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)

NRSN1		ENSSSCG00000001084	7:20013984-20032380	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
NRSN1		location ⇒	7:20013947-20014015	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
NRSN1		location ⇒	7:20014060-20014131	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
NRSN1		location ⇒	7:20021787-20021988	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
NRSN1		location ⇒	7:20031854-20032239	CU302418,CH242-240P19,7:19923339-20166719 (Clone quality: bE240P19 on chr=7; Num_of_Contigs=1; )
NRSN2		ENSSSCG00000007210	17:36775248-36780466		CU606854,CH242-254I19,17:36758384-36785232 (Clone quality: bE254I19 on chr=17; Num_of_Contigs=11; )
NRTN		ENSSSCG00000013529	2:49500143-49503515
NRXN1		ENSSSCG00000008420	3:84245471-84406411
NRXN1		location ⇒	3:84408084-84408144		CU463189,CH242-173M19,3:84404507-84489608 (Clone quality: bE173M19 on chr=3; Num_of_Contigs=6; )
NRXN1		location ⇒	3:84508365-84508452		CU463189,CH242-173M19,3:84493244-84536055 (Clone quality: bE173M19 on chr=3; Num_of_Contigs=6; )
NRXN1		location ⇒	3:84534179-84534413		CU463189,CH242-173M19,3:84493244-84536055 (Clone quality: bE173M19 on chr=3; Num_of_Contigs=6; )
NRXN1		location ⇒	3:84534476-84534667		CU463189,CH242-173M19,3:84493244-84536055 (Clone quality: bE173M19 on chr=3; Num_of_Contigs=6; )
NRXN2		ENSSSCG00000013024	2:5852514-5951864
NRXN2		location ⇒	2:5936597-5936804		CU468547,CH242-388P19,2:5923691-5950653 (Clone quality: bE388P19 on chr=2; Num_of_Contigs=12; )
NRXN2		location ⇒	2:5938786-5938870		CU468547,CH242-388P19,2:5923691-5950653 (Clone quality: bE388P19 on chr=2; Num_of_Contigs=12; )
NRXN3		ENSSSCG00000008419	3:84139589-84143189		CU855542,CH242-54I20,3:84059108-84153305 (Clone quality: bE54I20 on chr=3; Num_of_Contigs=3; )
NRXN3		location ⇒	7:109682180-109682301		FP085423,CH242-2F7,7:109674711-109709777 (Clone quality: bE2F7 on chr=7; Num_of_Contigs=3; )
NRXN3		location ⇒	7:109871151-109871323		FP085423,CH242-2F7,7:109866867-109878223 (Clone quality: bE2F7 on chr=7; Num_of_Contigs=3; )
NRXN3		location ⇒	7:110282076-110282258		CT954283,CH242-134I14,7:110242012-110395306 (Clone quality: bE134I14 on chr=7; Num_of_Contigs=1; )
NRXN3		location ⇒	7:21101315-21101385		CU468933,CH242-200A13,7:21100382-21104334 (Clone quality: bE200A13 on chr=7; Num_of_Contigs=28; )
NSD1		ENSSSCG00000014044	2:69760794-69854637
NSDHL		ENSSSCG00000012758	X:122076442-122091596	CU468868,CH242-187E18,X:122069416-122115029 (Clone quality: bE187E18 on chr=X; Num_of_Contigs=5; )
NSEP1		location ⇒	8:38089349-38089503		CU693419,CH242-30B6,8:38088161-38095809 (Clone quality: bE30B6 on chr=8; Num_of_Contigs=7; )
NSEP1		location ⇒	8:38089611-38090656		CU693419,CH242-30B6,8:38088161-38095809 (Clone quality: bE30B6 on chr=8; Num_of_Contigs=7; )
NSF		ENSSSCG00000017316	12:15338119-15503039
NSL1		ENSSSCG00000015593	9:123093429-123135938
NSMAF		ENSSSCG00000006236	4:77067737-77125223
NSMCE1		ENSSSCG00000007820	3:17802339-17805951
NSMCE2		ENSSSCG00000005968	4:14013065-14099824		CU463271,CH242-376H17,4:13997435-14158254 (Clone quality: bE376H17 on chr=4; Num_of_Contigs=1; )
NSMCE4A		ENSSSCG00000010700	14:137929291-137945825		CT990604,CH242-440O7,14:137857385-138026315 (Clone quality: bE440O7 on chr=14; Num_of_Contigs=1; )
NSUN2		ENSSSCG00000017104	16:72710029-72749948
NSUN4		ENSSSCG00000003902	6:118152819-118177147
NSUN6		ENSSSCG00000011041	10:43065454-43132403
NT5C		ENSSSCG00000017221	12:4487621-4489266		CU640421,CH242-384L19,12:4475907-4520854 (Clone quality: bE384L19 on chr=12; Num_of_Contigs=8; )
NT5C1A		ENSSSCG00000003662	6:65556682-65572930	CR956427,CH242-51O7,6:65474974-65651225 (No clone quality info on bE51O7)
NT5C1B		ENSSSCG00000008607	3:110883916-110905809		FP236372,CH242-16J2,3:110875808-110953282 (Clone quality: bE16J2 on chr=3; Num_of_Contigs=4; )
NT5C2		ENSSSCG00000010594	14:119144264-119225797
NT5C2L1		ENSSSCG00000004435	1:85722771-85857163
NT5C3L		ENSSSCG00000017425	12:18622989-18631118		CU928665,CH242-332K23,12:18588452-18636683 (Clone quality: bE332K23 on chr=12; Num_of_Contigs=7; )
NT5DC1		ENSSSCG00000004435	1:85722771-85857163
NT5DC2		ENSSSCG00000011444	13:29272455-29277173		CU550676,CH242-330J9,13:29268984-29292035 (Clone quality: bE330J9 on chr=13; Num_of_Contigs=4; )
NT5DC3		ENSSSCG00000000853	5:75865491-75907435
NT5DC4		ENSSSCG00000008092	3:39106491-39113280
NT5E		location ⇒	1:56621030-56621407		CU633512,CH242-380A21,1:56591790-56637959 (Clone quality: bE380A21 on chr=1; Num_of_Contigs=15; )
NT5E		location ⇒	1:56639281-56639495		CU633512,CH242-380A21,1:56638060-56648013 (Clone quality: bE380A21 on chr=1; Num_of_Contigs=15; )
NT5E		location ⇒	1:56847784-56848161		CU074281,CH242-116C18,1:56772555-56944639 (Clone quality: bE116C18 on chr=1; Num_of_Contigs=2; )
NT5E		location ⇒	1:56866002-56866216		CU074281,CH242-116C18,1:56772555-56944639 (Clone quality: bE116C18 on chr=1; Num_of_Contigs=2; )
NT5M		ENSSSCG00000018052	12:56926966-56941635		CU927962,CH242-273I13,12:56891060-57001521 (Clone quality: bE273I13 on chr=12; Num_of_Contigs=8; )
NTE		ENSSSCG00000013572	2:50955871-50984485
NTE		location ⇒	2:50959505-50959627		CU972392,CH242-85F14,2:50951770-50967555 (Clone quality: bE85F14 on chr=2; Num_of_Contigs=25; )

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).