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)

SSSCA1		ENSSSCG00000012990	2:5150538-5151815		CU914305,CH242-95H15,2:5149176-5153998 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
SSSCA1		location ⇒	2:5150917-5150583		CU914305,CH242-95H15,2:5149176-5153998 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
SSSCA1		location ⇒	2:5151401-5151318		CU914305,CH242-95H15,2:5149176-5153998 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
SSSCA1		location ⇒	2:5151685-5151533		CU914305,CH242-95H15,2:5149176-5153998 (Clone quality: bE95H15 on chr=2; Num_of_Contigs=19; )
SST		ENSSSCG00000011808	13:94724975-94726408		CU466378,CH242-185B2,13:94693645-94764313 (Clone quality: bE185B2 on chr=13; Num_of_Contigs=3; )
SST5		location ⇒	12:5896792-5896527		CU466404,CH242-455N10,12:5857365-5908364 (Clone quality: bE455N10 on chr=12; Num_of_Contigs=7; )
SSTR1		ENSSSCG00000001938	7:67641197-67642369	CT990617,CH242-94D11,7:67500927-67705976 (Clone quality: bE94D11 on chr=7; Num_of_Contigs=1; )
SSTR2		ENSSSCG00000017249	12:5895858-5896967		CU466404,CH242-455N10,12:5857365-5908364 (Clone quality: bE455N10 on chr=12; Num_of_Contigs=7; )
SSU72		ENSSSCG00000003348	6:42999078-43026098
SSU_rRNA_5		ENSSSCG00000018960	X:21037351-21037727		CU928861,CH242-88C2,X:21034792-21043096 (Clone quality: bE88C2 on chr=X; Num_of_Contigs=19; )
SSU_rRNA_5		ENSSSCG00000018376	17:64374926-64375578		FP016076,CH242-519M12,17:64356803-64376155 (Clone quality: bE519M12 on chr=17; Num_of_Contigs=14; )
SSU_rRNA_5		ENSSSCG00000019265	17:64159179-64159964
SSU_rRNA_5		ENSSSCG00000018481	X:20899594-20899970	FP101977,CH242-113I11,X:20869447-20900822 (Clone quality: bE113I11 on chr=X; Num_of_Contigs=2; )
SSU_rRNA_5		ENSSSCG00000018609	6:258810-259443		FP102614,CH242-198I21,6:256719-261768 (Clone quality: bE198I21 on chr=6; Num_of_Contigs=22; )
SSX2IP		ENSSSCG00000003757	6:89113038-89142240
SSX2IP		location ⇒	6:89124469-89124548		CU469250,CH242-520E12,6:89123613-89159801 (Clone quality: bE520E12 on chr=6; Num_of_Contigs=12; )
SSX2IP		location ⇒	6:89124626-89124808		CU469250,CH242-520E12,6:89123613-89159801 (Clone quality: bE520E12 on chr=6; Num_of_Contigs=12; )
SSX2IP		location ⇒	6:89128388-89128538		CU469250,CH242-520E12,6:89123613-89159801 (Clone quality: bE520E12 on chr=6; Num_of_Contigs=12; )
SSX2IP		location ⇒	6:89130114-89130251		CU469250,CH242-520E12,6:89123613-89159801 (Clone quality: bE520E12 on chr=6; Num_of_Contigs=12; )
ST14		ENSSSCG00000015246	9:55341969-55359518
ST18		ENSSSCG00000006266	4:80873721-80939825
ST3GAL-IV		location ⇒	9:51981803-51981956		CU463959,CH242-476I11,9:51964690-51995101 (Clone quality: bE476I11 on chr=9; Num_of_Contigs=5; )
ST3GAL-IV		location ⇒	9:51984250-51984444		CU463959,CH242-476I11,9:51964690-51995101 (Clone quality: bE476I11 on chr=9; Num_of_Contigs=5; )
ST3GAL-IV		location ⇒	9:51989285-51989431		CU463959,CH242-476I11,9:51964690-51995101 (Clone quality: bE476I11 on chr=9; Num_of_Contigs=5; )
ST3GAL-IV		location ⇒	9:51989696-51990354		CU463959,CH242-476I11,9:51964690-51995101 (Clone quality: bE476I11 on chr=9; Num_of_Contigs=5; )
ST3GAL1		ENSSSCG00000005943	4:6695726-6705795		CU179695,CH242-327C11,4:6638178-6710539 (Clone quality: bE327C11 on chr=4; Num_of_Contigs=5; )
ST3GAL4		ENSSSCG00000015232	9:51812632-51990371
ST3GAL5		ENSSSCG00000008227	3:53876865-53887643
ST3GAL5		location ⇒	3:53877166-53877074		CU862068,CH242-499L20,3:53854005-53881526 (Clone quality: bE499L20 on chr=3; Num_of_Contigs=8; )
ST3GAL5		location ⇒	3:53881467-53881350		CU862068,CH242-499L20,3:53854005-53881526 (Clone quality: bE499L20 on chr=3; Num_of_Contigs=8; )
ST3GAL5		location ⇒	3:53882336-53882148		CU862068,CH242-499L20,3:53881627-53888299 (Clone quality: bE499L20 on chr=3; Num_of_Contigs=8; )
ST3GAL5		location ⇒	3:53887612-53887265		CU862068,CH242-499L20,3:53881627-53888299 (Clone quality: bE499L20 on chr=3; Num_of_Contigs=8; )
ST3GAL6		ENSSSCG00000011976	13:118265176-118284771
ST5		ENSSSCG00000014568	9:106398-123464		FP102759,CH242-92D2,9:104962-128138 (Clone quality: bE92D2 on chr=9; Num_of_Contigs=7; )
ST6GAL2		ENSSSCG00000008141	3:43855839-43885293		FP236198,CH242-106F23,3:43852218-43902951 (Clone quality: bE106F23 on chr=3; Num_of_Contigs=2; )
ST6GALNAC-V		location ⇒	6:95291316-95291221		CU407301,CH242-75I5,6:95284937-95310763 (Clone quality: bE75I5 on chr=6; Num_of_Contigs=5; )
ST6GALNAC-V		location ⇒	6:95292344-95292137		CU407301,CH242-75I5,6:95284937-95310763 (Clone quality: bE75I5 on chr=6; Num_of_Contigs=5; )
ST6GALNAC1		ENSSSCG00000017172	12:3157987-3161180
ST6GALNAC2		ENSSSCG00000017177	12:3277247-3285641		CU928356,CH242-33I18,12:3274501-3286837 (Clone quality: bE33I18 on chr=12; Num_of_Contigs=10; )
ST6GALNAC4		ENSSSCG00000005628	1:282879087-282889624		CU638853,CH242-308I15,1:282840723-282900792 (Clone quality: bE308I15 on chr=1; Num_of_Contigs=4; )
ST6GALNAC6		ENSSSCG00000005623	1:282717340-282727272
ST7		ENSSSCG00000016629	18:27553433-27789512
ST7L		ENSSSCG00000006779	4:112274357-112340190		FP085533,CH242-398F22,4:112262268-112425068 (Clone quality: bE398F22 on chr=4; Num_of_Contigs=2; )
ST8SIA1		location ⇒	5:49287190-49287062		CU468664,CH242-282F10,5:49281752-49287798 (Clone quality: bE282F10 on chr=5; Num_of_Contigs=6; )
ST8SIA2		ENSSSCG00000002264	7:95755715-95787915
ST8SIA2		location ⇒	7:95755845-95755793		CT823558,CH242-5F18,7:95747102-95766942 (Clone quality: bE5F18 on chr=7; Num_of_Contigs=5; )
ST8SIA2		location ⇒	7:95760027-95759896		CT823558,CH242-5F18,7:95747102-95766942 (Clone quality: bE5F18 on chr=7; Num_of_Contigs=5; )
ST8SIA2		location ⇒	7:95765629-95765220		CT823558,CH242-5F18,7:95747102-95766942 (Clone quality: bE5F18 on chr=7; Num_of_Contigs=5; )
ST8SIA3		ENSSSCG00000004539	1:109851426-109859237		CU062560,CH242-388H12,1:109850833-109864102 (Clone quality: bE388H12 on chr=1; Num_of_Contigs=13; )
ST8SIA4		ENSSSCG00000014180	2:95983476-96075674

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).