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)

P79302_PIG		ENSSSCG00000011571	13:55704621-55704707		CU469341,CH242-394A9,13:55702257-55705779 (Clone quality: bE394A9 on chr=13; Num_of_Contigs=26; )
P79321_PIG		ENSSSCG00000015829	15:46933712-46943741		CU582801,CH242-263J16,15:46920043-46945113 (Clone quality: bE263J16 on chr=15; Num_of_Contigs=9; )
P79326_PIG		ENSSSCG00000002535	7:131807953-131809819		CU633632,CH242-139M12,7:131807603-131831335 (Clone quality: bE139M12 on chr=7; Num_of_Contigs=22; )
P8		ENSSSCG00000011300	13:23566444-23595944
P8		ENSSSCG00000016314	15:126944280-127020166	CU407086,CH242-496M8,15:126923063-127047825 (Clone quality: bE496M8 on chr=15; Num_of_Contigs=6; )
P8		ENSSSCG00000012816	X:123542283-123546487
PA2G4		ENSSSCG00000012159	X:15073685-15075486
PAAF1		ENSSSCG00000014831	9:7963652-8017022
PABPC1L		ENSSSCG00000007382	17:49128307-49158046		CU633343,CH242-147P9,17:49046271-49162684 (Clone quality: bE147P9 on chr=17; Num_of_Contigs=3; )
PABPC4		ENSSSCG00000003660	6:65403862-65420062	CR956622,PigE-219N9,6:65300804-65474973 (No clone quality info on bT219N9)
PABPC4		location ⇒	3:30232426-30231706		CU915426,CH242-478G12,3:30208153-30255890 (Clone quality: bE478G12 on chr=3; Num_of_Contigs=3; )
PABPC4L		ENSSSCG00000009067	8:78938084-78939031
PABPN1		ENSSSCG00000002023	7:82057753-82061913		CU633625,CH242-116C14,7:82041923-82116183 (Clone quality: bE116C14 on chr=7; Num_of_Contigs=8; )
PABPN1L		ENSSSCG00000002647	6:388288-391016		FP102571,CH242-151H1,6:382867-395224 (Clone quality: bE151H1 on chr=6; Num_of_Contigs=15; )
PACAP		ENSSSCG00000016672	18:40391249-40433540
PACAP		ENSSSCG00000016403	18:91259-132891
PACAP		ENSSSCG00000011280	13:21872535-21944268
PACAP		ENSSSCG00000003698	6:72333470-72337631		CU467582,CH242-420P11,6:72324388-72354995 (Clone quality: bE420P11 on chr=6; Num_of_Contigs=8; )
PACAP		location ⇒	2:128340124-128339766		FP101965,CH242-45H7,2:128263088-128357212 (Clone quality: bE45H7 on chr=2; Num_of_Contigs=5; )
PACAP		location ⇒	2:128341831-128341631		FP101965,CH242-45H7,2:128263088-128357212 (Clone quality: bE45H7 on chr=2; Num_of_Contigs=5; )
PACAP		location ⇒	2:128459878-128460078		FP102079,CH242-22H3,2:128458813-128522338 (Clone quality: bE22H3 on chr=2; Num_of_Contigs=6; )
PACAP		location ⇒	2:128461585-128461943		FP102079,CH242-22H3,2:128458813-128522338 (Clone quality: bE22H3 on chr=2; Num_of_Contigs=6; )
PACRGL		ENSSSCG00000008750	8:12068355-12087786
PACS1		ENSSSCG00000012956	2:4512679-4650114
PACS1		location ⇒	2:4524025-4524163		CU462998,CH242-142J19,2:4503241-4539956 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
PACS1		location ⇒	2:4524262-4524378		CU462998,CH242-142J19,2:4503241-4539956 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
PACS1		location ⇒	2:4530773-4530936		CU462998,CH242-142J19,2:4503241-4539956 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
PACS1		location ⇒	2:4531673-4531732		CU462998,CH242-142J19,2:4503241-4539956 (Clone quality: bE142J19 on chr=2; Num_of_Contigs=8; )
PACSIN2		ENSSSCG00000000036	5:2502656-2679140
PACSIN3		ENSSSCG00000013244	2:13405836-13413834		CU469364,CH242-119B4,2:13316728-13478061 (Clone quality: bE119B4 on chr=2; Num_of_Contigs=2; )
PADI1		ENSSSCG00000003481	6:52207524-52247247		CU929901,CH242-259H17,6:52206564-52306325 (Clone quality: bE259H17 on chr=6; Num_of_Contigs=3; )
PADI3		ENSSSCG00000003482	6:52251605-52285904		CU929901,CH242-259H17,6:52206564-52306325 (Clone quality: bE259H17 on chr=6; Num_of_Contigs=3; )
PADI4		ENSSSCG00000003483	6:52333151-52344191
PADI4		location ⇒	6:52243724-52243799		CU929901,CH242-259H17,6:52206564-52306325 (Clone quality: bE259H17 on chr=6; Num_of_Contigs=3; )
PADI4		location ⇒	6:52285670-52285917		CU929901,CH242-259H17,6:52206564-52306325 (Clone quality: bE259H17 on chr=6; Num_of_Contigs=3; )
PADI4		location ⇒	6:52341785-52341931		CU929743,CH242-257G20,6:52334986-52347017 (Clone quality: bE257G20 on chr=6; Num_of_Contigs=9; )
PADI4		location ⇒	6:52343960-52344293		CU929743,CH242-257G20,6:52334986-52347017 (Clone quality: bE257G20 on chr=6; Num_of_Contigs=9; )
PADI6		ENSSSCG00000003484	6:52348084-52365554		CU929743,CH242-257G20,6:52347118-52390944 (Clone quality: bE257G20 on chr=6; Num_of_Contigs=9; )
PAEP		ENSSSCG00000005752	1:289683588-289841532
PAEP		location ⇒	1:289687035-289686893		FP074863,CH242-151E10,1:289681425-289688852 (Clone quality: bE151E10 on chr=1; Num_of_Contigs=9; )
PAEP		location ⇒	1:289687796-289687674		FP074863,CH242-151E10,1:289681425-289688852 (Clone quality: bE151E10 on chr=1; Num_of_Contigs=9; )
PAEP		location ⇒	1:289840742-289840600		FP102268,CH242-95K10,1:289832708-289844981 (Clone quality: bE95K10 on chr=1; Num_of_Contigs=5; )
PAEP		location ⇒	1:289841503-289841381		FP102268,CH242-95K10,1:289832708-289844981 (Clone quality: bE95K10 on chr=1; Num_of_Contigs=5; )
PAF1		ENSSSCG00000010707	14:138658743-138663949		FP236263,CH242-159G20,14:138633964-138675291 (Clone quality: bE159G20 on chr=14; Num_of_Contigs=8; )
PAFAH1B1		ENSSSCG00000017836	12:46162294-46249005
PAFAH1B1		location ⇒	12:46163073-46162704		CU469125,CH242-167E20,12:46146931-46210392 (Clone quality: bE167E20 on chr=12; Num_of_Contigs=10; )
PAFAH1B1		location ⇒	12:46169639-46169410		CU469125,CH242-167E20,12:46146931-46210392 (Clone quality: bE167E20 on chr=12; Num_of_Contigs=10; )
PAFAH1B1		location ⇒	12:46182664-46182453		CU469125,CH242-167E20,12:46146931-46210392 (Clone quality: bE167E20 on chr=12; Num_of_Contigs=10; )
PAFAH1B1		location ⇒	12:46207788-46207568		CU469125,CH242-167E20,12:46146931-46210392 (Clone quality: bE167E20 on chr=12; Num_of_Contigs=10; )
PAFAH1B2		ENSSSCG00000015075	9:43326428-43336855		CU633260,CH242-267D22,9:43314501-43344182 (Clone quality: bE267D22 on chr=9; Num_of_Contigs=9; )

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, 2201-21

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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).