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)

C8B		ENSSSCG00000003834	6:110258223-110299283		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8B		location ⇒	6:110279182-110279382		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8B		location ⇒	6:110281129-110281370		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8B		location ⇒	6:110286265-110286431		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8B		location ⇒	6:110298535-110299274		CT025767,XX-1E1,6:110170538-110364429 (Clone quality: bEE1E1 on chr=6; Num_of_Contigs=1; )
C8G		ENSSSCG00000005840	1:294236972-294238512		FP236151,CH242-517G10,1:294232528-294238661 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
C8G		location ⇒	1:294237045-294237234		FP236151,CH242-517G10,1:294232528-294238661 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
C8G		location ⇒	1:294237316-294237456		FP236151,CH242-517G10,1:294232528-294238661 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
C8G		location ⇒	1:294237734-294237842		FP236151,CH242-517G10,1:294232528-294238661 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
C8G		location ⇒	1:294238347-294238511		FP236151,CH242-517G10,1:294232528-294238661 (Clone quality: bE517G10 on chr=1; Num_of_Contigs=14; )
C8orf33		ENSSSCG00000005880	4:131960-132889		CU914810,CH242-87G5,4:131735-166992 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
C8orf33		location ⇒	4:132106-131968		CU914810,CH242-87G5,4:131735-166992 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
C8orf33		location ⇒	4:132330-132268		CU914810,CH242-87G5,4:131735-166992 (Clone quality: bE87G5 on chr=4; Num_of_Contigs=8; )
C8orf34		ENSSSCG00000006198	4:68886863-69041196
C8orf37		ENSSSCG00000006092	4:41914598-41933543		CU407168,CH242-230I12,4:41827613-42007263 (Clone quality: bE230I12 on chr=4; Num_of_Contigs=1; )
C8orf38		ENSSSCG00000006093	4:42022563-42054698
C8orf40		ENSSSCG00000007024	17:11405872-11422006		CU628001,CH242-85P17,17:11399977-11434096 (Clone quality: bE85P17 on chr=17; Num_of_Contigs=5; )
C8orf41		ENSSSCG00000015833	15:49325016-49335920
C8orf46		ENSSSCG00000006212	4:70793864-70813993		CU855750,CH242-30I10,4:70739858-70897572 (Clone quality: bE30I10 on chr=4; Num_of_Contigs=1; )
C8orf47		ENSSSCG00000006080	4:38874851-38885900		CU234130,CH242-486G18,4:38849917-38907420 (Clone quality: bE486G18 on chr=4; Num_of_Contigs=7; )
C8orf48		ENSSSCG00000006972	17:1227284-1228123		CU104687,CH242-88D5,17:1227132-1238678 (Clone quality: bE88D5 on chr=17; Num_of_Contigs=5; )
C8orf58		ENSSSCG00000009627	14:6845664-6849577		CU407060,CH242-266L24,14:6832388-6900516 (Clone quality: bE266L24 on chr=14; Num_of_Contigs=5; )
C8orf59		ENSSSCG00000006144	4:53313301-53323241
C8orf73		ENSSSCG00000006948	4:135754052-135912660
C8orf79		ENSSSCG00000006969	17:640892-683076
C8orf80		ENSSSCG00000009673	14:11783006-11826089		CU468329,CH242-220E13,14:11669700-11856557 (Clone quality: bE220E13 on chr=14; Num_of_Contigs=1; )
C8orf83		ENSSSCG00000006112	4:44283186-44366668
C8orf84		ENSSSCG00000006183	4:64938016-64957511		CU469056,CH242-70H23,4:64933009-64980124 (Clone quality: bE70H23 on chr=4; Num_of_Contigs=4; )
C8orf85		ENSSSCG00000006013	4:21430316-21434396		CU467777,CH242-481P3,4:21409812-21444668 (Clone quality: bE481P3 on chr=4; Num_of_Contigs=9; )
C9		ENSSSCG00000016856	16:21882480-21918668
C9		ENSSSCG00000001754	7:53558430-53566497		CU469426,CH242-238I15,7:53527495-53574187 (Clone quality: bE238I15 on chr=7; Num_of_Contigs=3; )
C9		location ⇒	16:21882672-21882495		CU466476,CH242-400A5,16:21873758-21887137 (Clone quality: bE400A5 on chr=16; Num_of_Contigs=14; )
C9		location ⇒	16:21885485-21885237		CU466476,CH242-400A5,16:21873758-21887137 (Clone quality: bE400A5 on chr=16; Num_of_Contigs=14; )
C9		location ⇒	16:21889559-21889292		CU466476,CH242-400A5,16:21887238-21905598 (Clone quality: bE400A5 on chr=16; Num_of_Contigs=14; )
C9		location ⇒	16:21918666-21918503		CU466476,CH242-400A5,16:21905699-21928965 (Clone quality: bE400A5 on chr=16; Num_of_Contigs=14; )
C9orf100		ENSSSCG00000005314	1:247476786-247479985		CU062658,CH242-97C14,1:247426659-247546707 (Clone quality: bE97C14 on chr=1; Num_of_Contigs=2; )
C9orf102		ENSSSCG00000010941	10:25752908-25834734
C9orf114		ENSSSCG00000005662	1:283831386-283841321		FP236218,CH242-328B23,1:283815054-283846030 (Clone quality: bE328B23 on chr=1; Num_of_Contigs=4; )
C9orf116		ENSSSCG00000005760	1:289871390-289875744		FP102268,CH242-95K10,1:289867363-289878318 (Clone quality: bE95K10 on chr=1; Num_of_Contigs=5; )
C9orf117		ENSSSCG00000005618	1:282571537-282575117		CU407281,CH242-506D15,1:282547408-282575119 (Clone quality: bE506D15 on chr=1; Num_of_Contigs=13; )
C9orf119		ENSSSCG00000005644	1:283354868-283361026		CU234126,CH242-282L14,1:283270038-283452033 (Clone quality: bE282L14 on chr=1; Num_of_Contigs=4; )
C9orf123		ENSSSCG00000005196	1:224027764-224029470		CU074323,CH242-153K16,1:224011953-224099666 (Clone quality: bE153K16 on chr=1; Num_of_Contigs=6; )
C9orf125		ENSSSCG00000005396	1:254683447-254685741
C9orf126		ENSSSCG00000005598	1:280566436-280630711		FP067359,CH242-297H23,1:280534139-280638618 (Clone quality: bE297H23 on chr=1; Num_of_Contigs=4; )
C9orf127		ENSSSCG00000005325	1:247648895-247675337
C9orf127		location ⇒	1:247658052-247658312		CU074289,CH242-130G19,1:247583036-247668986 (Clone quality: bE130G19 on chr=1; Num_of_Contigs=3; )
C9orf127		location ⇒	1:247658924-247659205		CU074289,CH242-130G19,1:247583036-247668986 (Clone quality: bE130G19 on chr=1; Num_of_Contigs=3; )
C9orf128		ENSSSCG00000005324	1:247631705-247639584		CU074289,CH242-130G19,1:247583036-247668986 (Clone quality: bE130G19 on chr=1; Num_of_Contigs=3; )
C9orf131		ENSSSCG00000005298	1:246875549-246879563		FP102396,CH242-207N19,1:246822188-246892961 (Clone quality: bE207N19 on chr=1; Num_of_Contigs=1; )
C9orf134		ENSSSCG00000005129	1:207322647-207326193		CU570865,CH242-7J19,1:207242814-207378480 (Clone quality: bE7J19 on chr=1; Num_of_Contigs=1; )

Go to records:
1-49, 50-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 601-650, 651-700, 701-750, 751-800, 801-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-3750, 3751-3800, 3801-3850, 3851-3900, 3901-12

Report problems to zhu

iastate.edu

$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).