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)

NANOS1		ENSSSCG00000010678	14:134952280-134953134		CU407047,CH242-224G2,14:134885099-135000492 (Clone quality: bE224G2 on chr=14; Num_of_Contigs=3; )
NANOS2		ENSSSCG00000003096	6:36111941-36112357		FP102597,CH242-173N22,6:36105371-36127546 (Clone quality: bE173N22 on chr=6; Num_of_Contigs=4; )
NANOS3		ENSSSCG00000013759	2:56890994-56893899		FP016000,CH242-10C10,2:56824783-56952713 (Clone quality: bE10C10 on chr=2; Num_of_Contigs=2; )
NANP		ENSSSCG00000007134	17:32630393-32639250
NANS		ENSSSCG00000005373	1:251431918-251463134
NAP1L1		ENSSSCG00000000522	5:39352048-39384982		CU915734,CH242-236O16,5:39334338-39397758 (Clone quality: bE236O16 on chr=5; Num_of_Contigs=8; )
NAP1L2		ENSSSCG00000012415	X:58327021-58328442		FP236342,CH242-421O6,X:58260875-58341096 (Clone quality: bE421O6 on chr=X; Num_of_Contigs=8; )
NAP1L4		ENSSSCG00000012856	2:395740-421651
NAP1L5		ENSSSCG00000009209	8:112057551-112058138		CU915521,CH242-67L24,8:112030423-112089206 (Clone quality: bE67L24 on chr=8; Num_of_Contigs=4; )
NAP1L6		ENSSSCG00000012414	X:58298670-58298975		FP236342,CH242-421O6,X:58260875-58341096 (Clone quality: bE421O6 on chr=X; Num_of_Contigs=8; )
NAPA		ENSSSCG00000003120	6:37158698-37170163	FP104555,CH242-158J7,6:37157842-37175931 (Clone quality: bE158J7 on chr=6; Num_of_Contigs=11; )
NAPB		ENSSSCG00000007118	17:31844773-31859631		CU606974,CH242-23K16,17:31836000-31892949 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
NARF		ENSSSCG00000017126	12:76019-94328
NARFL		ENSSSCG00000008002	3:35702474-35708696
NARG1		ENSSSCG00000009061	8:75339995-75402575
NARG1L		ENSSSCG00000009435	11:24504756-24569908		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG1L		ENSSSCG00000009435	11:24504756-24569908		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG1L		location ⇒	11:24510669-24510491		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG1L		location ⇒	11:24519679-24519517		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG1L		location ⇒	11:24520226-24520056		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG1L		location ⇒	11:24553293-24553139		CU062515,CH242-111E23,11:24503434-24582003 (Clone quality: bE111E23 on chr=11; Num_of_Contigs=4; )
NARG2		ENSSSCG00000004577	1:115035179-115192127
NARS		ENSSSCG00000004542	1:110057789-110074140
NARS2		ENSSSCG00000014893	9:12843705-12983403
NAT10		ENSSSCG00000013304	2:25195366-25236183	CU929607,CH242-257K17,2:25128827-25332127 (Clone quality: bE257K17 on chr=2; Num_of_Contigs=6; )
NAT13		ENSSSCG00000011917	13:109150674-109172711		CU915398,CH242-257L23,13:109145832-109269113 (Clone quality: bE257L23 on chr=13; Num_of_Contigs=2; )
NAT14		ENSSSCG00000003298	6:41397645-41426849
NAT5		ENSSSCG00000007101	17:29001362-29010994
NAT5		ENSSSCG00000011917	13:109150674-109172711		CU915398,CH242-257L23,13:109145832-109269113 (Clone quality: bE257L23 on chr=13; Num_of_Contigs=2; )
NAT5		location ⇒	17:29005352-29005485		CU694798,CH242-394D15,17:29005272-29010120 (Clone quality: bE394D15 on chr=17; Num_of_Contigs=17; )
NAT5		location ⇒	17:29009917-29010047		CU694798,CH242-394D15,17:29005272-29010120 (Clone quality: bE394D15 on chr=17; Num_of_Contigs=17; )
NAT8		ENSSSCG00000008296	3:63635048-63635722		CU463123,CH242-385I3,3:63620104-63635885 (Clone quality: bE385I3 on chr=3; Num_of_Contigs=11; )
NAT8L		ENSSSCG00000008683	8:394877-399289
NAT9		ENSSSCG00000017231	12:4683111-4687325	CU928524,CH242-307O4,12:4671735-4885844 (Clone quality: bE307O4 on chr=12; Num_of_Contigs=13; )
NAV1		ENSSSCG00000011259	13:19268539-19355430
NAV1		ENSSSCG00000000228	5:15775900-15830824
NAV1		ENSSSCG00000000227	5:15660451-15661659		CU914420,CH242-302G7,5:15656171-15666934 (Clone quality: bE302G7 on chr=5; Num_of_Contigs=10; )
NAV1		ENSSSCG00000010915	10:24194506-24265570
NAV1		ENSSSCG00000017282	12:12591089-12619924		CU466386,CH242-271O11,12:12583385-12667411 (Clone quality: bE271O11 on chr=12; Num_of_Contigs=5; )
NAV1		ENSSSCG00000015913	15:68206582-68283686
NAV1		ENSSSCG00000015905	15:67147950-67223934
NAV1		ENSSSCG00000011260	13:19472027-19517737
NAV2		ENSSSCG00000013351	2:36689468-36730205		CU571227,CH242-358C11,2:36681710-36731953 (Clone quality: bE358C11 on chr=2; Num_of_Contigs=10; )
NAV3		ENSSSCG00000000953	5:98135299-98217284
NBAS		ENSSSCG00000008620	3:113396698-113507557
NBEA		ENSSSCG00000009350	11:10757689-11290827
NBEAL2		ENSSSCG00000011330	13:24884468-25042580
NBN		ENSSSCG00000006127	4:47957663-47976943
NBPF5		ENSSSCG00000006710	4:105391530-105391709		CU856064,CH242-73D8,4:105385418-105397018 (Clone quality: bE73D8 on chr=4; Num_of_Contigs=13; )
NCALD		ENSSSCG00000006059	4:35501437-35703848

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).