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)

C22orf41		ENSSSCG00000000963	5:99667554-99687463
C22orf46		ENSSSCG00000000056	5:3423805-3425914		CU633382,CH242-275I12,5:3423272-3428475 (Clone quality: bE275I12 on chr=5; Num_of_Contigs=9; )
C2CD2		ENSSSCG00000012086	13:144833475-144833687		CU928443,CH242-84M16,13:144823808-144839384 (Clone quality: bE84M16 on chr=13; Num_of_Contigs=3; )
C2CD2L		ENSSSCG00000015111	9:44934537-44943438		CU639481,CH242-263G17,9:44899832-45096295 (Clone quality: bE263G17 on chr=9; Num_of_Contigs=2; )
C2CD4D		ENSSSCG00000006613	4:101180992-101182050		CU582876,CH242-155P3,4:101180772-101190545 (Clone quality: bE155P3 on chr=4; Num_of_Contigs=6; )
C2orf16		ENSSSCG00000008544	3:104139942-104145275		CU972435,CH242-399O12,3:104138679-104155293 (Clone quality: bE399O12 on chr=3; Num_of_Contigs=8; )
C2orf18		ENSSSCG00000008562	3:104745186-104758776		CU914418,CH242-286P5,3:104742456-104775942 (Clone quality: bE286P5 on chr=3; Num_of_Contigs=6; )
C2orf21		ENSSSCG00000016153	15:105615334-105757767
C2orf24		ENSSSCG00000016206	15:114196546-114200278		CU467077,CH242-178P16,15:114185678-114214521 (Clone quality: bE178P16 on chr=15; Num_of_Contigs=9; )
C2orf29		ENSSSCG00000008167	3:48719552-48734844
C2orf30		ENSSSCG00000008414	3:81261173-81288594		CU855592,CH242-276B14,3:81162359-81308523 (Clone quality: bE276B14 on chr=3; Num_of_Contigs=5; )
C2orf34		ENSSSCG00000008447	3:89446727-89472273		CU942401,CH242-321A5,3:89361347-89524389 (Clone quality: bE321A5 on chr=3; Num_of_Contigs=2; )
C2orf37		ENSSSCG00000015947	15:72788692-72824224
C2orf40		ENSSSCG00000008142	3:43974258-43985344
C2orf42		ENSSSCG00000008332	3:66318347-66341865
C2orf44		ENSSSCG00000008589	3:106798721-106808163		CU928810,CH242-168M14,3:106748766-106849093 (Clone quality: bE168M14 on chr=3; Num_of_Contigs=3; )
C2orf47		ENSSSCG00000016088	15:97328770-97340439		CU694839,CH242-200F17,15:97222410-97396477 (Clone quality: bE200F17 on chr=15; Num_of_Contigs=1; )
C2orf49		ENSSSCG00000008146	3:44501848-44508804
C2orf50		ENSSSCG00000008632	3:116340691-116482050
C2orf51		ENSSSCG00000008209	3:52598361-52603491		CU464187,CH242-105C21,3:52460473-52637141 (Clone quality: bE105C21 on chr=3; Num_of_Contigs=1; )
C2orf53		ENSSSCG00000008552	3:104425632-104426825		CU896571,CH242-143O19,3:104398046-104492436 (Clone quality: bE143O19 on chr=3; Num_of_Contigs=6; )
C2orf54		ENSSSCG00000016400	15:134379788-134388863
C2orf55		ENSSSCG00000008187	3:51060788-51079966		CU407144,CH242-156F8,3:51057894-51127185 (Clone quality: bE156F8 on chr=3; Num_of_Contigs=4; )
C2orf56		ENSSSCG00000008494	3:96038482-96061720		CU695023,CH242-129E17,3:96011217-96129629 (Clone quality: bE129E17 on chr=3; Num_of_Contigs=2; )
C2orf57		ENSSSCG00000016278	15:124582747-124583778		CU856676,CH242-83A8,15:124567279-124585602 (Clone quality: bE83A8 on chr=15; Num_of_Contigs=8; )
C2orf60		ENSSSCG00000016087	15:97309953-97328488		CU694839,CH242-200F17,15:97222410-97396477 (Clone quality: bE200F17 on chr=15; Num_of_Contigs=1; )
C2orf61		ENSSSCG00000008432	3:86750021-86797476
C2orf62		ENSSSCG00000016187	15:113489734-113496237
C2orf63		ENSSSCG00000008402	3:79833628-79884011
C2orf64		ENSSSCG00000008189	3:51268814-51278875		CU694916,CH242-454K11,3:51231234-51347424 (Clone quality: bE454K11 on chr=3; Num_of_Contigs=2; )
C2orf65		ENSSSCG00000008263	3:62804078-62884319
C2orf66		ENSSSCG00000016072	15:94440434-94441904		CU466965,CH242-344E23,15:94439552-94447396 (Clone quality: bE344E23 on chr=15; Num_of_Contigs=13; )
C2orf68		ENSSSCG00000008234	3:54064066-54066603		CU928286,CH242-219K12,3:54043219-54085564 (Clone quality: bE219K12 on chr=3; Num_of_Contigs=4; )
C2orf69		ENSSSCG00000016086	15:97292734-97303257		CU694839,CH242-200F17,15:97222410-97396477 (Clone quality: bE200F17 on chr=15; Num_of_Contigs=1; )
C2orf7		ENSSSCG00000008304	3:63908320-63912805		FP089556,CH242-274G10,3:63904593-63934044 (Clone quality: bE274G10 on chr=3; Num_of_Contigs=6; )
C2orf70		ENSSSCG00000008565	3:104915142-104930459		CU550723,CH242-158M4,3:104903273-104931631 (Clone quality: bE158M4 on chr=3; Num_of_Contigs=9; )
C2orf72		ENSSSCG00000016270	15:124194604-124201768		CU466944,CH242-462A10,15:124189987-124206317 (Clone quality: bE462A10 on chr=15; Num_of_Contigs=10; )
C2orf73		ENSSSCG00000008410	3:80990736-81195812
C2orf74		ENSSSCG00000008384	3:74221297-74224599
C2orf76		ENSSSCG00000015718	15:23528096-23544004		CU861525,CH242-168K13,15:23527317-23663672 (Clone quality: bE168K13 on chr=15; Num_of_Contigs=2; )
C2orf77		ENSSSCG00000015935	15:71412980-71436255
C2orf78		ENSSSCG00000008299	3:63689813-63693651
C2orf79		ENSSSCG00000008580	3:106203684-106207424		CU929972,CH242-90C18,3:106191128-106234756 (Clone quality: bE90C18 on chr=3; Num_of_Contigs=2; )
C2orf80		ENSSSCG00000016146	15:104175503-104194413
C2orf82		ENSSSCG00000016294	15:125754115-125760726		CU571212,CH242-232E19,15:125722666-125764144 (Clone quality: bE232E19 on chr=15; Num_of_Contigs=8; )
C2orf84		ENSSSCG00000008584	3:106719528-106734966
C2orf86		ENSSSCG00000008370	3:72531715-72531882		FP236233,CH242-133O13,3:72516141-72584832 (Clone quality: bE133O13 on chr=3; Num_of_Contigs=4; )
C2orf88		ENSSSCG00000016048	15:89313671-89313955		CU928188,CH242-102H22,15:89306714-89337168 (Clone quality: bE102H22 on chr=15; Num_of_Contigs=16; )
C3		ENSSSCG00000000664	5:59354247-59385516
C3		ENSSSCG00000001422	7:27842472-27862549	CT956038,CH242-183N12,7:27767223-27953076 (Clone quality: bE183N12 on chr=7; 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).