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)

SERPINA12		ENSSSCG00000002478	7:124229372-124351718
SERPINA12		location ⇒	7:124141844-124141934		CU652780,CH242-302G10,7:124140037-124147324 (Clone quality: bE302G10 on chr=7; Num_of_Contigs=22; )
SERPINA12		location ⇒	7:124232021-124232111		CU633316,CH242-69M9,7:124201197-124252438 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA12		location ⇒	7:124235723-124235820		CU633316,CH242-69M9,7:124201197-124252438 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA13		ENSSSCG00000002485	7:124488365-124546592
SERPINA3		ENSSSCG00000002483	7:124442778-124451547		CU468597,CH242-186K9,7:124431975-124466966 (Clone quality: bE186K9 on chr=7; Num_of_Contigs=21; )
SERPINA3		ENSSSCG00000002487	7:124550458-124559551
SERPINA3		location ⇒	7:124388248-124387592		CU468597,CH242-186K9,7:124386198-124389750 (Clone quality: bE186K9 on chr=7; Num_of_Contigs=21; )
SERPINA3		location ⇒	7:124451467-124451529		CU468597,CH242-186K9,7:124431975-124466966 (Clone quality: bE186K9 on chr=7; Num_of_Contigs=21; )
SERPINA3		location ⇒	7:124525963-124526611		CU468597,CH242-186K9,7:124525900-124528104 (Clone quality: bE186K9 on chr=7; Num_of_Contigs=21; )
SERPINA3		location ⇒	7:124557351-124556695		CU302448,CH242-17C18,7:124548762-124558660 (Clone quality: bE17C18 on chr=7; Num_of_Contigs=5; )
SERPINA5		ENSSSCG00000002481	7:124359044-124369881		CU633316,CH242-69M9,7:124319189-124372263 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA5		location ⇒	7:124365807-124366008		CU633316,CH242-69M9,7:124319189-124372263 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA5		location ⇒	7:124367666-124367939		CU633316,CH242-69M9,7:124319189-124372263 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA5		location ⇒	7:124368302-124368451		CU633316,CH242-69M9,7:124319189-124372263 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA5		location ⇒	7:124369397-124369535		CU633316,CH242-69M9,7:124319189-124372263 (Clone quality: bE69M9 on chr=7; Num_of_Contigs=4; )
SERPINA6		ENSSSCG00000002475	7:123932180-123951199
SERPINA7		ENSSSCG00000012547	X:84691441-84697113		CU694910,CH242-427M6,X:84616132-84699773 (Clone quality: bE427M6 on chr=X; Num_of_Contigs=4; )
SERPINB1		ENSSSCG00000001011	7:3025102-3034222
SERPINB1		location ⇒	7:3028110-3027941		CU041352,CH242-333I16,7:3001628-3033508 (Clone quality: bE333I16 on chr=7; Num_of_Contigs=9; )
SERPINB1		location ⇒	7:3033077-3032908		CU041352,CH242-333I16,7:3001628-3033508 (Clone quality: bE333I16 on chr=7; Num_of_Contigs=9; )
SERPINB10		ENSSSCG00000004889	1:164926724-164951511		CU234209,CH242-429G16,1:164915641-164951957 (Clone quality: bE429G16 on chr=1; Num_of_Contigs=4; )
SERPINB2		ENSSSCG00000004890	1:164957077-164967152	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB2		location ⇒	1:164956769-164956517	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB2		location ⇒	1:164957479-164956808	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB2		location ⇒	1:164957965-164957800	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB2		location ⇒	1:164967163-164966983	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB5		ENSSSCG00000004894	1:165269250-165287936		CU694588,CH242-25E9,1:165262269-165295154 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
SERPINB5		location ⇒	1:165269812-165269480		CU694588,CH242-25E9,1:165262269-165295154 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
SERPINB5		location ⇒	1:165276242-165276070		CU694588,CH242-25E9,1:165262269-165295154 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
SERPINB5		location ⇒	1:165280821-165280678		CU694588,CH242-25E9,1:165262269-165295154 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
SERPINB5		location ⇒	1:165284968-165284829		CU694588,CH242-25E9,1:165262269-165295154 (Clone quality: bE25E9 on chr=1; Num_of_Contigs=5; )
SERPINB7		ENSSSCG00000004891	1:165039220-165083424	CU074278,CH242-106E19,1:164951958-165118980 (Clone quality: bE106E19 on chr=1; Num_of_Contigs=1; )
SERPINB8		ENSSSCG00000004888	1:164907399-164917059
SERPINC1		ENSSSCG00000015493	9:108945335-108956842		FP102036,CH242-81O13,9:108937651-108962833 (Clone quality: bE81O13 on chr=9; Num_of_Contigs=6; )
SERPINC1		location ⇒	9:108947754-108948127		FP102036,CH242-81O13,9:108937651-108962833 (Clone quality: bE81O13 on chr=9; Num_of_Contigs=6; )
SERPINC1		location ⇒	9:108951427-108951821		FP102036,CH242-81O13,9:108937651-108962833 (Clone quality: bE81O13 on chr=9; Num_of_Contigs=6; )
SERPINC1		location ⇒	9:108956320-108956568		FP102036,CH242-81O13,9:108937651-108962833 (Clone quality: bE81O13 on chr=9; Num_of_Contigs=6; )
SERPINC1		location ⇒	9:96351836-96351780		CU570825,CH242-232P7,9:96290209-96447239 (Clone quality: bE232P7 on chr=9; Num_of_Contigs=1; )
SERPIND1		ENSSSCG00000010093	14:51526269-51532480		CU468899,CH242-236E21,14:51456577-51553624 (Clone quality: bE236E21 on chr=14; Num_of_Contigs=7; )
SERPIND1		location ⇒	14:51526463-51527146		CU468899,CH242-236E21,14:51456577-51553624 (Clone quality: bE236E21 on chr=14; Num_of_Contigs=7; )
SERPIND1		location ⇒	14:51528528-51528804		CU468899,CH242-236E21,14:51456577-51553624 (Clone quality: bE236E21 on chr=14; Num_of_Contigs=7; )
SERPIND1		location ⇒	14:51531148-51531294		CU468899,CH242-236E21,14:51456577-51553624 (Clone quality: bE236E21 on chr=14; Num_of_Contigs=7; )
SERPIND1		location ⇒	14:51531680-51532476		CU468899,CH242-236E21,14:51456577-51553624 (Clone quality: bE236E21 on chr=14; Num_of_Contigs=7; )
SERPINE1		ENSSSCG00000003798	6:102195509-102208960		CU442704,CH242-111N2,6:102164133-102241390 (Clone quality: bE111N2 on chr=6; Num_of_Contigs=4; )
SERPINE2		ENSSSCG00000016233	15:118156165-118250911
SERPINF1		ENSSSCG00000017818	12:45372872-45415798
SERPINF2		ENSSSCG00000017820	12:45423069-45428117		FP016227,CH242-99J5,12:45391979-45428198 (Clone quality: bE99J5 on chr=12; Num_of_Contigs=5; )
SERPINF2		location ⇒	12:45423639-45422532		FP016227,CH242-99J5,12:45391979-45428198 (Clone quality: bE99J5 on chr=12; Num_of_Contigs=5; )
SERPINF2		location ⇒	12:45424493-45424286		FP016227,CH242-99J5,12:45391979-45428198 (Clone quality: bE99J5 on chr=12; Num_of_Contigs=5; )

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).