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)

MYO1F		ENSSSCG00000013604	2:51781731-51795930		FP090904,CH242-212F1,2:51700191-51798128 (Clone quality: bE212F1 on chr=2; Num_of_Contigs=2; )
MYO1G		ENSSSCG00000016742	18:49129782-49140280
MYO1H		ENSSSCG00000009935	14:41707610-41752659		CU638684,CH242-434M9,14:41660146-41771253 (Clone quality: bE434M9 on chr=14; Num_of_Contigs=2; )
MYO3A		ENSSSCG00000011059	10:46378767-46543200
MYO5C		ENSSSCG00000004621	1:124287507-124398504		CU062444,CH242-111O18,1:124272857-124446865 (Clone quality: bE111O18 on chr=1; Num_of_Contigs=1; )
MYO6		ENSSSCG00000004478	1:94966774-95136736
MYO7A		ENSSSCG00000014876	9:11143814-11206961		CU951449,CH242-131D10,9:11110960-11206962 (Clone quality: bE131D10 on chr=9; Num_of_Contigs=4; )
MYO9A		ENSSSCG00000004979	1:177177017-177331065
MYO9B		ENSSSCG00000013876	2:61701778-61716228		CU914416,CH242-266I16,2:61677550-61716362 (Clone quality: bE266I16 on chr=2; Num_of_Contigs=8; )
MYOC		ENSSSCG00000015481	9:107078630-107089440		CU928019,CH242-102L6,9:107032719-107220326 (Clone quality: bE102L6 on chr=9; Num_of_Contigs=1; )
MYOC		location ⇒	9:107079415-107078065		CU928019,CH242-102L6,9:107032719-107220326 (Clone quality: bE102L6 on chr=9; Num_of_Contigs=1; )
MYOC		location ⇒	9:107081189-107081061		CU928019,CH242-102L6,9:107032719-107220326 (Clone quality: bE102L6 on chr=9; Num_of_Contigs=1; )
MYOC		location ⇒	9:107089427-107088766		CU928019,CH242-102L6,9:107032719-107220326 (Clone quality: bE102L6 on chr=9; Num_of_Contigs=1; )
MYOCD		ENSSSCG00000018017	12:54184661-54191192
MYOCD		location ⇒	12:54148674-54148730		CU466334,CH242-429C20,12:54098576-54160861 (Clone quality: bE429C20 on chr=12; Num_of_Contigs=6; )
MYOCD		location ⇒	12:54154161-54154325		CU466334,CH242-429C20,12:54098576-54160861 (Clone quality: bE429C20 on chr=12; Num_of_Contigs=6; )
MYOCD		location ⇒	12:54184817-54184662		FP016121,CH242-301L17,12:54180281-54187568 (Clone quality: bE301L17 on chr=12; Num_of_Contigs=19; )
MYOCD		location ⇒	12:54186567-54186415		FP016121,CH242-301L17,12:54180281-54187568 (Clone quality: bE301L17 on chr=12; Num_of_Contigs=19; )
MYOD1		ENSSSCG00000013375	2:38709241-38710956		CU914672,CH242-409N20,2:38693857-38778694 (Clone quality: bE409N20 on chr=2; Num_of_Contigs=5; )
MYOF		ENSSSCG00000010476	14:110024838-110097302
MYOG		ENSSSCG00000015475	9:106802307-106804777		CU694815,CH242-126M16,9:106764994-106805328 (Clone quality: bE126M16 on chr=9; Num_of_Contigs=9; )
MYOM1		ENSSSCG00000003693	6:70794741-70931819
MYOM1		location ⇒	6:70919132-70919238		CU929646,CH242-413G2,6:70816571-70938296 (Clone quality: bE413G2 on chr=6; Num_of_Contigs=3; )
MYOM1		location ⇒	6:70922733-70922896		CU929646,CH242-413G2,6:70816571-70938296 (Clone quality: bE413G2 on chr=6; Num_of_Contigs=3; )
MYOM1		location ⇒	6:70931464-70931806		CU929646,CH242-413G2,6:70816571-70938296 (Clone quality: bE413G2 on chr=6; Num_of_Contigs=3; )
MYOM1		location ⇒	6:70931802-70931938		CU929646,CH242-413G2,6:70816571-70938296 (Clone quality: bE413G2 on chr=6; Num_of_Contigs=3; )
MYOM2		ENSSSCG00000015747	15:30805632-30891963
MYOM2		location ⇒	15:30869596-30869735		CU929022,CH242-202G15,15:30858897-30920945 (Clone quality: bE202G15 on chr=15; Num_of_Contigs=6; )
MYOM2		location ⇒	15:30872077-30872223		CU929022,CH242-202G15,15:30858897-30920945 (Clone quality: bE202G15 on chr=15; Num_of_Contigs=6; )
MYOM2		location ⇒	15:30876492-30876607		CU929022,CH242-202G15,15:30858897-30920945 (Clone quality: bE202G15 on chr=15; Num_of_Contigs=6; )
MYOM2		location ⇒	15:30876792-30876881		CU929022,CH242-202G15,15:30858897-30920945 (Clone quality: bE202G15 on chr=15; Num_of_Contigs=6; )
MYOT		ENSSSCG00000014324	2:126969357-126989069
MYOZ1		ENSSSCG00000010304	14:79709549-79718718		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
MYOZ1		location ⇒	14:79710863-79711074		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
MYOZ1		location ⇒	14:79713403-79713584		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
MYOZ1		location ⇒	14:79715970-79716218		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
MYOZ1		location ⇒	14:79718188-79718699		CT827821,CH242-151I16,14:79697766-79768615 (Clone quality: bE151I16 on chr=14; Num_of_Contigs=5; )
MYOZ2		ENSSSCG00000009110	8:90168377-90169837		CU856165,CH242-61P16,8:90168017-90171679 (Clone quality: bE61P16 on chr=8; Num_of_Contigs=12; )
MYPOP		ENSSSCG00000003097	6:36120469-36442882
MYRIP		ENSSSCG00000011269	13:20214546-20223864
MYSM1		ENSSSCG00000003830	6:108993513-109035677
MYST1		ENSSSCG00000007762	3:15866990-15877914		CU464163,CH242-418M3,3:15802333-15893853 (Clone quality: bE418M3 on chr=3; Num_of_Contigs=3; )
MYST2		ENSSSCG00000017553	12:23394660-23427719		CU442715,CH242-56F15,12:23390749-23462544 (Clone quality: bE56F15 on chr=12; Num_of_Contigs=9; )
MYST3		ENSSSCG00000007023	17:11264826-11311874		CU627979,CH242-228P8,17:11264462-11313342 (Clone quality: bE228P8 on chr=17; Num_of_Contigs=13; )
MYST4		ENSSSCG00000010316	14:80747464-80811705
MYT1L		ENSSSCG00000008652	3:121086691-121133547

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, 1401-46

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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).