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)

C1QR1		location ⇒	17:31705508-31704704		CU407182,CH242-263H13,17:31698231-31705569 (Clone quality: bE263H13 on chr=17; Num_of_Contigs=6; )
C1QR1		location ⇒	17:31706845-31706326		CU407182,CH242-263H13,17:31705670-31737715 (Clone quality: bE263H13 on chr=17; Num_of_Contigs=6; )
C1QR1		location ⇒	17:31746865-31744992		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
C1qRP		ENSSSCG00000007116	17:31744235-31746961		CU606974,CH242-23K16,17:31739767-31793889 (Clone quality: bE23K16 on chr=17; Num_of_Contigs=5; )
C1QTNF2		location ⇒	16:60661899-60661248		CU928350,CH242-226E17,16:60643711-60718469 (Clone quality: bE226E17 on chr=16; Num_of_Contigs=6; )
C1QTNF2		location ⇒	16:60664497-60664241		CU928350,CH242-226E17,16:60643711-60718469 (Clone quality: bE226E17 on chr=16; Num_of_Contigs=6; )
C1QTNF2		location ⇒	16:60774586-60774842		CU571129,CH242-2E15,16:60758885-60798250 (Clone quality: bE2E15 on chr=16; Num_of_Contigs=4; )
C1QTNF2		location ⇒	16:60777458-60778109		CU571129,CH242-2E15,16:60758885-60798250 (Clone quality: bE2E15 on chr=16; Num_of_Contigs=4; )
C1QTNF3		ENSSSCG00000016823	16:17548763-17575781		CU928963,CH242-104B16,16:17505139-17604356 (Clone quality: bE104B16 on chr=16; Num_of_Contigs=4; )
C1QTNF3		location ⇒	16:17550827-17550223		CU928963,CH242-104B16,16:17505139-17604356 (Clone quality: bE104B16 on chr=16; Num_of_Contigs=4; )
C1QTNF4		ENSSSCG00000013231	2:13092097-13093059		CU856103,CH242-271O6,2:12985573-13119992 (Clone quality: bE271O6 on chr=2; Num_of_Contigs=3; )
C1QTNF4		location ⇒	2:13092798-13091959		CU856103,CH242-271O6,2:12985573-13119992 (Clone quality: bE271O6 on chr=2; Num_of_Contigs=3; )
C1QTNF5		ENSSSCG00000015119	9:45162257-45167389		CU915638,CH242-115L13,9:45139059-45168315 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
C1QTNF5		location ⇒	9:45160381-45159766		CU915638,CH242-115L13,9:45139059-45168315 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
C1QTNF5		location ⇒	9:45161567-45161386		CU915638,CH242-115L13,9:45139059-45168315 (Clone quality: bE115L13 on chr=9; Num_of_Contigs=6; )
C1QTNF5		location ⇒	9:45250082-45249467		CU951455,CH242-416J8,9:45248065-45272580 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
C1QTNF5		location ⇒	9:45251268-45251087		CU951455,CH242-416J8,9:45248065-45272580 (Clone quality: bE416J8 on chr=9; Num_of_Contigs=2; )
C1QTNF6		location ⇒	5:18873449-18873511		CU464167,CH242-45P10,5:18873317-18877461 (Clone quality: bE45P10 on chr=5; Num_of_Contigs=3; )
C1QTNF6		location ⇒	5:45716503-45716439		CU467699,CH242-230O19,5:45617298-45778082 (Clone quality: bE230O19 on chr=5; Num_of_Contigs=1; )
C1QTNF6		location ⇒	5:46837638-46837703		FP102575,CH242-152I15,5:46808901-46859110 (Clone quality: bE152I15 on chr=5; Num_of_Contigs=10; )
C1QTNF6		location ⇒	5:82806554-82806618		CU442719,CH242-91J22,5:82799634-82806728 (Clone quality: bE91J22 on chr=5; Num_of_Contigs=5; )
C1QTNF7		ENSSSCG00000008737	8:7889160-7905206		CU928759,CH242-80M6,8:7860052-7935328 (Clone quality: bE80M6 on chr=8; Num_of_Contigs=5; )
C1QTNF7		location ⇒	8:7904587-7905223		CU928759,CH242-80M6,8:7860052-7935328 (Clone quality: bE80M6 on chr=8; Num_of_Contigs=5; )
C1R		ENSSSCG00000000675	5:59762099-59773034		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1R		ENSSSCG00000000674	5:59745215-59757097		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1R		location ⇒	5:59756392-59756472		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1R		location ⇒	5:59762934-59763162		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1R		location ⇒	5:59764699-59764893		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1R		location ⇒	5:59772150-59773031		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1RL		ENSSSCG00000000674	5:59745215-59757097		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1RL		location ⇒	5:59745233-59745299		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1RL		location ⇒	5:59746050-59746326		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1RL		location ⇒	5:59752724-59752908		CU929436,CH242-260C21,5:59719409-59776366 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1S		ENSSSCG00000000676	5:59788135-59799275		CU929436,CH242-260C21,5:59776467-59801643 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1S		location ⇒	5:59789358-59788551		CU929436,CH242-260C21,5:59776467-59801643 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1S		location ⇒	5:59794516-59794315		CU929436,CH242-260C21,5:59776467-59801643 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1S		location ⇒	5:59796556-59796377		CU929436,CH242-260C21,5:59776467-59801643 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C1S		location ⇒	5:59797250-59797042		CU929436,CH242-260C21,5:59776467-59801643 (Clone quality: bE260C21 on chr=5; Num_of_Contigs=5; )
C2		location ⇒	7:27854644-27854712	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C2		location ⇒	7:27854875-27854930	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C2		location ⇒	7:27855429-27855482	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C2		location ⇒	7:27856012-27856066	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; Num_of_Contigs=3; )
C20orf100		ENSSSCG00000007368	17:48262911-48460020
C20orf108		ENSSSCG00000007492	17:59476535-59488099	CR956640,CH242-155M9,17:59463698-59643740 (No clone quality info on bE155M9)
C20orf111		ENSSSCG00000007374	17:48618603-48622167
C20orf112		ENSSSCG00000007249	17:38087874-38096306		CU075917,CH242-158M7,17:38014651-38109830 (Clone quality: bE158M7 on chr=17; Num_of_Contigs=7; )
C20orf114		ENSSSCG00000007261	17:38702396-38729891		CU467098,CH242-181C3,17:38585383-38773516 (Clone quality: bE181C3 on chr=17; Num_of_Contigs=1; )
C20orf114		ENSSSCG00000007257	17:38545150-38552803		CU861496,CH242-97E15,17:38541073-38553058 (Clone quality: bE97E15 on chr=17; Num_of_Contigs=6; )
C20orf114		location ⇒	17:38545150-38545298		CU861496,CH242-97E15,17:38541073-38553058 (Clone quality: bE97E15 on chr=17; Num_of_Contigs=6; )
C20orf114		location ⇒	17:38552629-38552790		CU861496,CH242-97E15,17:38541073-38553058 (Clone quality: bE97E15 on chr=17; Num_of_Contigs=6; )

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).