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)

CTPS		ENSSSCG00000003973	6:121597240-121628289		FP016067,CH242-126M8,6:121551012-121676967 (Clone quality: bE126M8 on chr=6; Num_of_Contigs=2; )
CTPS2		ENSSSCG00000012146	X:12510127-12660153
CTR9		ENSSSCG00000013406	2:45192141-45220403
CTSA		ENSSSCG00000007431	17:50146758-50153335
CTSC		ENSSSCG00000014924	9:21822223-21856922		CU855751,CH242-343O24,9:21819212-21862877 (Clone quality: bE343O24 on chr=9; Num_of_Contigs=3; )
CTSC		location ⇒	9:21822958-21822118		CU855751,CH242-343O24,9:21819212-21862877 (Clone quality: bE343O24 on chr=9; Num_of_Contigs=3; )
CTSC		location ⇒	9:21834123-21833967		CU855751,CH242-343O24,9:21819212-21862877 (Clone quality: bE343O24 on chr=9; Num_of_Contigs=3; )
CTSC		location ⇒	9:21837631-21837461		CU855751,CH242-343O24,9:21819212-21862877 (Clone quality: bE343O24 on chr=9; Num_of_Contigs=3; )
CTSC		location ⇒	9:21856923-21856637		CU855751,CH242-343O24,9:21819212-21862877 (Clone quality: bE343O24 on chr=9; Num_of_Contigs=3; )
CTSF		location ⇒	2:4136972-4137092		CU928093,CH242-168G1,2:4131589-4155461 (Clone quality: bE168G1 on chr=2; Num_of_Contigs=25; )
CTSF		location ⇒	2:4137316-4137411		CU928093,CH242-168G1,2:4131589-4155461 (Clone quality: bE168G1 on chr=2; Num_of_Contigs=25; )
CTSF		location ⇒	2:4419414-4419319		CU928034,CH242-426E24,2:4401193-4424111 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
CTSF		location ⇒	2:4419758-4419638		CU928034,CH242-426E24,2:4401193-4424111 (Clone quality: bE426E24 on chr=2; Num_of_Contigs=5; )
CTSG		ENSSSCG00000001980	7:81140765-81143404		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CTSG		location ⇒	7:81129456-81129393		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CTSG		location ⇒	7:81140949-81141012		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CTSG		location ⇒	7:81142569-81142627		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CTSG		location ⇒	7:81165901-81165956		CT997804,CH242-280B15,7:81125347-81169003 (Clone quality: bE280B15 on chr=7; Num_of_Contigs=5; )
CTSH		ENSSSCG00000001770	7:54119425-54140625		CU326382,CH242-204O9,7:54055646-54191837 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )
CTSH		location ⇒	7:54119821-54119630		CU326382,CH242-204O9,7:54055646-54191837 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )
CTSH		location ⇒	7:54121268-54121135		CU326382,CH242-204O9,7:54055646-54191837 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )
CTSH		location ⇒	7:54133647-54133538		CU326382,CH242-204O9,7:54055646-54191837 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )
CTSH		location ⇒	7:54140554-54140438		CU326382,CH242-204O9,7:54055646-54191837 (Clone quality: bE204O9 on chr=7; Num_of_Contigs=8; )
CTSK		ENSSSCG00000006647	4:102342678-102354617		CU463875,CH242-217B6,4:102327469-102356902 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
CTSK		location ⇒	4:102342677-102342803		CU463875,CH242-217B6,4:102327469-102356902 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
CTSK		location ⇒	4:102343623-102343780		CU463875,CH242-217B6,4:102327469-102356902 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
CTSK		location ⇒	4:102345440-102345662		CU463875,CH242-217B6,4:102327469-102356902 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
CTSK		location ⇒	4:102350047-102350217		CU463875,CH242-217B6,4:102327469-102356902 (Clone quality: bE217B6 on chr=4; Num_of_Contigs=12; )
CTSL2		location ⇒	10:26751286-26751356		CU927895,CH242-175K13,10:26727966-26753278 (Clone quality: bE175K13 on chr=10; Num_of_Contigs=17; )
CTSL2		location ⇒	10:26755701-26755785		CU927895,CH242-175K13,10:26753379-26755906 (Clone quality: bE175K13 on chr=10; Num_of_Contigs=17; )
CTSL2		location ⇒	10:26906165-26906081		CU571031,CH242-270H6,10:26897910-26971773 (Clone quality: bE270H6 on chr=10; Num_of_Contigs=6; )
CTSL2		location ⇒	10:26910830-26910760		CU571031,CH242-270H6,10:26897910-26971773 (Clone quality: bE270H6 on chr=10; Num_of_Contigs=6; )
CTSO		ENSSSCG00000008867	8:38712697-38725139		CU855637,CH242-199L13,8:38712595-38842897 (Clone quality: bE199L13 on chr=8; Num_of_Contigs=2; )
CTSS		ENSSSCG00000006648	4:102368163-102393283		CU655899,CH242-160A10,4:102356903-102440553 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
CTSS		location ⇒	4:102373578-102373729		CU655899,CH242-160A10,4:102356903-102440553 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
CTSS		location ⇒	4:102375924-102376154		CU655899,CH242-160A10,4:102356903-102440553 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
CTSS		location ⇒	4:102377893-102378061		CU655899,CH242-160A10,4:102356903-102440553 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
CTSS		location ⇒	4:102392828-102393266		CU655899,CH242-160A10,4:102356903-102440553 (Clone quality: bE160A10 on chr=4; Num_of_Contigs=7; )
CTSW		ENSSSCG00000012970	2:4823483-4827562		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CTSW		location ⇒	2:4823723-4823483		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CTSW		location ⇒	2:4823996-4823810		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CTSW		location ⇒	2:4824716-4824590		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CTSW		location ⇒	2:4825342-4825185		CU928325,CH242-208C18,2:4805866-4836669 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
CTSZ		ENSSSCG00000007522	17:61758359-61766242	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
CTSZ		location ⇒	17:61758846-61758358	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
CTSZ		location ⇒	17:61760002-61759836	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
CTSZ		location ⇒	17:61762344-61762164	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
CTSZ		location ⇒	17:61765557-61765391	CR956646,CH242-247L10,17:61655968-61825296 (No clone quality info on bE247L10)
CTTN		ENSSSCG00000012867	2:1431275-1461457
CTTN		location ⇒	2:1453751-1453639		CU469203,CH242-236K15,2:1451789-1460862 (Clone quality: bE236K15 on chr=2; Num_of_Contigs=23; )

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, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

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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).