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)

WDR26		ENSSSCG00000010849	10:13579283-13617906		CU927957,CH242-267J14,10:13562338-13618285 (Clone quality: bE267J14 on chr=10; Num_of_Contigs=3; )
WDR27		ENSSSCG00000004008	1:399819-708754
WDR3		ENSSSCG00000006727	4:106902536-106940455
WDR32		ENSSSCG00000005356	1:249971264-250030925
WDR33		ENSSSCG00000015861	15:55704291-55780442
WDR34		ENSSSCG00000005655	1:283683460-283711719		CU862000,CH242-4D17,1:283660123-283729806 (Clone quality: bE4D17 on chr=1; Num_of_Contigs=2; )
WDR35		ENSSSCG00000008604	3:109800613-109856310
WDR36		ENSSSCG00000014199	2:104448602-104488964		CU928266,CH242-209C17,2:104442193-104490507 (Clone quality: bE209C17 on chr=2; Num_of_Contigs=4; )
WDR38		ENSSSCG00000005594	1:280470424-280474008		CU468031,CH242-524N14,1:280318183-280492192 (Clone quality: bE524N14 on chr=1; Num_of_Contigs=1; )
WDR40A		ENSSSCG00000010986	10:31224091-31264265		CU928632,CH242-256F17,10:31181963-31275322 (Clone quality: bE256F17 on chr=10; Num_of_Contigs=6; )
WDR41		ENSSSCG00000014098	2:75224638-75279591
WDR42A		ENSSSCG00000006388	4:93661714-93708268	CU207285,CH242-406N12,4:93542791-93708820 (Clone quality: bE406N12 on chr=4; Num_of_Contigs=3; )
WDR42B		ENSSSCG00000012192	X:22564378-22566192		CU855538,CH242-516J15,X:22560833-22605638 (Clone quality: bE516J15 on chr=X; Num_of_Contigs=7; )
WDR43		ENSSSCG00000008536	3:103276871-103292188		CU915390,CH242-227M18,3:103263888-103292948 (Clone quality: bE227M18 on chr=3; Num_of_Contigs=14; )
WDR44		ENSSSCG00000012635	X:97515691-97591790
WDR45		ENSSSCG00000012290	X:42586747-42592039		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
WDR45		location ⇒	X:42587210-42586748		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
WDR45		location ⇒	X:42587606-42587461		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
WDR45		location ⇒	X:42588080-42587871		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
WDR45		location ⇒	X:42589161-42589053		FP067404,CH242-247J8,X:42575088-42641365 (Clone quality: bE247J8 on chr=X; Num_of_Contigs=5; )
WDR46		ENSSSCG00000001504	7:34052487-34060763	CU607018,CH242-138E20,7:33930957-34116846 (Clone quality: bE138E20 on chr=7; Num_of_Contigs=1; )
WDR47		ENSSSCG00000006840	4:115508278-115574988
WDR48		ENSSSCG00000011261	13:19660875-19710093		CU856480,CH242-203F12,13:19659552-19771103 (Clone quality: bE203F12 on chr=13; Num_of_Contigs=3; )
WDR49		ENSSSCG00000011738	13:81386272-81479777		CU582954,CH242-37M21,13:81344340-81513789 (Clone quality: bE37M21 on chr=13; Num_of_Contigs=1; )
WDR5		ENSSSCG00000005744	1:288655578-288672266
WDR51A		ENSSSCG00000011426	13:28743848-28778994
WDR51B		ENSSSCG00000000920	5:87863412-87950558
WDR54		ENSSSCG00000008282	3:63131763-63136101		CU856063,CH242-70N7,3:63122986-63137576 (Clone quality: bE70N7 on chr=3; Num_of_Contigs=22; )
WDR55		ENSSSCG00000014373	2:129386983-129392711		CU459055,CH242-430O11,2:129383345-129419222 (Clone quality: bE430O11 on chr=2; Num_of_Contigs=5; )
WDR59		ENSSSCG00000002714	6:9296295-9325405
WDR5B		ENSSSCG00000005748	1:289051263-289109834
WDR6		ENSSSCG00000011369	13:26592882-26601047
WDR61		ENSSSCG00000001757	7:53665590-53683767		CU467054,CH242-222N19,7:53664834-53710059 (Clone quality: bE222N19 on chr=7; Num_of_Contigs=8; )
WDR62		ENSSSCG00000002923	6:30513182-30568001
WDR63		ENSSSCG00000006950	4:135773615-135834733		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
WDR63		location ⇒	4:135787934-135788083		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
WDR63		location ⇒	4:135789105-135789289		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
WDR63		location ⇒	4:135802177-135802250		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
WDR63		location ⇒	4:135819592-135819652		CU595636,CH242-517I9,4:135754241-135836671 (Clone quality: bE517I9 on chr=4; Num_of_Contigs=3; )
WDR64		ENSSSCG00000010839	10:11874298-11919411
WDR66		ENSSSCG00000009802	14:30767698-30845244
WDR67		ENSSSCG00000005987	4:15797614-15835076
WDR69		ENSSSCG00000016255	15:121932962-121968232
WDR7		ENSSSCG00000004538	1:109244025-109343312
WDR70		ENSSSCG00000016846	16:20105325-20294858
WDR72		ENSSSCG00000004615	1:122632639-122821081
WDR75		ENSSSCG00000016036	15:88282774-88325496		CU927954,CH242-251G6,15:88276169-88334941 (Clone quality: bE251G6 on chr=15; Num_of_Contigs=5; )
WDR76		ENSSSCG00000004695	1:133730890-133801724
WDR77		ENSSSCG00000006790	4:113267829-113275740		CU311186,CH242-230C12,4:113251594-113376287 (Clone quality: bE230C12 on chr=4; Num_of_Contigs=3; )
WDR8		ENSSSCG00000003360	6:43684338-43696220		FP102698,CH242-39I24,6:43627875-43737015 (Clone quality: bE39I24 on chr=6; Num_of_Contigs=5; )

Go to records:
1-49, 50-100, 101-150, 151-200

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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).