000011446	13:29393149-29429468
NEK5		ENSSSCG00000009380	11:15822807-15868816
NEK6		ENSSSCG00000005587	1:279894624-280010071
NEK7		ENSSSCG00000010904	10:22158521-22256461
NEK8		ENSSSCG00000017766	12:42619871-42629292		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
NEK9		ENSSSCG00000002381	7:106533146-106575806	CT737372,CH242-134B18,7:106458379-106624048 (Clone quality: bE134B18 on chr=7; Num_of_Contigs=4; )
NELF		ENSSSCG00000005851	1:294355182-294356788		CU928955,CH242-34I15,1:294355036-294362230 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
NELL1		ENSSSCG00000013345	2:35177819-35952290
NELL1		location ⇒	2:35179788-35179715		CU856267,CH242-266N1,2:35149924-35206930 (Clone quality: bE266N1 on chr=2; Num_of_Contigs=5; )
NELL1		location ⇒	2:35182145-35181966		CU856267,CH242-266N1,2:35149924-35206930 (Clone quality: bE266N1 on chr=2; Num_of_Contigs=5; )
NELL1		location ⇒	2:35221211-35221015		CU856267,CH242-266N1,2:35211441-35281476 (Clone quality: bE266N1 on chr=2; Num_of_Contigs=5; )
NELL1		location ⇒	2:35440975-35440916		CU856420,CH242-64G6,2:35419911-35448662 (Clone quality: bE64G6 on chr=2; Num_of_Contigs=5; )
NELL2		ENSSSCG00000000802	5:71567867-71863023
NELL2		location ⇒	5:71627200-71627053		CU861985,CH242-383A4,5:71594530-71638873 (Clone quality: bE383A4 on chr=5; Num_of_Contigs=3; )
NELL2		location ⇒	5:71629143-71628964		CU861985,CH242-383A4,5:71594530-71638873 (Clone quality: bE383A4 on chr=5; Num_of_Contigs=3; )
NELL2		location ⇒	5:71631052-71630857		CU861985,CH242-383A4,5:71594530-71638873 (Clone quality: bE383A4 on chr=5; Num_of_Contigs=3; )
NELL2		location ⇒	5:71641187-71641045		CU861985,CH242-383A4,5:71638974-71690682 (Clone quality: bE383A4 on chr=5; Num_of_Contigs=3; )
NENF		ENSSSCG00000015597	9:123411172-123422059
NEO1		ENSSSCG00000001921	7:65557820-65791036
NEO1		location ⇒	7:42915542-42915693		CU695159,CH242-195C12,7:42913166-42916748 (Clone quality: bE195C12 on chr=7; Num_of_Contigs=29; )
NEO1		location ⇒	7:65471617-65471767		CU076090,CH242-417D16,7:65462934-65471808 (Clone quality: bE417D16 on chr=7; Num_of_Contigs=2; )
NEO1		location ⇒	7:65599791-65599640		CU856111,CH242-39I16,7:65533880-65670752 (Clone quality: bE39I16 on chr=7; Num_of_Contigs=2; )
NEO1		location ⇒	7:65603926-65603776		CU856111,CH242-39I16,7:65533880-65670752 (Clone quality: bE39I16 on chr=7; Num_of_Contigs=2; )
NETO1		ENSSSCG00000004876	1:157926617-158110034
NEU1		ENSSSCG00000007164	17:34178421-34179296		CU302217,CH242-196N9,17:34159575-34193292 (Clone quality: bE196N9 on chr=17; Num_of_Contigs=10; )
NEU1		ENSSSCG00000001418	7:27775646-27780585	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
NEU2		ENSSSCG00000016297	15:125906142-125908774		CU928130,CH242-481I23,15:125903359-125912303 (Clone quality: bE481I23 on chr=15; Num_of_Contigs=18; )

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, 951-29

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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).