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)

C9orf135		ENSSSCG00000005251	1:233379783-233504353
C9orf144		ENSSSCG00000005295	1:246694298-246701774
C9orf150		ENSSSCG00000005192	1:218993972-219045663
C9orf152		ENSSSCG00000005452	1:263930632-263936943
C9orf153		ENSSSCG00000010954	10:27934850-27947895		CU694299,CH242-250G4,10:27769603-27962750 (Clone quality: bE250G4 on chr=10; Num_of_Contigs=2; )
C9orf156		ENSSSCG00000005370	1:251284374-251338835
C9orf167		ENSSSCG00000005845	1:294323846-294325093		CU928955,CH242-34I15,1:294322778-294354935 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
C9orf169		ENSSSCG00000005857	1:294435302-294435700		CU928955,CH242-34I15,1:294431557-294452171 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
C9orf171		ENSSSCG00000005727	1:287919626-287955448
C9orf173		ENSSSCG00000005847	1:294339898-294341272		CU928955,CH242-34I15,1:294322778-294354935 (Clone quality: bE34I15 on chr=1; Num_of_Contigs=4; )
C9orf21		ENSSSCG00000011169	10:65022123-65036695		CU972489,CH242-181E4,10:65004607-65041493 (Clone quality: bE181E4 on chr=10; Num_of_Contigs=9; )
C9orf23		ENSSSCG00000010973	10:30634527-30635018		CU928717,CH242-142N10,10:30613639-30641888 (Clone quality: bE142N10 on chr=10; Num_of_Contigs=7; )
C9orf24		ENSSSCG00000010980	10:30897430-30912519
C9orf25		ENSSSCG00000010979	10:30888918-30894231		CU571264,CH242-10D18,10:30874192-30908800 (Clone quality: bE10D18 on chr=10; Num_of_Contigs=8; )
C9orf3		ENSSSCG00000010943	10:26147406-26497159
C9orf30		ENSSSCG00000005390	1:253828230-253853025		CU928622,CH242-112O3,1:253823561-253939042 (Clone quality: bE112O3 on chr=1; Num_of_Contigs=5; )
C9orf4		ENSSSCG00000005445	1:262858810-262885183		CU550650,CH242-116A3,1:262838524-262995303 (Clone quality: bE116A3 on chr=1; Num_of_Contigs=1; )
C9orf40		ENSSSCG00000005270	1:238516112-238521583		CU633596,CH242-504A9,1:238508848-238577312 (Clone quality: bE504A9 on chr=1; Num_of_Contigs=3; )
C9orf41		ENSSSCG00000005271	1:238534036-238568665		CU633596,CH242-504A9,1:238508848-238577312 (Clone quality: bE504A9 on chr=1; Num_of_Contigs=3; )
C9orf43		ENSSSCG00000005479	1:266804361-266824826		FP102008,CH242-508O3,1:266799704-266845426 (Clone quality: bE508O3 on chr=1; Num_of_Contigs=5; )
C9orf46		ENSSSCG00000005212	1:226602148-226657186
C9orf5		ENSSSCG00000005444	1:262845595-262846149		CU550650,CH242-116A3,1:262838524-262995303 (Clone quality: bE116A3 on chr=1; Num_of_Contigs=1; )
C9orf50		ENSSSCG00000005674	1:284480442-284483972
C9orf57		ENSSSCG00000005263	1:235744107-235896350
C9orf6		ENSSSCG00000005440	1:262654624-262660553
C9orf61		ENSSSCG00000005249	1:232991855-233036866		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
C9orf61		location ⇒	1:233006641-233006750		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
C9orf61		location ⇒	1:233017334-233017463		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
C9orf61		location ⇒	1:233019426-233019560		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
C9orf61		location ⇒	1:233032660-233032944		CU407274,CH242-482L1,1:232970429-233107951 (Clone quality: bE482L1 on chr=1; Num_of_Contigs=3; )
C9orf68		ENSSSCG00000005221	1:227470150-227482372		CU041279,CH242-42M5,1:227466825-227496173 (Clone quality: bE42M5 on chr=1; Num_of_Contigs=7; )
C9orf71		ENSSSCG00000005244	1:232221668-232226105		CU896594,CH242-392F14,1:232177818-232233439 (Clone quality: bE392F14 on chr=1; Num_of_Contigs=9; )
C9orf72		ENSSSCG00000011010	10:37528575-37553211		CU571192,CH242-151L17,10:37521948-37561116 (Clone quality: bE151L17 on chr=10; Num_of_Contigs=4; )
C9orf80		ENSSSCG00000005470	1:266288232-266305217
C9orf82		ENSSSCG00000005127	1:205470610-205513983
C9orf84		ENSSSCG00000005463	1:265352042-265377522		FP016086,CH242-109H23,1:265346767-265380976 (Clone quality: bE109H23 on chr=1; Num_of_Contigs=3; )
C9orf89		ENSSSCG00000008077	3:37784228-37788164
C9orf9		ENSSSCG00000005734	1:288269851-288273817		CU469088,CH242-113L1,1:288269560-288273931 (Clone quality: bE113L1 on chr=1; Num_of_Contigs=17; )
C9orf91		ENSSSCG00000005492	1:268217597-268241609
C9orf93		ENSSSCG00000005182	1:215980480-216284203
C9orf95		ENSSSCG00000005272	1:238590339-238617454
C9orf97		ENSSSCG00000005367	1:250965726-250985143
C9orf98		ENSSSCG00000005732	1:288220580-288222646		CU326339,CH242-262P16,1:288172771-288226948 (Clone quality: bE262P16 on chr=1; Num_of_Contigs=6; )
CA1		ENSSSCG00000006142	4:53187533-53197072		CU151857,CH242-236F19,4:53183914-53263009 (Clone quality: bE236F19 on chr=4; Num_of_Contigs=10; )
CA10		ENSSSCG00000017594	12:25783748-25828445
CA11		ENSSSCG00000003147	6:37712606-37717860		CU929759,CH242-294C24,6:37595303-37722216 (Clone quality: bE294C24 on chr=6; Num_of_Contigs=3; )
CA12		ENSSSCG00000004565	1:112045924-112116177
CA13		ENSSSCG00000006143	4:53253553-53293677
CA14		ENSSSCG00000006658	4:102779631-102781045		CU468675,CH242-4P3,4:102770988-102781211 (Clone quality: bE4P3 on chr=4; Num_of_Contigs=11; )
CA2		ENSSSCG00000006140	4:52952120-52968873		CU571274,CH242-157O11,4:52933471-52993062 (Clone quality: bE157O11 on chr=4; Num_of_Contigs=3; )

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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).