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)

CXCL9		location ⇒	8:61049521-61049350		CU672252,CH242-392J2,8:61030020-61058295 (Clone quality: bE392J2 on chr=8; Num_of_Contigs=2; )
CXCL9		location ⇒	8:61051011-61050958		CU672252,CH242-392J2,8:61030020-61058295 (Clone quality: bE392J2 on chr=8; Num_of_Contigs=2; )
CXCL9		location ⇒	8:61052733-61052605		CU672252,CH242-392J2,8:61030020-61058295 (Clone quality: bE392J2 on chr=8; Num_of_Contigs=2; )
CXCL9		location ⇒	8:61054161-61054053		CU672252,CH242-392J2,8:61030020-61058295 (Clone quality: bE392J2 on chr=8; Num_of_Contigs=2; )
CXCR3		ENSSSCG00000012402	X:57213490-57216859		FP015848,CH242-94E16,X:57182938-57245160 (Clone quality: bE94E16 on chr=X; Num_of_Contigs=6; )
CXCR3		location ⇒	X:57215026-57213491		FP015848,CH242-94E16,X:57182938-57245160 (Clone quality: bE94E16 on chr=X; Num_of_Contigs=6; )
CXCR3		location ⇒	X:57216859-57216775		FP015848,CH242-94E16,X:57182938-57245160 (Clone quality: bE94E16 on chr=X; Num_of_Contigs=6; )
CXCR4		ENSSSCG00000015688	15:14081271-14084327
CXCR4		location ⇒	15:14083281-14084327		CU463931,CH242-461D1,15:14082364-14086873 (Clone quality: bE461D1 on chr=15; Num_of_Contigs=8; )
CXCR4		location ⇒	15:14083281-14084327		CU463931,CH242-461D1,15:14082364-14086873 (Clone quality: bE461D1 on chr=15; Num_of_Contigs=8; )
CXCR5		ENSSSCG00000015098	9:44724736-44735301		FP089499,CH242-36G7,9:44609302-44750256 (Clone quality: bE36G7 on chr=9; Num_of_Contigs=3; )
CXCR5		ENSSSCG00000015098	9:44724736-44735301		FP089499,CH242-36G7,9:44609302-44750256 (Clone quality: bE36G7 on chr=9; Num_of_Contigs=3; )
CXCR6		ENSSSCG00000011318	13:24506685-24511451		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CXCR6		ENSSSCG00000011318	13:24506685-24511451		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CXCR6		location ⇒	13:24506685-24506785		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CXCR6		location ⇒	13:24509572-24511451		CU469254,CH242-75A24,13:24398824-24519472 (Clone quality: bE75A24 on chr=13; Num_of_Contigs=4; )
CXCR7		ENSSSCG00000016322	15:128776144-128777232		CU929109,CH242-312D3,15:128751699-128807860 (Clone quality: bE312D3 on chr=15; Num_of_Contigs=8; )
CXCR7		location ⇒	15:128776335-128775696		CU929109,CH242-312D3,15:128751699-128807860 (Clone quality: bE312D3 on chr=15; Num_of_Contigs=8; )
CXG1_PIG		ENSSSCG00000017350	12:16489508-16490839		FP102430,CH242-164B23,12:16487389-16513482 (Clone quality: bE164B23 on chr=12; Num_of_Contigs=11; )
CXG1_PIG		ENSSSCG00000017348	12:16407255-16408586		CU896578,CH242-101E18,12:16390983-16436613 (Clone quality: bE101E18 on chr=12; Num_of_Contigs=7; )
CXorf15		location ⇒	X:12757222-12757393		CU463287,CH242-124N9,X:12731155-12802306 (Clone quality: bE124N9 on chr=X; Num_of_Contigs=6; )
CXorf15		location ⇒	X:12758581-12758778		CU463287,CH242-124N9,X:12731155-12802306 (Clone quality: bE124N9 on chr=X; Num_of_Contigs=6; )
CXorf15		location ⇒	X:12770672-12770792		CU463287,CH242-124N9,X:12731155-12802306 (Clone quality: bE124N9 on chr=X; Num_of_Contigs=6; )
CXorf15		location ⇒	X:12770895-12771352		CU463287,CH242-124N9,X:12731155-12802306 (Clone quality: bE124N9 on chr=X; Num_of_Contigs=6; )
CXorf21		ENSSSCG00000012201	X:25791423-25792322	CU210922,CH242-479E6,X:25682979-25864194 (Clone quality: bE479E6 on chr=X; Num_of_Contigs=1; )
CXorf22		ENSSSCG00000012219	X:31509339-31545878
CXorf26		ENSSSCG00000012429	X:60225399-60228940
CXorf27		ENSSSCG00000012231	X:33344116-33344457	CU695110,CH242-281O17,X:33271124-33401329 (Clone quality: bE281O17 on chr=X; Num_of_Contigs=4; )
CXorf36		ENSSSCG00000012263	X:40288991-40289236		FP102177,CH242-210O3,X:40287967-40291040 (Clone quality: bE210O3 on chr=X; Num_of_Contigs=23; )
CXorf38		ENSSSCG00000012249	X:36046286-36065965
CXorf39		ENSSSCG00000012542	X:82748675-82771454
CXorf40A		ENSSSCG00000012737	X:120049493-120050886		FP102033,CH242-101J9,X:120045833-120065226 (Clone quality: bE101J9 on chr=X; Num_of_Contigs=8; )
CXorf41		ENSSSCG00000012558	X:85791716-85829214
CXorf48		ENSSSCG00000012693	X:109070761-109087685		CU928850,CH242-30L9,X:109056727-109092602 (Clone quality: bE30L9 on chr=X; Num_of_Contigs=6; )
CXorf56		ENSSSCG00000012622	X:96639705-96650622
CXorf57		ENSSSCG00000012549	X:84944696-84958351
CXORF57		ENSSSCG00000012549	X:84944696-84958351
CXORF57		location ⇒	X:84944890-84944695		FP103051,CH242-71D22,X:84939944-84957232 (Clone quality: bE71D22 on chr=X; Num_of_Contigs=4; )
CXORF57		location ⇒	X:84958483-84957712		FP103051,CH242-71D22,X:84957333-84976454 (Clone quality: bE71D22 on chr=X; Num_of_Contigs=4; )
CXORF57		location ⇒	X:85068339-85069110		CU914612,CH242-85J15,X:85065194-85079466 (Clone quality: bE85J15 on chr=X; Num_of_Contigs=6; )
CXORF57		location ⇒	X:85119623-85119364		CU914612,CH242-85J15,X:85117874-85126528 (Clone quality: bE85J15 on chr=X; Num_of_Contigs=6; )
CXorf58		ENSSSCG00000012175	X:18858499-18888878
CXORF6		ENSSSCG00000012741	X:120339479-120389000		FP102038,CH242-116A16,X:120329164-120398795 (Clone quality: bE116A16 on chr=X; Num_of_Contigs=5; )
CXorf64		ENSSSCG00000012647	X:101410509-101412337		FP102440,CH242-251N15,X:101407809-101423016 (Clone quality: bE251N15 on chr=X; Num_of_Contigs=13; )
CXorf65		ENSSSCG00000012398	X:56857854-56859680		CU468205,CH242-6A14,X:56849541-56908124 (Clone quality: bE6A14 on chr=X; Num_of_Contigs=4; )
CXorf66		ENSSSCG00000012714	X:112553305-112677871
CXorf67		ENSSSCG00000012316	X:44379404-44381686		FP102067,CH242-300C18,X:44377037-44405705 (Clone quality: bE300C18 on chr=X; Num_of_Contigs=4; )
CXXC1		ENSSSCG00000004517	1:102963474-102968962		CU914451,CH242-152J17,1:102889373-103019647 (Clone quality: bE152J17 on chr=1; Num_of_Contigs=3; )
CXXC4		ENSSSCG00000009159	8:100648256-100649130		CU928701,CH242-400B5,8:100647554-100668664 (Clone quality: bE400B5 on chr=8; Num_of_Contigs=9; )
CXXC5		ENSSSCG00000014357	2:128559980-128562712		CU928373,CH242-379D14,2:128553450-128585205 (Clone quality: bE379D14 on chr=2; Num_of_Contigs=17; )

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).