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)

C11orf30		ENSSSCG00000014868	9:10459581-10505742		CU928935,CH242-34M6,9:10455925-10506297 (Clone quality: bE34M6 on chr=9; Num_of_Contigs=2; )
C11orf34		ENSSSCG00000015041	9:38887144-38900478		CU657951,CH242-322L21,9:38838246-38903616 (Clone quality: bE322L21 on chr=9; Num_of_Contigs=9; )
C11orf41		ENSSSCG00000013311	2:25649687-25776410
C11orf42		ENSSSCG00000014634	9:2822586-2827636		CU915603,CH242-135E13,9:2821746-2828209 (Clone quality: bE135E13 on chr=9; Num_of_Contigs=12; )
C11orf46		ENSSSCG00000014222	2:108916501-108920755		CU856265,CH242-232F2,2:108874333-108958027 (Clone quality: bE232F2 on chr=2; Num_of_Contigs=4; )
C11orf49		ENSSSCG00000013246	2:13427096-13636928
C11orf51		ENSSSCG00000014806	9:6120751-6122221
C11orf53		ENSSSCG00000015018	9:38042270-38044397		CU856590,CH242-307A12,9:38028698-38049795 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
C11orf54		ENSSSCG00000014948	9:26550833-26561207
C11orf58		ENSSSCG00000013383	2:39669405-39708473		CU468201,CH242-353I19,2:39590631-39746097 (Clone quality: bE353I19 on chr=2; Num_of_Contigs=2; )
C11orf59		ENSSSCG00000014804	9:6108886-6114894		FP102867,CH242-179D20,9:6102602-6119094 (Clone quality: bE179D20 on chr=9; Num_of_Contigs=3; )
C11orf61		ENSSSCG00000015201	9:50455603-50486118
C11orf63		ENSSSCG00000015138	9:48366187-48435629
C11orf65		ENSSSCG00000015008	9:36028302-36108084
C11orf66		ENSSSCG00000013081	2:8352566-8361814
C11orf67		ENSSSCG00000014883	9:12139891-12189349
C11orf68		ENSSSCG00000012966	2:4790094-4790849		CU928325,CH242-208C18,2:4762275-4805765 (Clone quality: bE208C18 on chr=2; Num_of_Contigs=5; )
C11orf70		ENSSSCG00000014980	9:32575628-32666794
C11orf71		ENSSSCG00000015058	9:40755376-40755492		CU856090,CH242-161C5,9:40675140-40798853 (Clone quality: bE161C5 on chr=9; Num_of_Contigs=4; )
C11orf73		ENSSSCG00000014916	9:20445260-20453055		CU914737,CH242-142G5,9:20440430-20459477 (Clone quality: bE142G5 on chr=9; Num_of_Contigs=19; )
C11orf8		ENSSSCG00000013327	2:28031590-28211524	CU463210,CH242-12K2,2:28008472-28224382 (Clone quality: bE12K2 on chr=2; Num_of_Contigs=7; )
C11orf82		ENSSSCG00000014898	9:17088435-17100040
C11orf84		ENSSSCG00000013048	2:6553559-6635817
C11orf85		ENSSSCG00000013014	2:5621411-5642123		CU606982,CH242-431G15,2:5575891-5703518 (Clone quality: bE431G15 on chr=2; Num_of_Contigs=4; )
C11orf86		ENSSSCG00000012924	2:3879440-3880843		FP089559,CH242-217L14,2:3868885-3887517 (Clone quality: bE217L14 on chr=2; Num_of_Contigs=11; )
C11orf87		ENSSSCG00000015012	9:37031149-37031745		CU655915,CH242-248F15,9:37009874-37032637 (Clone quality: bE248F15 on chr=9; Num_of_Contigs=11; )
C11orf88		ENSSSCG00000015021	9:38327015-38352688		FP015891,CH242-190F19,9:38300003-38361484 (Clone quality: bE190F19 on chr=9; Num_of_Contigs=1; )
C11orf9		ENSSSCG00000013078	2:8014755-8047559
C11orf90		ENSSSCG00000014950	9:26598095-26619829		CU464153,CH242-27K5,9:26560904-26638658 (Clone quality: bE27K5 on chr=9; Num_of_Contigs=3; )
C11orf91		ENSSSCG00000013310	2:25622827-25624741	CU896538,CH242-498B6,2:25615450-25717737 (Clone quality: bE498B6 on chr=2; Num_of_Contigs=8; )
C11orf93		ENSSSCG00000015019	9:38085689-38090173		CU856590,CH242-307A12,9:38084595-38103087 (Clone quality: bE307A12 on chr=9; Num_of_Contigs=14; )
C11orf94		ENSSSCG00000013268	2:14863004-14863760		FP101987,CH242-521A18,2:14831953-14928280 (Clone quality: bE521A18 on chr=2; Num_of_Contigs=9; )
C11orf95		ENSSSCG00000013053	2:6819349-6821684		FP089542,CH242-41F12,2:6778030-6836536 (Clone quality: bE41F12 on chr=2; Num_of_Contigs=6; )
C12orf10		ENSSSCG00000000267	5:17059988-17065529		CU570852,CH242-3N12,5:17057869-17089247 (Clone quality: bE3N12 on chr=5; Num_of_Contigs=3; )
C12orf12		ENSSSCG00000000919	5:86929576-86930796		CU468030,CH242-511M16,5:86928922-86932533 (Clone quality: bE511M16 on chr=5; Num_of_Contigs=1; )
C12orf23		ENSSSCG00000000166	5:11596010-11600941
C12orf24		ENSSSCG00000009822	14:31876737-31886595
C12orf26		ENSSSCG00000000941	5:95488133-95521294
C12orf28		ENSSSCG00000000501	5:32959666-33067586
C12orf29		ENSSSCG00000000925	5:90234022-90248424		CU468671,CH242-415O13,5:90211693-90383459 (Clone quality: bE415O13 on chr=5; Num_of_Contigs=1; )
C12orf32		ENSSSCG00000000738	5:63116863-63122079
C12orf34		ENSSSCG00000009927	14:41232088-41326221
C12orf39		ENSSSCG00000000578	5:49921468-49928336
C12orf4		ENSSSCG00000000723	5:61640802-61682779
C12orf40		ENSSSCG00000000782	5:67148076-67217875
C12orf41		ENSSSCG00000000842	5:75047920-75070553
C12orf43		ENSSSCG00000009920	14:41050659-41060729		CU467935,CH242-88C19,14:41029822-41073842 (Clone quality: bE88C19 on chr=14; Num_of_Contigs=7; )
C12orf48		ENSSSCG00000000859	5:77417578-77439472
C12orf49		ENSSSCG00000009863	14:35976703-35992574		CU694246,CH242-503C19,14:35947395-36003276 (Clone quality: bE503C19 on chr=14; Num_of_Contigs=6; )
C12orf5		ENSSSCG00000000726	5:61803651-61815808		CU457725,CH242-403B8,5:61794410-61821976 (Clone quality: bE403B8 on chr=5; Num_of_Contigs=3; )

Go to records:
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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).