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)

SFTPA2		location ⇒	14:85573962-85573097		CU469045,CH242-504L17,14:85552217-85591006 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPB		ENSSSCG00000008229	3:53976698-53987113		CU928286,CH242-219K12,3:53963583-54011045 (Clone quality: bE219K12 on chr=3; Num_of_Contigs=4; )
SFTPC		ENSSSCG00000009619	14:6387471-6399944		CT827951,CH242-289H4,14:6374382-6404490 (Clone quality: bE289H4 on chr=14; Num_of_Contigs=6; )
SFTPD		ENSSSCG00000010334	14:85508342-85523061		CU469045,CH242-504L17,14:85482673-85525440 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPD		location ⇒	14:85511171-85511374		CU469045,CH242-504L17,14:85482673-85525440 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPD		location ⇒	14:85518278-85518398		CU469045,CH242-504L17,14:85482673-85525440 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPD		location ⇒	14:85519543-85519663		CU469045,CH242-504L17,14:85482673-85525440 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPD		location ⇒	14:85522506-85523060		CU469045,CH242-504L17,14:85482673-85525440 (Clone quality: bE504L17 on chr=14; Num_of_Contigs=9; )
SFTPG		ENSSSCG00000001385	7:27377788-27378770	CT971577,CH242-239H1,7:27216113-27394697 (Clone quality: bE239H1 on chr=7; Num_of_Contigs=1; )
SFXN1		ENSSSCG00000014063	2:70963767-70978871
SFXN2		ENSSSCG00000010589	14:118805493-118815668		CU570855,CH242-447M15,14:118779172-118818079 (Clone quality: bE447M15 on chr=14; Num_of_Contigs=8; )
SFXN4		ENSSSCG00000010681	14:135033679-135058961
SFXN5		ENSSSCG00000008307	3:63967002-64135884
SGCA		ENSSSCG00000017583	12:24695484-24707267		CU694879,CH242-301O20,12:24690355-24707749 (Clone quality: bE301O20 on chr=12; Num_of_Contigs=13; )
SGCB		ENSSSCG00000008833	8:33692777-33711354		CU928766,CH242-128N5,8:33662044-33745367 (Clone quality: bE128N5 on chr=8; Num_of_Contigs=5; )
SGCD		ENSSSCG00000017063	16:64147594-64250935
SGCE		ENSSSCG00000015328	9:69730669-69802813
SGCG		ENSSSCG00000009281	11:1255956-1368986
SGCZ		ENSSSCG00000006974	17:1771221-1891512
SGK3		ENSSSCG00000006206	4:70394037-70419900
SGK493		ENSSSCG00000008468	3:91829397-91838545		CU929292,CH242-243I20,3:91819586-91838849 (Clone quality: bE243I20 on chr=3; Num_of_Contigs=33; )
SGMS1		ENSSSCG00000010433	14:103817282-103909542
SGMS2		ENSSSCG00000009152	8:97892312-97980529
SGOL1		ENSSSCG00000011207	13:6135200-6149308		CU639466,CH242-422B18,13:6134935-6150519 (Clone quality: bE422B18 on chr=13; Num_of_Contigs=8; )
SGOL2		ENSSSCG00000016092	15:97860527-97892880		CU915540,CH242-160L13,15:97806887-97896803 (Clone quality: bE160L13 on chr=15; Num_of_Contigs=3; )
SGPL1		ENSSSCG00000010274	14:76875949-76932192	CT737289,CH242-133B3,14:76783692-76995335 (Clone quality: bE133B3 on chr=14; Num_of_Contigs=4; )
SGPP1		ENSSSCG00000005111	1:203357008-203366758		CU618319,CH242-25H18,1:203352954-203375604 (Clone quality: bE25H18 on chr=1; Num_of_Contigs=12; )
SGPP1		location ⇒	1:203238838-203238930		CU606882,CH242-508F6,1:203234062-203252164 (Clone quality: bE508F6 on chr=1; Num_of_Contigs=17; )
SGPP1		location ⇒	1:203248044-203248846		CU606882,CH242-508F6,1:203234062-203252164 (Clone quality: bE508F6 on chr=1; Num_of_Contigs=17; )
SGPP1		location ⇒	1:203366216-203367018		CU618319,CH242-25H18,1:203352954-203375604 (Clone quality: bE25H18 on chr=1; Num_of_Contigs=12; )
SGPP1		location ⇒	1:203485107-203484418		CU618319,CH242-25H18,1:203476820-203498980 (Clone quality: bE25H18 on chr=1; Num_of_Contigs=12; )
SGPP2		ENSSSCG00000016227	15:115261237-115301811		CU861974,CH242-297O1,15:115246187-115311887 (Clone quality: bE297O1 on chr=15; Num_of_Contigs=4; )
SGSH		ENSSSCG00000017152	12:1202710-1363070
SGSM1		ENSSSCG00000009951	14:43176343-43237875
SGSM2		ENSSSCG00000017829	12:45867769-45911357
SGSM3		ENSSSCG00000000076	5:4244540-4286170		CU639392,CH242-157D22,5:4238817-4335426 (Clone quality: bE157D22 on chr=5; Num_of_Contigs=2; )
SGTA		ENSSSCG00000013467	2:47393028-47409568		CU972376,CH242-107L7,2:47367584-47461889 (Clone quality: bE107L7 on chr=2; Num_of_Contigs=6; )
SGTB		ENSSSCG00000016950	16:41558448-41596116		CU856268,CH242-30E20,16:41457783-41623625 (Clone quality: bE30E20 on chr=16; Num_of_Contigs=2; )
SH2B1		ENSSSCG00000007804	3:16647622-16654744
SH2B2		ENSSSCG00000007682	3:7974200-7980581		CU914498,CH242-199C11,3:7962532-7980583 (Clone quality: bE199C11 on chr=3; Num_of_Contigs=7; )
SH2B3		ENSSSCG00000009833	14:32684696-32711754		CT737146,CH242-55G24,14:32654913-32799551 (Clone quality: bE55G24 on chr=14; Num_of_Contigs=2; )
SH2D1A		ENSSSCG00000012643	X:99581220-99604600
SH2D1A		location ⇒	X:99581442-99581580	FP085529,CH242-373I23,X:99533515-99598484 (Clone quality: bE373I23 on chr=X; Num_of_Contigs=3; )
SH2D1A		location ⇒	X:99597425-99597487	FP085529,CH242-373I23,X:99533515-99598484 (Clone quality: bE373I23 on chr=X; Num_of_Contigs=3; )
SH2D1A		location ⇒	X:99602533-99602678	FP085529,CH242-373I23,X:99598585-99671293 (Clone quality: bE373I23 on chr=X; Num_of_Contigs=3; )
SH2D1B		ENSSSCG00000006341	4:91816581-91821027		CU468663,CH242-271J5,4:91816325-91826602 (Clone quality: bE271J5 on chr=4; Num_of_Contigs=24; )
SH2D1B		location ⇒	4:107274916-107274992		CU469418,CH242-264L10,4:107154030-107294999 (Clone quality: bE264L10 on chr=4; Num_of_Contigs=1; )
SH2D1B		location ⇒	4:37662014-37662083		CU469046,CH242-505O12,4:37591932-37692638 (Clone quality: bE505O12 on chr=4; Num_of_Contigs=2; )
SH2D1B		location ⇒	4:78406674-78406751		CU462960,CH242-392H23,4:78385334-78466679 (Clone quality: bE392H23 on chr=4; Num_of_Contigs=4; )
SH2D1B		location ⇒	4:91984746-91984667		CU234128,CH242-455O10,4:91952162-92014654 (Clone quality: bE455O10 on chr=4; Num_of_Contigs=9; )

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, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-16

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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).