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)

snoU6-53		ENSSSCG00000018404	7:84625248-84625359		CT797461,CH242-33P22,7:84554488-84717081 (Clone quality: bE33P22 on chr=7; Num_of_Contigs=7; )
snoU6-53		ENSSSCG00000018824	7:84237840-84237949		CU468936,CH242-31A5,7:84202898-84292931 (Clone quality: bE31A5 on chr=7; Num_of_Contigs=6; )
snoU6-53		ENSSSCG00000019563	7:84620470-84620579		CT797461,CH242-33P22,7:84554488-84717081 (Clone quality: bE33P22 on chr=7; Num_of_Contigs=7; )
snoU6-53		ENSSSCG00000019581	7:84242610-84242721		CU468936,CH242-31A5,7:84202898-84292931 (Clone quality: bE31A5 on chr=7; Num_of_Contigs=6; )
snoU6-53		ENSSSCG00000019877	7:84154510-84154619		CU695130,CH242-313K14,7:84149987-84156255 (Clone quality: bE313K14 on chr=7; Num_of_Contigs=19; )
snoU6-77		ENSSSCG00000019619	12:50065788-50065928	CU914279,CH242-411E2,12:49887557-50072341 (Clone quality: bE411E2 on chr=10; Num_of_Contigs=3; )
snoU82P		ENSSSCG00000018752	5:5238835-5238889		CU686742,CH242-39B7,5:5238369-5240834 (Clone quality: bE39B7 on chr=5; Num_of_Contigs=13; )
snoU83B		ENSSSCG00000018184	5:5240518-5240611		CU686742,CH242-39B7,5:5238369-5240834 (Clone quality: bE39B7 on chr=5; Num_of_Contigs=13; )
snoU97		ENSSSCG00000019944	2:45164997-45165137		CU606995,CH242-524E9,2:45156442-45179549 (Clone quality: bE524E9 on chr=2; Num_of_Contigs=8; )
snoZ17		ENSSSCG00000019446	12:42633846-42633922		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
snoZ17		ENSSSCG00000020020	12:42634786-42634857		FP016171,CH242-62B5,12:42618725-42654541 (Clone quality: bE62B5 on chr=12; Num_of_Contigs=5; )
snoZ30		ENSSSCG00000018995	12:37741813-37741909		CU927946,CH242-204J8,12:37724810-37778976 (Clone quality: bE204J8 on chr=12; Num_of_Contigs=6; )
snoZ39		ENSSSCG00000018631	2:83938903-83938965		CU855504,CH242-232C14,2:83908383-83956815 (Clone quality: bE232C14 on chr=2; Num_of_Contigs=8; )
snoZ40		ENSSSCG00000018558	9:26391550-26391622		CU694898,CH242-364L8,9:26386311-26391934 (Clone quality: bE364L8 on chr=9; Num_of_Contigs=25; )
SNP		location ⇒	1:188087537-188087465		CU606975,CH242-251A8,1:188036812-188088768 (Clone quality: bE251A8 on chr=1; Num_of_Contigs=5; )
SNP		location ⇒	1:228874400-228874328		CU618324,CH242-276M24,1:228857825-228880847 (Clone quality: bE276M24 on chr=1; Num_of_Contigs=4; )
SNPH		ENSSSCG00000007190	17:35685638-35724371		CU638675,CH242-204E6,17:35560423-35742963 (Clone quality: bE204E6 on chr=17; Num_of_Contigs=1; )
snR39B		ENSSSCG00000018746	13:94182264-94182332		CU633961,CH242-82L2,13:94145951-94228460 (Clone quality: bE82L2 on chr=13; Num_of_Contigs=4; )
snR39B		ENSSSCG00000018621	8:46421930-46421998		CU984585,CH242-214K24,8:46419225-46466714 (Clone quality: bE214K24 on chr=8; Num_of_Contigs=2; )
snR39B		ENSSSCG00000018708	7:97083693-97083758	CT842159,CH242-270B4,7:97057191-97273886 (Clone quality: bE270B4 on chr=7; Num_of_Contigs=6; )
SNRK		ENSSSCG00000011295	13:22564687-22600658		CU928338,CH242-289H19,13:22524239-22648223 (Clone quality: bE289H19 on chr=13; Num_of_Contigs=2; )
SNRNP200		ENSSSCG00000004358	1:70749012-70810129
SNRNP25		ENSSSCG00000007962	3:34904512-35098101
SNRNP27		ENSSSCG00000009484	11:54309410-54309884		CT963120,CH242-10B20,11:54303082-54466111 (Clone quality: bE10B20 on chr=11; Num_of_Contigs=1; )
SNRNP48		ENSSSCG00000001026	7:4951255-4966416		CT990631,CH242-417G22,7:4950508-5112484 (Clone quality: bE417G22 on chr=7; Num_of_Contigs=2; )
SNRP70		location ⇒	6:37811431-37811577		FP102974,CH242-517N5,6:37807668-37815371 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
SNRP70		location ⇒	6:37812334-37812492		FP102974,CH242-517N5,6:37807668-37815371 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
SNRP70		location ⇒	6:37813880-37813944		FP102974,CH242-517N5,6:37807668-37815371 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
SNRP70		location ⇒	6:37814051-37814108		FP102974,CH242-517N5,6:37807668-37815371 (Clone quality: bE517N5 on chr=6; Num_of_Contigs=15; )
SNRPA		ENSSSCG00000002998	6:33697057-33708517		CU928654,CH242-130A3,6:33678287-33731769 (Clone quality: bE130A3 on chr=6; Num_of_Contigs=6; )
SNRPA1		ENSSSCG00000005786	1:292344640-292356715
SNRPB		ENSSSCG00000011966	13:116604487-116605242		CU861635,CH242-475E6,13:116604478-116619240 (Clone quality: bE475E6 on chr=13; Num_of_Contigs=6; )
SNRPB2		ENSSSCG00000007081	17:25844388-25877148
SNRPC		ENSSSCG00000001531	7:35170389-35185639	CT797453,CH242-109D12,7:35137121-35327761 (Clone quality: bE109D12 on chr=7; Num_of_Contigs=2; )
SNRPD1		ENSSSCG00000003701	6:72867850-72879730		CU633960,CH242-6K3,6:72853193-72892970 (Clone quality: bE6K3 on chr=6; Num_of_Contigs=6; )
SNRPD3		ENSSSCG00000010058	14:50638308-50651031		CU468600,CH242-236F16,14:50621163-50709737 (Clone quality: bE236F16 on chr=14; Num_of_Contigs=6; )
SNRPF		ENSSSCG00000000895	5:82631990-82639939		CU633406,CH242-359G18,5:82626648-82645738 (Clone quality: bE359G18 on chr=5; Num_of_Contigs=3; )
SNRPG		ENSSSCG00000008328	3:66198631-66206792		CU929337,CH242-249L10,3:66190660-66207181 (Clone quality: bE249L10 on chr=3; Num_of_Contigs=18; )
SNTA1		ENSSSCG00000007265	17:38837615-38865965
SNTB1		ENSSSCG00000005994	4:18029517-18150654
SNTN		ENSSSCG00000011492	13:38180537-38191355
SNUPN		ENSSSCG00000001877	7:63263657-63290647		CU582918,CH242-27K6,7:63261045-63302782 (Clone quality: bE27K6 on chr=7; Num_of_Contigs=5; )
SNX1		ENSSSCG00000004556	1:111157927-111179288		CU302261,CH242-182N21,1:111146176-111189442 (Clone quality: bE182N21 on chr=1; Num_of_Contigs=3; )
SNX10		ENSSSCG00000016709	18:44950731-44979087
SNX10		location ⇒	18:44949875-44949762		CU655935,CH242-367O12,18:44876784-44955235 (Clone quality: bE367O12 on chr=18; Num_of_Contigs=3; )
SNX10		location ⇒	18:44951528-44951254		CU655935,CH242-367O12,18:44876784-44955235 (Clone quality: bE367O12 on chr=18; Num_of_Contigs=3; )
SNX10		location ⇒	18:44952188-44951980		CU655935,CH242-367O12,18:44876784-44955235 (Clone quality: bE367O12 on chr=18; Num_of_Contigs=3; )
SNX10		location ⇒	18:44964514-44964426		FP236743,CH242-201O19,18:44955236-44965897 (Clone quality: bE201O19 on chr=18; Num_of_Contigs=8; )
SNX11		ENSSSCG00000017528	12:21895352-21903717		FP016123,CH242-397L8,12:21776694-21937896 (Clone quality: bE397L8 on chr=12; Num_of_Contigs=6; )
SNX12		ENSSSCG00000012400	X:56891561-56899136		CU468205,CH242-6A14,X:56849541-56908124 (Clone quality: bE6A14 on chr=X; Num_of_Contigs=4; )

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).