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)

CA3		ENSSSCG00000006141	4:52985168-52995436
CA6		ENSSSCG00000003391	6:46776211-46798106
CA8		ENSSSCG00000006233	4:75641998-75712815
CA9		ENSSSCG00000005315	1:247486665-247493333		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
CAB39		ENSSSCG00000016266	15:123918421-124009247
CAB39L		ENSSSCG00000009397	11:18285223-18322932
CABLES1		ENSSSCG00000003705	6:73661712-73753577
CABLES2		ENSSSCG00000007540	17:64006676-64018123
CABLES2		location ⇒	17:64016347-64016452		CU607084,CH242-119P9,17:64010245-64020547 (Clone quality: bE119P9 on chr=17; Num_of_Contigs=6; )
CABLES2		location ⇒	17:64016593-64016700		CU607084,CH242-119P9,17:64010245-64020547 (Clone quality: bE119P9 on chr=17; Num_of_Contigs=6; )
CABLES2		location ⇒	17:64017598-64017804		CU607084,CH242-119P9,17:64010245-64020547 (Clone quality: bE119P9 on chr=17; Num_of_Contigs=6; )
CABLES2		location ⇒	17:64017953-64018123		CU607084,CH242-119P9,17:64010245-64020547 (Clone quality: bE119P9 on chr=17; Num_of_Contigs=6; )
CABP1		ENSSSCG00000009913	14:40640432-40651116		CU062553,CH242-319N22,14:40627030-40656411 (Clone quality: bE319N22 on chr=14; Num_of_Contigs=5; )
CABP2		ENSSSCG00000012900	2:3359516-3363140
CABP4		ENSSSCG00000012906	2:3450459-3453455		CU633429,CH242-6G2,2:3403551-3456026 (Clone quality: bE6G2 on chr=2; Num_of_Contigs=8; )
CABP5		ENSSSCG00000003126	6:37287363-37298222		FP102640,CH242-235B10,6:37275907-37358125 (Clone quality: bE235B10 on chr=6; Num_of_Contigs=12; )
CABP7		ENSSSCG00000009985	14:47258740-47268242		CU633725,CH242-61M8,14:47183164-47366877 (Clone quality: bE61M8 on chr=14; Num_of_Contigs=1; )
CABYR		ENSSSCG00000003711	6:74346051-74370917		CU457767,CH242-245O7,6:74312546-74409001 (Clone quality: bE245O7 on chr=6; Num_of_Contigs=3; )
CACHD1		ENSSSCG00000004829	1:148924355-149045229
CACNA1A		ENSSSCG00000013754	2:56394573-56648933
CACNA1C		ENSSSCG00000000763	5:65002112-65141065
CACNA1C775		location ⇒	6:33557577-33557617		FP102369,CH242-128M4,6:33522006-33560344 (Clone quality: bE128M4 on chr=6; Num_of_Contigs=3; )
CACNA1D		ENSSSCG00000011455	13:29986203-30144848
CACNA1E		ENSSSCG00000015543	9:115629053-115731238
CACNA1F		ENSSSCG00000012298	X:42760501-42794033
CACNA1G		ENSSSCG00000017562	12:24060894-24094898
CACNA1I		ENSSSCG00000000082	5:4916295-4970998
CACNA1S		location ⇒	5:65107347-65107403		CU467896,CH242-34G22,5:65102199-65110639 (Clone quality: bE34G22 on chr=5; Num_of_Contigs=20; )
CACNA1S		location ⇒	5:65114903-65114969		CU467896,CH242-34G22,5:65110740-65141248 (Clone quality: bE34G22 on chr=5; Num_of_Contigs=20; )
CACNA1S		location ⇒	5:65152528-65152473		CU467896,CH242-34G22,5:65141349-65164940 (Clone quality: bE34G22 on chr=5; Num_of_Contigs=20; )
CACNA1S		location ⇒	5:65209738-65209677		CU467896,CH242-34G22,5:65200988-65210509 (Clone quality: bE34G22 on chr=5; Num_of_Contigs=20; )
CACNA2D1		ENSSSCG00000015402	9:91842222-92058797
CACNA2D2		ENSSSCG00000011412	13:27507680-27538828		CU861907,CH242-10C8,13:27490820-27610755 (Clone quality: bE10C8 on chr=13; Num_of_Contigs=3; )
CACNA2D4		ENSSSCG00000000758	5:64495022-64497952		FP102363,CH242-96D13,5:64494009-64498768 (Clone quality: bE96D13 on chr=5; Num_of_Contigs=18; )
CACNB1		ENSSSCG00000017510	12:21078286-21099106		FP085518,CH242-274F4,12:21003722-21101963 (Clone quality: bE274F4 on chr=12; Num_of_Contigs=3; )
CACNB2		ENSSSCG00000011040	10:43004842-43059614		FP102227,CH242-200J12,10:42987985-43075271 (Clone quality: bE200J12 on chr=10; Num_of_Contigs=3; )
CACNB3		ENSSSCG00000000176	5:13383979-13392426		CU914692,CH242-143P14,5:13374362-13396730 (Clone quality: bE143P14 on chr=5; Num_of_Contigs=6; )
CACNB4		location ⇒	8:36690707-36690862		FP016030,CH242-203L13,8:36675472-36701432 (Clone quality: bE203L13 on chr=8; Num_of_Contigs=3; )
CACNG1		ENSSSCG00000017271	12:11479591-11490680		CU639426,CH242-257I15,12:11407624-11507935 (Clone quality: bE257I15 on chr=12; Num_of_Contigs=3; )
CACNG2		ENSSSCG00000000140	5:7581330-7599506		CU861543,CH242-228E12,5:7494498-7671966 (Clone quality: bE228E12 on chr=5; Num_of_Contigs=1; )
CACNG3		ENSSSCG00000007831	3:20457027-20468701		FP102288,CH242-12G14,3:20444578-20575371 (Clone quality: bE12G14 on chr=3; Num_of_Contigs=1; )
CACNG4		ENSSSCG00000017270	12:11407711-11468596		CU639426,CH242-257I15,12:11407624-11507935 (Clone quality: bE257I15 on chr=12; Num_of_Contigs=3; )
CACNG5		ENSSSCG00000017269	12:11336894-11343225
CACNG6		ENSSSCG00000003257	6:40359754-40378232
CACNG7		ENSSSCG00000003254	6:40221171-40241085		CU855513,CH242-259K4,6:40218722-40247521 (Clone quality: bE259K4 on chr=6; Num_of_Contigs=12; )
CACNG8		ENSSSCG00000003255	6:40279060-40293544		CU855513,CH242-259K4,6:40278937-40293545 (Clone quality: bE259K4 on chr=6; Num_of_Contigs=12; )
CACYBP		ENSSSCG00000015504	9:109993270-110006558		CU856703,CH242-461F11,9:109957487-110007620 (Clone quality: bE461F11 on chr=9; Num_of_Contigs=13; )
CADM1		location ⇒	9:41559127-41558498		CU571118,CH242-229F5,9:41547760-41603997 (Clone quality: bE229F5 on chr=9; Num_of_Contigs=4; )
CADM1		location ⇒	9:41559753-41559162		CU571118,CH242-229F5,9:41547760-41603997 (Clone quality: bE229F5 on chr=9; Num_of_Contigs=4; )
CADM1		location ⇒	9:41559855-41559815		CU571118,CH242-229F5,9:41547760-41603997 (Clone quality: bE229F5 on chr=9; Num_of_Contigs=4; )

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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).