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)

NUAK1		ENSSSCG00000000172	5:12455313-12527633
NUB1		ENSSSCG00000016438	18:5091817-5120321
NUBP2		ENSSSCG00000008014	3:35878650-35884819		CU929968,CH242-75C10,3:35871551-35889570 (Clone quality: bE75C10 on chr=3; Num_of_Contigs=6; )
NUBPL		ENSSSCG00000001968	7:73590890-73759318
NUCB1		ENSSSCG00000003150	6:37735144-37877074
NUDC		ENSSSCG00000003566	6:57907201-57920554		FP015947,CH242-485K18,6:57822585-57995160 (Clone quality: bE485K18 on chr=6; Num_of_Contigs=2; )
NUDCD2		ENSSSCG00000017023	16:57826205-57835233		CU694497,CH242-321D12,16:57793714-57884951 (Clone quality: bE321D12 on chr=16; Num_of_Contigs=4; )
NUDCD3		ENSSSCG00000016747	18:49310463-49381597
NUDT12		ENSSSCG00000014187	2:98014596-98024376
NUDT14		ENSSSCG00000002557	7:133180952-133185165		CU695123,CH242-103I13,7:133176800-133187547 (Clone quality: bE103I13 on chr=7; Num_of_Contigs=13; )
NUDT16		ENSSSCG00000011180	13:899466-901273		CU633332,CH242-130E2,13:864497-950101 (Clone quality: bE130E2 on chr=13; Num_of_Contigs=3; )
NUDT17		ENSSSCG00000006690	4:103557029-103562426		CU606940,CH242-153I6,4:103542731-103564425 (Clone quality: bE153I6 on chr=4; Num_of_Contigs=12; )
NUDT18		ENSSSCG00000009615	14:6334443-6336714		CT737273,CH242-75B21,14:6289244-6343920 (Clone quality: bE75B21 on chr=14; Num_of_Contigs=4; )
NUDT19		ENSSSCG00000002861	6:28549611-28558497
NUDT2		ENSSSCG00000010981	10:30918388-30962603
NUDT22		ENSSSCG00000013039	2:6265656-6268567
NUDT4		ENSSSCG00000000909	5:84017945-84029464		CU915373,CH242-67L15,5:84016329-84029623 (Clone quality: bE67L15 on chr=5; Num_of_Contigs=3; )
NUDT5		ENSSSCG00000011113	10:56691724-56713510
NUDT6		ENSSSCG00000009085	8:86812294-86855056
NUDT7		ENSSSCG00000002697	6:7258791-7270636		CU929768,CH242-317J11,6:7258703-7280594 (Clone quality: bE317J11 on chr=6; Num_of_Contigs=9; )
NUDT8		ENSSSCG00000012894	2:3294498-3309019		CU856401,CH242-191A12,2:3294296-3314165 (Clone quality: bE191A12 on chr=2; Num_of_Contigs=8; )
NUDT9		ENSSSCG00000009223	8:112940456-112967502
NUF2		ENSSSCG00000006333	4:90917402-90948694
NUFIP1		ENSSSCG00000009420	11:21135666-21170899		CU928345,CH242-142F4,11:21026915-21175302 (Clone quality: bE142F4 on chr=11; Num_of_Contigs=1; )
NUFIP2		ENSSSCG00000017785	12:43280789-43288321		CU694816,CH242-127B5,12:43266869-43320143 (Clone quality: bE127B5 on chr=12; Num_of_Contigs=7; )
NUMA1		ENSSSCG00000014802	9:5998138-6069102
NUMB		ENSSSCG00000000791	5:69164686-69235000
NUMB		ENSSSCG00000002342	7:104607816-104664693
NUMB		ENSSSCG00000004677	1:132394055-132404337		CU459107,CH242-257E14,1:132383826-132520076 (Clone quality: bE257E14 on chr=1; Num_of_Contigs=5; )
NUMB		ENSSSCG00000008838	8:34629526-34740040
NUMB		ENSSSCG00000009308	11:4144670-4180545
NUMB		ENSSSCG00000011521	13:46253260-46271541		CU861920,CH242-148F5,13:46248984-46315362 (Clone quality: bE148F5 on chr=13; Num_of_Contigs=2; )
NUMB		location ⇒	7:104617677-104617500		CU914658,CH242-289F14,7:104591764-104620514 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
NUMB		location ⇒	7:104621686-104621543		CU914658,CH242-289F14,7:104620615-104648105 (Clone quality: bE289F14 on chr=7; Num_of_Contigs=6; )
NUMB		location ⇒	7:104664693-104664550		FP236303,PigE-216C18,7:104658608-104667877 (No clone quality info on )
NUMB		location ⇒	7:104803605-104803748		CU861939,CH242-201I13,7:104800247-104809838 (Clone quality: bE201I13 on chr=7; Num_of_Contigs=14; )
NUP107		ENSSSCG00000000486	5:32195256-32244265
NUP133		ENSSSCG00000010189	14:62652910-62705275
NUP155		ENSSSCG00000016845	16:20026160-20095176
NUP160		ENSSSCG00000013223	2:12859947-12910150
NUP188		ENSSSCG00000005667	1:283933901-283987210	CU076102,CH242-68C14,1:283855073-284074390 (Clone quality: bE68C14 on chr=1; Num_of_Contigs=6; )
NUP210		ENSSSCG00000011610	13:59006527-59045849		CU928600,CH242-260O3,13:59006397-59083909 (Clone quality: bE260O3 on chr=13; Num_of_Contigs=4; )
NUP210L		ENSSSCG00000006563	4:99889896-99925289
NUP214		ENSSSCG00000005711	1:286341534-286451095
NUP214		location ⇒	1:286194984-286195085		CU407178,CH242-255P5,1:286175308-286212177 (Clone quality: bE255P5 on chr=1; Num_of_Contigs=12; )
NUP214		location ⇒	1:286198152-286198352		CU407178,CH242-255P5,1:286175308-286212177 (Clone quality: bE255P5 on chr=1; Num_of_Contigs=12; )
NUP214		location ⇒	1:286199122-286199278		CU407178,CH242-255P5,1:286175308-286212177 (Clone quality: bE255P5 on chr=1; Num_of_Contigs=12; )
NUP214		location ⇒	1:286200141-286200338		CU407178,CH242-255P5,1:286175308-286212177 (Clone quality: bE255P5 on chr=1; Num_of_Contigs=12; )
NUP35		ENSSSCG00000016021	15:83324014-83329880		CU570843,CH242-321B10,15:83323100-83332831 (Clone quality: bE321B10 on chr=15; Num_of_Contigs=11; )
NUP37		ENSSSCG00000000860	5:77458299-77485535

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).